Contacts of the strand formed by residues 1161 - 1174 (chain A) in PDB entry 4UHW


Residue contacts within the protein are derived with the CSU software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332). A short description of the analytical approach is given at the end of the page.
For CSU analysis of other PDB entry

Note:
Non-standard 3 letter residue codes indicate a heterogroup. To identify and analyse, use LPC software

Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB   - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC   - hydrophobic-hydrophilic contact (destabilizing contact)
+/-  - indicates presence/absence of a specific contacts
*    - indicates residues forming contacts  by their side chain
       (including CA atoms)
Residues in contact with TYR1161 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1015A  PRO*     3.7     0.5    -      -       -      +
   1016A  VAL*     3.0    62.8    +      -       +      +
   1090A  VAL*     4.1     0.9    -      -       -      +
   1093A  ASP*     2.7    29.0    +      -       -      -
   1145A  TYR*     4.5     6.1    -      +       -      -
   1159A  PHE*     3.5     2.4    -      -       -      +
   1160A  GLU*     1.3    88.5    -      -       +      +
   1162A  PHE*     1.3    79.9    +      -       -      +
   1163A  VAL*     4.2     3.1    -      -       +      -
   1258A  ASN*     5.8     4.5    -      -       -      +
   1260A  ASN*     4.7     4.5    -      -       -      +
   1261A  THR*     3.5    26.7    -      -       +      -
   1266A  LYS*     3.9    32.3    -      -       +      -
   1267A  GLY*     2.9    29.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE1162 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    964A  TYR*     3.7    15.3    -      -       -      -
    966A  GLN*     3.8    32.5    -      -       -      -
    967A  GLU      4.7     1.8    -      -       -      -
    968A  ILE*     3.5    31.2    -      -       +      -
   1013A  LYS*     3.6    24.7    -      -       +      -
   1014A  PHE      3.5     3.4    -      -       -      +
   1015A  PRO*     3.5    30.3    -      -       +      -
   1159A  PHE*     4.0     6.3    -      -       +      -
   1160A  GLU      5.4     0.2    -      -       -      -
   1161A  TYR*     1.3    88.7    -      -       -      +
   1163A  VAL*     1.3    58.6    +      -       -      +
   1164A  TYR*     3.6    31.9    -      -       +      +
   1266A  LYS*     2.7    32.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL1163 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1012A  LEU*     3.8     2.4    -      -       +      +
   1013A  LYS*     3.5     2.9    -      -       -      -
   1014A  PHE*     2.7    47.9    +      -       +      +
   1016A  VAL*     4.2     8.1    -      -       +      -
   1161A  TYR*     4.2     8.9    -      -       +      -
   1162A  PHE*     1.3    73.0    -      -       -      +
   1164A  TYR*     1.3    66.2    +      -       -      +
   1189A  MET*     4.3    12.3    -      -       +      -
   1190A  ASP      3.6    18.2    -      -       -      +
   1191A  VAL*     5.5     0.2    -      -       -      -
   1266A  LYS*     4.2    12.3    -      -       +      -
   1267A  GLY      3.8    23.3    -      -       -      +
   1268A  LEU*     4.6     6.3    -      -       +      -
   1271A  SER*     3.7    29.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR1164 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    968A  ILE*     4.1     7.3    -      -       -      +
    969A  ASN      3.4    29.0    +      -       -      -
    970A  ALA*     4.1     8.2    -      -       +      +
    972A  ASN*     4.0    13.9    -      -       +      +
    973A  LEU*     3.8    36.6    -      -       +      +
    976A  CYS*     3.8     1.6    -      -       -      -
   1012A  LEU*     3.3    14.6    -      -       -      +
   1013A  LYS*     3.6    29.5    -      -       +      +
   1162A  PHE*     3.6    38.4    -      +       +      +
   1163A  VAL*     1.3    77.0    -      -       -      +
   1165A  GLY*     1.3    58.8    +      -       -      +
   1189A  MET*     3.7     4.9    -      -       -      +
   1190A  ASP*     2.8    56.1    +      -       +      +
   1266A  LYS*     4.4     3.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY1165 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    973A  LEU*     4.4     2.9    -      -       -      +
    976A  CYS*     3.6    11.4    -      -       -      +
   1011A  PRO*     3.5     2.8    -      -       -      +
   1012A  LEU*     2.7    50.1    +      -       -      +
   1164A  TYR*     1.3    76.6    -      -       -      +
   1166A  ALA*     1.3    60.4    +      -       -      +
   1188A  VAL      3.3    12.6    -      -       -      -
   1189A  MET*     4.2     4.0    -      -       -      -
   1275A  LEU*     4.9     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA1166 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    976A  CYS*     3.5    28.2    -      -       -      +
    977A  TRP*     4.1    14.6    -      -       +      +
    980A  CYS*     4.0    11.2    -      -       +      -
   1009A  MET*     5.1     0.4    -      -       +      -
   1010A  VAL      3.4    12.6    -      -       -      +
   1011A  PRO*     4.1     4.9    -      -       +      -
   1012A  LEU      4.5     0.4    -      -       -      +
   1165A  GLY*     1.3    74.8    -      -       -      +
   1167A  ALA*     1.3    65.1    +      -       -      +
   1187A  ILE*     3.6     3.6    -      -       -      +
   1188A  VAL      3.0    29.0    +      -       -      +
   1275A  LEU*     4.3     4.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA1167 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    980A  CYS*     3.9     1.3    -      -       -      -
   1009A  MET*     3.3     5.9    -      -       -      +
   1010A  VAL*     2.9    32.4    +      -       +      +
   1166A  ALA*     1.3    79.1    -      -       -      +
   1168A  CYS*     1.3    61.2    +      -       -      +
   1185A  THR*     5.2     0.9    -      -       +      -
   1186A  ASP      3.2    10.3    -      -       -      +
   1187A  ILE*     4.1    11.9    -      -       +      -
   1208A  PHE*     5.4     0.2    -      -       +      -
   1275A  LEU*     4.0    30.1    -      -       +      +
   1278A  SER*     3.8    17.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS1168 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    980A  CYS*     3.7     8.3    -      -       -      -
    984A  SER*     3.8    21.3    -      -       -      -
    986A  TYR*     4.0    12.1    -      -       -      -
    989A  ARG*     3.9    12.3    -      -       -      -
   1007A  LEU*     3.8    22.0    -      -       -      -
   1008A  ALA      3.3    11.7    -      -       -      -
   1009A  MET*     3.7    18.2    -      -       +      -
   1167A  ALA*     1.3    74.8    -      -       -      +
   1169A  SER*     1.3    65.8    +      -       -      +
   1185A  THR*     3.2     4.5    -      -       -      +
   1186A  ASP*     2.8    34.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with SER1169 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1007A  LEU*     3.4     5.7    -      -       -      +
   1008A  ALA      3.0    29.9    +      -       -      -
   1168A  CYS*     1.3    72.6    +      -       -      +
   1170A  GLU*     1.3    62.0    +      -       -      +
   1171A  VAL*     5.6     0.4    -      -       -      -
   1184A  ARG      3.4     4.7    -      -       -      -
   1185A  THR*     2.6    24.8    +      -       -      +
   1278A  SER*     2.8    42.0    +      -       -      -
   1279A  VAL*     3.8    13.4    -      -       -      +
   1282A  ALA*     3.3     7.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU1170 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    989A  ARG*     2.8    41.6    +      -       -      +
    992A  ALA*     5.8     1.9    -      -       -      +
    993A  VAL*     3.5    23.7    -      -       +      +
   1005A  LYS*     3.8    15.4    +      -       +      +
   1006A  GLY      3.3    11.4    -      -       -      +
   1007A  LEU*     3.5     7.9    -      -       +      -
   1169A  SER*     1.3    73.2    -      -       -      +
   1171A  VAL*     1.3    65.2    +      -       -      +
   1182A  ASN*     3.7     1.6    -      -       -      +
   1183A  ILE*     2.8    57.9    +      -       +      +
   1184A  ARG*     2.9    11.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL1171 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1005A  LYS*     3.2     7.4    -      -       -      +
   1006A  GLY      3.0    32.5    +      -       -      +
   1169A  SER*     5.6     0.2    -      -       -      -
   1170A  GLU*     1.3    80.3    -      -       -      +
   1172A  GLU*     1.3    58.9    +      -       -      +
   1173A  ILE*     4.5     8.7    -      -       +      -
   1180A  HIS*     4.2     3.8    -      -       +      -
   1181A  LYS      3.2     9.0    -      -       -      +
   1182A  ASN*     3.4    25.4    -      -       -      +
   1183A  ILE*     3.4     7.8    -      -       -      +
   1279A  VAL*     4.1    13.9    -      -       +      -
   1282A  ALA*     3.6    20.0    -      -       +      +
   1283A  ILE*     3.6    39.9    -      -       +      +
   1286A  ALA*     4.6     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU1172 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    551A  SER*     5.4     1.2    -      -       -      -
    556A  LEU*     3.4    31.9    -      -       +      +
    996A  PHE*     3.3    26.0    -      -       +      -
   1003A  LYS*     3.7    13.0    -      -       +      +
   1004A  LYS      3.3    12.8    -      -       -      +
   1005A  LYS*     3.9    17.0    +      -       +      -
   1171A  VAL*     1.3    74.8    -      -       -      +
   1173A  ILE*     1.3    70.3    +      -       -      +
   1180A  HIS*     3.3     2.5    -      -       -      -
   1181A  LYS*     3.0    33.9    +      -       +      +
   1183A  ILE*     3.5    15.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE1173 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    556A  LEU*     4.4     1.1    -      -       -      -
   1003A  LYS*     3.3    13.9    -      -       -      +
   1004A  LYS*     2.8    33.0    +      -       +      +
   1171A  VAL*     4.5     5.8    -      -       +      -
   1172A  GLU*     1.3    76.5    -      -       -      +
   1174A  ASP*     1.3    60.9    +      -       -      +
   1175A  CYS*     4.0    13.7    -      -       -      +
   1179A  ASP      3.4     8.7    -      -       -      +
   1180A  HIS*     3.9    15.3    -      -       +      -
   1283A  ILE*     4.2    16.8    -      -       +      -
   1286A  ALA*     3.9    28.9    -      -       +      +
   1287A  VAL*     4.0    16.8    -      -       +      +
   1311A  ILE*     4.0    10.3    -      -       +      -
   1315A  CYS*     3.9    27.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP1174 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    525A  LYS*     3.4    19.2    +      -       -      -
    552A  ALA*     5.7     0.3    -      -       -      -
    555A  ASP*     3.4    16.9    -      -       -      +
    556A  LEU*     4.2     5.1    -      -       +      +
   1002A  TRP      3.9     2.1    -      -       -      +
   1003A  LYS*     3.3    24.4    -      -       -      +
   1173A  ILE*     1.3    71.6    -      -       -      +
   1175A  CYS*     1.3    59.5    +      -       -      +
   1176A  LEU*     3.0    22.5    +      -       -      +
   1177A  THR*     3.2    28.8    +      -       -      +
   1178A  GLY*     2.8    32.2    +      -       -      -
   1179A  ASP*     3.0    17.7    +      -       +      +
   1311A  ILE*     4.8     0.7    -      -       -      +
----------------------------------------------------------
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A short description of the analytical approach
The contact analysis used in this page is based upon the approach developed in: Sobolev V., Wade R.C., Vriend G. and Edelman M. PROTEINS (1996) 25, 120-129. Contact legitimacy depends on the hydrophobic-hydrophilic properties of the contacting atoms. In order to define it, for each inter-atomic contact, eight atom classes have been introduced:


   I  Hydrophilic      - N and O that can donate and accept hydrogen bonds
                         (e.g., oxygen of hydroxyl group of Ser. or Thr)
  II  Acceptor         - N or O that can only accept a hydrogen bond
 III  Donor            - N that can only donate a hydrogen bond
  IV  Hydrophobic      - Cl, Br, I and all C atoms that are not in
                         aromatic rings and do not have a covalent bond to
                         a N or O atom
   V  Aromatic         - C in aromatic rings irrespective of any other 
                         bonds formed by the atom
  VI  Neutral          - C atoms that have a covalent bond to at least one
                         atom of class I or two or more atoms from class II
                         or III; atoms; S, F, P, and metal atoms in all cases
 VII  Neutral-donor    - C atoms that have a covalent bond with only one
                         atom of class III
VIII  Neutral-acceptor - C atoms that have a covalent bond with only 
                         one atom of class II
For each pair of contacts the state of legitimacy is shown below:

Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
  Atomic class           I  II  III   IV   V   VI  VII  VIII
------------------------------------------------------------
   I  (Hydrophilic)      +   +    +    -   +   +    +    +
  II  (Acceptor)         +   -    +    -   +   +    +    -
 III  (Donor)            +   +    -    -   +   +    -    +
  IV  (Hydrophobic)      -   -    -    +   +   +    +    +
   V  (Aromatic)         +   +    +    +   +   +    +    +
  VI  (Neutral)          +   +    +    +   +   +    +    +
 VII  (Neutral-donor)    +   +    -    +   +   +    -    +
VIII  (Neutral-acceptor) +   -    +    +   +   +    +    -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically assigned based on the atomic coordinates. However, in three cases (see below) the automatic assignment is currently ambiguous. In these cases, the user is advised to manually analyse the full list of contacts using LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are 
   considered "aromatic" (Class V) if the ring is approximately
   planar, and "hydrophobic" (Class IV) or "neutral" (Classes
   VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
   "hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
   "carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).

Please E-mail any questions and/or suggestions concerning this page to Vladimir.Sobolev@weizmann.ac.il