# 61 # Error: Abnormally short interatomic distances The pairs of atoms listed in the table below have an unusually short interactomic distance; each bump is listed in only one direction. The contact distances of all atom pairs have been checked. Two atoms are said to `bump' if they are closer than the sum of their Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom is used. The first number in the table tells you how much shorter that specific contact is than the acceptable limit. The second distance is the distance between the centres of the two atoms. Although we believe that two water atoms at 2.4 A distance are too close, we only report water pairs that are closer than this rather short distance. The last text-item on each line represents the status of the atom pair. If the final column contains the text 'HB', the bump criterion was relaxed because there could be a hydrogen bond. Similarly relaxed criteria are used for 1-3 and 1-4 interactions (listed as 'B2' and 'B3', respectively). BL indicates that the B-factors of the clashing atoms have a low B-factor thereby making this clash even more worrisome. INTRA and INTER indicate whether the clashes are between atoms in the same asymmetric unit, or atoms in symmetry related asymmetric units, respectively. 83 CYS ( 83-) A - SG <-> 99 CYS ( 99-) A - CA 0.50 2.50 INTRA BF 83 CYS ( 83-) A - SG <-> 99 CYS ( 99-) A - N 0.43 2.87 INTRA BF 64 ASN ( 64-) A - CA <-> 65 PRO ( 65-) A - CD 0.35 2.45 INTRA BF 45 ASN ( 45-) A - CG <-> 130 TRP ( 130-) A - NE1 0.32 2.78 INTRA BF 41 ILE ( 41-) A - CG1 <-> 124 ILE ( 124-) A - CD1 0.28 2.92 INTRA BF 44 ALA ( 44-) A - CB <-> 139 VAL ( 139-) A - CG1 0.28 2.92 INTRA BL 41 ILE ( 41-) A - CD1 <-> 46 TRP ( 46-) A - NE1 0.28 2.82 INTRA BF 47 VAL ( 47-) A - CG1 <-> 142 TYR ( 142-) A - CB 0.27 2.93 INTRA BF 53 GLU ( 53-) A - CG <-> 76 GLN ( 76-) A - CB 0.27 2.93 INTRA BF 82 TRP ( 82-) A - CZ3 <-> 116 ARG ( 116-) A - CD 0.27 2.93 INTRA BF 70 THR ( 70-) A - CG2 <-> 72 TYR ( 72-) A - CE2 0.27 2.93 INTRA BF 71 ASP ( 71-) A - CB <-> 76 GLN ( 76-) A - CG 0.27 2.93 INTRA BF 25 GLU ( 25-) A - CA <-> 28 ARG ( 28-) A - CD 0.26 2.94 INTRA BF 33 LEU ( 33-) A - CD2 <-> 111 VAL ( 111-) A - CB 0.26 2.94 INTRA BL 95 CYS ( 95-) A - CB <-> 97 ILE ( 97-) A - CD1 0.26 2.94 INTRA BF 33 LEU ( 33-) A - CD2 <-> 111 VAL ( 111-) A - CG2 0.26 2.94 INTRA BL 117 VAL ( 117-) A - CG1 <-> 127 TRP ( 127-) A - CH2 0.26 2.94 INTRA BF 33 LEU ( 33-) A - CG <-> 35 LEU ( 35-) A - CD2 0.26 2.94 INTRA BL 41 ILE ( 41-) A - CG2 <-> 46 TRP ( 46-) A - CZ2 0.26 2.94 INTRA BF 18 GLY ( 18-) A - CA <-> 59 GLN ( 59-) A - CD 0.25 2.95 INTRA BF 70 THR ( 70-) A - CG2 <-> 72 TYR ( 72-) A - CZ 0.25 2.95 INTRA BF 41 ILE ( 41-) A - CD1 <-> 45 ASN ( 45-) A - CB 0.25 2.95 INTRA BF 41 ILE ( 41-) A - CD1 <-> 46 TRP ( 46-) A - CD1 0.25 2.95 INTRA BF 139 VAL ( 139-) A - CG1 <-> 142 TYR ( 142-) A - CD2 0.25 2.95 INTRA BL 24 CYS ( 24-) A - SG <-> 146 CYS ( 146-) A - N 0.25 3.05 INTRA BL 82 TRP ( 82-) A - CZ2 <-> 117 VAL ( 117-) A - CG2 0.25 2.95 INTRA BF 122 GLN ( 122-) A - CD <-> 125 ARG ( 125-) A - CD 0.25 2.95 INTRA BF 122 GLN ( 122-) A - CG <-> 125 ARG ( 125-) A - CB 0.24 2.96 INTRA BF 19 LYS ( 19-) A - CD <-> 21 PHE ( 21-) A - CZ 0.24 2.96 INTRA BF 33 LEU ( 33-) A - CB <-> 35 LEU ( 35-) A - CD2 0.24 2.96 INTRA BL 18 GLY ( 18-) A - CA <-> 59 GLN ( 59-) A - NE2 0.24 2.86 INTRA BF 104 GLN ( 104-) A - NE2 <-> 106 ASN ( 106-) A - CG 0.24 2.86 INTRA BF 41 ILE ( 41-) A - CG1 <-> 45 ASN ( 45-) A - ND2 0.24 2.86 INTRA BF 41 ILE ( 41-) A - CG2 <-> 46 TRP ( 46-) A - NE1 0.24 2.86 INTRA BF 116 ARG ( 116-) A - NH2 <-> 119 ARG ( 119-) A - CB 0.24 2.86 INTRA BF 82 TRP ( 82-) A - CE2 <-> 117 VAL ( 117-) A - CG2 0.23 2.97 INTRA BF 39 ARG ( 39-) A - NH2 <-> 123 GLY ( 123-) A - CA 0.23 2.87 INTRA BF 46 TRP ( 46-) A - CH2 <-> 118 VAL ( 118-) A - CG1 0.22 2.98 INTRA BL 81 TYR ( 81-) A - CA <-> 92 VAL ( 92-) A - CG2 0.22 2.98 INTRA BF 80 HIS ( 80-) A - CD2 <-> 81 TYR ( 81-) A - CE2 0.20 3.00 INTRA BF 35 LEU ( 35-) A - CD1 <-> 115 LYS ( 115-) A - NZ 0.19 2.91 INTRA BL 80 HIS ( 80-) A - CD2 <-> 81 TYR ( 81-) A - CZ 0.19 3.01 INTRA BF 41 ILE ( 41-) A - CD1 <-> 45 ASN ( 45-) A - ND2 0.19 2.91 INTRA BF 35 LEU ( 35-) A - CA <-> 115 LYS ( 115-) A - NZ 0.18 2.92 INTRA BL 1 MET ( 1-) A - CG <-> 2 LYS ( 2-) A - N 0.18 2.82 INTRA BF 137 ARG ( 137-) A - CG <-> 138 ASP ( 138-) A - N 0.18 2.82 INTRA BF 112 THR ( 112-) A - CG2 <-> 113 CYS ( 113-) A - N 0.18 2.82 INTRA BL 29 THR ( 29-) A - CG2 <-> 30 LEU ( 30-) A - N 0.18 2.82 INTRA BL 117 VAL ( 117-) A - CG1 <-> 118 VAL ( 118-) A - N 0.17 2.83 INTRA BF 45 ASN ( 45-) A - CG <-> 130 TRP ( 130-) A - CD1 0.17 3.03 INTRA BF 74 ILE ( 74-) A - CG2 <-> 75 PHE ( 75-) A - N 0.17 2.83 INTRA BF 144 GLN ( 144-) A - CG <-> 145 GLY ( 145-) A - N 0.17 2.83 INTRA BF 26 LEU ( 26-) A - CD1 <-> 30 LEU ( 30-) A - CD1 0.17 3.03 INTRA BL 41 ILE ( 41-) A - CG2 <-> 46 TRP ( 46-) A - CE2 0.17 3.03 INTRA BF 33 LEU ( 33-) A - CD2 <-> 35 LEU ( 35-) A - CD2 0.16 3.04 INTRA BL 41 ILE ( 41-) A - CG1 <-> 45 ASN ( 45-) A - CB 0.16 3.04 INTRA BF 122 GLN ( 122-) A - CD <-> 125 ARG ( 125-) A - CG 0.15 3.05 INTRA BF 130 TRP ( 130-) A - CD1 <-> 134 CYS ( 134-) A - CB 0.15 3.05 INTRA BL 111 VAL ( 111-) A - CG1 <-> 112 THR ( 112-) A - N 0.15 2.85 INTRA BL 41 ILE ( 41-) A - CD1 <-> 46 TRP ( 46-) A - CE2 0.14 3.06 INTRA BF 72 TYR ( 72-) A - CE2 <-> 99 CYS ( 99-) A - SG 0.14 3.26 INTRA BF 49 LEU ( 49-) A - CD2 <-> 127 TRP ( 127-) A - CD2 0.13 3.07 INTRA BL 124 ILE ( 124-) A - CG2 <-> 130 TRP ( 130-) A - CG 0.13 3.07 INTRA BF 19 LYS ( 19-) A - CG <-> 21 PHE ( 21-) A - CE1 0.12 3.08 INTRA BF 64 ASN ( 64-) A - C <-> 66 GLY ( 66-) A - N 0.11 2.79 INTRA BF 23 ARG ( 23-) A - CG <-> 24 CYS ( 24-) A - N 0.10 2.90 INTRA BF 14 VAL ( 14-) A - CG1 <-> 15 THR ( 15-) A - N 0.09 2.91 INTRA BF 38 TYR ( 38-) A - O <-> 41 ILE ( 41-) A - CG2 0.08 2.72 INTRA BF 104 GLN ( 104-) A - OE1 <-> 106 ASN ( 106-) A - N 0.08 2.62 INTRA BF 64 ASN ( 64-) A - CB <-> 65 PRO ( 65-) A - CD 0.08 3.02 INTRA BF 72 TYR ( 72-) A - CE2 <-> 99 CYS ( 99-) A - CB 0.08 3.12 INTRA BF 18 GLY ( 18-) A - C <-> 105 ASP ( 105-) A - OD1 0.08 2.72 INTRA BF 67 ASP ( 67-) A - OD1 <-> 69 SER ( 69-) A - N 0.08 2.62 INTRA BF 12 LEU ( 12-) A - CD2 <-> 13 SER ( 13-) A - N 0.08 2.92 INTRA BF 58 THR ( 58-) A - CG2 <-> 104 GLN ( 104-) A - O 0.07 2.73 INTRA BF 18 GLY ( 18-) A - CA <-> 59 GLN ( 59-) A - OE1 0.07 2.73 INTRA BF 104 GLN ( 104-) A - OE1 <-> 106 ASN ( 106-) A - CG 0.07 2.73 INTRA BF 81 TYR ( 81-) A - O <-> 92 VAL ( 92-) A - CG2 0.07 2.73 INTRA BF 108 ALA ( 108-) A - O <-> 111 VAL ( 111-) A - CG1 0.06 2.74 INTRA BL 80 HIS ( 80-) A - O <-> 91 ALA ( 91-) A - CA 0.06 2.74 INTRA BF 109 ASP ( 109-) A - O <-> 112 THR ( 112-) A - CG2 0.06 2.74 INTRA BL 64 ASN ( 64-) A - CB <-> 67 ASP ( 67-) A - OD1 0.06 2.74 INTRA BF 85 ASN ( 85-) A - OD1 <-> 87 LYS ( 87-) A - CG 0.06 2.74 INTRA BF 26 LEU ( 26-) A - O <-> 29 THR ( 29-) A - CG2 0.06 2.74 INTRA BL 26 LEU ( 26-) A - O <-> 30 LEU ( 30-) A - CD1 0.06 2.74 INTRA BL 117 VAL ( 117-) A - O <-> 120 ASP ( 120-) A - CG 0.06 2.74 INTRA BF 88 THR ( 88-) A - CA <-> 89 PRO ( 89-) A - CD 0.06 2.74 INTRA BF 19 LYS ( 19-) A - CB <-> 105 ASP ( 105-) A - OD1 0.06 2.74 INTRA BF 114 ALA ( 114-) A - O <-> 117 VAL ( 117-) A - CG1 0.06 2.74 INTRA BF 48 CYS ( 48-) A - O <-> 52 TRP ( 52-) A - CD1 0.05 2.75 INTRA BF 124 ILE ( 124-) A - CG2 <-> 130 TRP ( 130-) A - CD2 0.05 3.15 INTRA BF 17 GLN ( 17-) A - CG <-> 105 ASP ( 105-) A - OD2 0.05 2.75 INTRA BF 101 ALA ( 101-) A - CB <-> 109 ASP ( 109-) A - OD2 0.05 2.75 INTRA BL 17 GLN ( 17-) A - CD <-> 105 ASP ( 105-) A - OD2 0.05 2.75 INTRA BF 24 CYS ( 24-) A - O <-> 28 ARG ( 28-) A - CD 0.05 2.75 INTRA BF 122 GLN ( 122-) A - CD <-> 125 ARG ( 125-) A - CB 0.05 3.15 INTRA BF 115 LYS ( 115-) A - O <-> 118 VAL ( 118-) A - CG2 0.05 2.75 INTRA BL 120 ASP ( 120-) A - CA <-> 121 PRO ( 121-) A - CD 0.05 2.75 INTRA BF 65 PRO ( 65-) A - C <-> 66 GLY ( 66-) A - CA 0.05 2.25 INTRA BF 104 GLN ( 104-) A - CD <-> 106 ASN ( 106-) A - CG 0.05 3.15 INTRA BF 49 LEU ( 49-) A - CD1 <-> 127 TRP ( 127-) A - CB 0.04 3.16 INTRA BL 23 ARG ( 23-) A - NH1 <-> 142 TYR ( 142-) A - O 0.04 2.66 INTRA BF 59 GLN ( 59-) A - NE2 <-> 103 LEU ( 103-) A - O 0.04 2.66 INTRA BF 124 ILE ( 124-) A - C <-> 126 ALA ( 126-) A - N 0.04 2.86 INTRA BF 125 ARG ( 125-) A - O <-> 131 ARG ( 131-) A - NH1 0.04 2.66 INTRA BF 122 GLN ( 122-) A - OE1 <-> 125 ARG ( 125-) A - CD 0.04 2.76 INTRA BF 64 ASN ( 64-) A - N <-> 69 SER ( 69-) A - O 0.04 2.66 INTRA BF 104 GLN ( 104-) A - NE2 <-> 106 ASN ( 106-) A - O 0.04 2.66 INTRA BF 83 CYS ( 83-) A - SG <-> 98 SER ( 98-) A - C 0.04 3.36 INTRA BF 26 LEU ( 26-) A - CG <-> 30 LEU ( 30-) A - CD1 0.04 3.16 INTRA BL 17 GLN ( 17-) A - O <-> 59 GLN ( 59-) A - NE2 0.04 2.66 INTRA BF 17 GLN ( 17-) A - CG <-> 18 GLY ( 18-) A - N 0.03 2.97 INTRA BF 104 GLN ( 104-) A - CD <-> 106 ASN ( 106-) A - O 0.03 2.77 INTRA BF 64 ASN ( 64-) A - O <-> 66 GLY ( 66-) A - N 0.03 2.67 INTRA BF 64 ASN ( 64-) A - ND2 <-> 69 SER ( 69-) A - O 0.03 2.67 INTRA BF 55 GLY ( 55-) A - N <-> 56 TYR ( 56-) A - N 0.03 2.57 INTRA BL 29 THR ( 29-) A - CG2 <-> 30 LEU ( 30-) A - CD1 0.02 3.18 INTRA BL 70 THR ( 70-) A - CG2 <-> 72 TYR ( 72-) A - OH 0.01 2.79 INTRA BF 54 SER ( 54-) A - OG <-> 74 ILE ( 74-) A - CA 0.01 2.79 INTRA BF 93 ASN ( 93-) A - OD1 <-> 96 HIS ( 96-) A - N 0.01 2.69 INTRA BF 52 TRP ( 52-) A - NE1 <-> 133 HIS ( 133-) A - CB 0.01 3.09 INTRA BL 24 CYS ( 24-) A - SG <-> 146 CYS ( 146-) A - CA 0.01 2.99 INTRA BL 63 TYR ( 63-) A - OH <-> 68 GLN ( 68-) A - CD 0.01 2.79 INTRA BF 19 LYS ( 19-) A - CD <-> 21 PHE ( 21-) A - CE2 0.01 3.19 INTRA BF 64 ASN ( 64-) A - CB <-> 69 SER ( 69-) A - O 0.00 2.80 INTRA BF 64 ASN ( 64-) A - CA <-> 65 PRO ( 65-) A - N 0.00 2.20 INTRA BF 75 PHE ( 75-) A - O <-> 127 TRP ( 127-) A - NE1 0.00 2.70 INTRA BF 83 CYS ( 83-) A - SG <-> 102 LEU ( 102-) A - CD1 0.00 3.40 INTRA BF # 71 # Error: HIS, ASN, GLN side chain flips Listed here are Histidine, Asparagine or Glutamine residues for which the orientation determined from hydrogen bonding analysis are different from the assignment given in the input. Either they could form energetically more favourable hydrogen bonds if the terminal group was rotated by 180 degrees, or there is no assignment in the input file (atom type 'A') but an assignment could be made. Be aware, though, that if the topology could not be determined for one or more ligands, then this option will make errors. 62 ASN ( 62-) A - 106 ASN ( 106-) A -