Contacts of the strand formed by residues 1053 - 1066 (chain A) in PDB entry 2PC0


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 PHE1053 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1046A  MET*     3.6    41.4    -      -       +      +
   1047A  ILE      3.3    21.3    -      -       -      +
   1048A  GLY      4.1     4.3    -      -       -      -
   1049A  GLY*     3.4    26.9    -      -       -      -
   1052A  GLY*     1.3    76.8    -      -       -      -
   1054A  ILE*     1.3    70.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE1054 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1045A  LYS      3.6     0.5    -      -       -      +
   1046A  MET*     3.4     4.6    -      -       -      -
   1047A  ILE*     2.9    46.3    +      -       +      +
   1048A  GLY*     5.7     1.8    -      -       -      -
   1052A  GLY      5.4     2.0    -      -       -      +
   1053A  PHE*     1.3    80.2    -      -       -      +
   1055A  LYS*     1.3    74.4    +      -       -      +
   1056A  VAL*     4.4     6.7    -      -       +      -
   1079A  PRO*     4.1    28.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS1055 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1044A  PRO*     4.2    21.3    -      -       +      -
   1045A  LYS      3.5     4.9    -      -       -      +
   1046A  MET*     3.6    29.1    -      -       +      +
   1054A  ILE*     1.3    74.1    -      -       -      +
   1056A  VAL*     1.3    76.3    +      -       -      +
   1079A  PRO*     3.7    17.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL1056 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1032A  VAL*     4.3     8.7    -      -       +      -
   1044A  PRO*     3.3     5.9    -      -       -      +
   1045A  LYS*     2.9    44.1    +      -       +      +
   1047A  ILE*     3.8    29.4    -      -       +      -
   1054A  ILE*     4.4     4.7    -      -       +      -
   1055A  LYS*     1.3    81.9    -      -       -      +
   1057A  ARG*     1.3    64.3    +      -       -      +
   1076A  LEU*     3.8    33.9    -      -       +      -
   1077A  VAL      3.5    11.2    -      -       -      +
   1078A  GLY*     4.1    16.8    -      -       -      -
   1079A  PRO*     4.3     4.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG1057 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1035A  GLU*     2.9    41.2    +      -       -      -
   1036A  MET      3.3    14.3    +      -       -      -
   1037A  ASN*     5.3     1.4    +      -       -      +
   1042A  TRP*     3.6    43.9    -      -       +      +
   1043A  LYS      3.7     4.7    -      -       -      -
   1044A  PRO*     5.6     0.2    -      -       +      -
   1056A  VAL*     1.3    73.5    -      -       -      +
   1058A  GLN*     1.3    61.2    +      -       -      +
   1059A  TYR*     2.9    39.1    +      -       +      -
   1075A  VAL      3.7     1.2    -      -       -      +
   1076A  LEU*     3.3     5.3    -      -       -      -
   1077A  VAL*     2.8    49.5    +      -       -      +
   1078A  GLY*     5.4     0.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN1058 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1041A  ARG      4.0     1.4    -      -       -      +
   1042A  TRP*     3.1    23.1    -      -       -      -
   1043A  LYS*     2.8    49.0    +      -       +      +
   1045A  LYS*     3.7    29.6    +      -       +      +
   1056A  VAL      4.0     0.8    +      -       -      -
   1057A  ARG*     1.3    71.4    -      -       -      +
   1059A  TYR*     1.3    60.3    +      -       -      +
   1060A  ASP*     3.0    30.1    +      -       -      +
   1074A  THR*     3.7    13.4    +      -       +      +
   1076A  LEU*     3.6    23.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR1059 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1038A  LEU*     3.3    37.7    +      -       +      -
   1039A  PRO      3.6    18.2    -      -       -      -
   1040A  GLY      4.1     6.5    -      -       -      -
   1041A  ARG      4.5     5.4    -      -       -      -
   1042A  TRP*     3.6    30.2    +      +       +      -
   1057A  ARG*     2.9    57.3    +      -       +      -
   1058A  GLN*     1.3    73.7    -      -       -      +
   1060A  ASP*     1.3    62.7    +      -       -      +
   1062A  ILE*     3.8    18.8    -      -       +      +
   1074A  THR*     3.3     3.3    -      -       -      +
   1075A  VAL      2.9    37.7    +      -       -      +
   1077A  VAL*     3.9    24.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP1060 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1039A  PRO      5.2     1.4    -      -       -      +
   1041A  ARG      4.8     6.2    +      -       -      +
   1043A  LYS*     5.0     5.2    +      -       -      -
   1058A  GLN*     3.0    30.2    +      -       -      +
   1059A  TYR*     1.3    74.1    -      -       -      +
   1061A  GLN*     1.3    79.9    +      -       +      +
   1062A  ILE*     3.3    11.4    +      -       -      +
   1074A  THR*     2.8    27.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN1061 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1060A  ASP*     1.3    81.2    -      -       +      +
   1062A  ILE*     1.3    62.8    +      -       -      +
   1063A  LEU      4.1     0.7    +      -       -      -
   1072A  ILE*     3.6    25.0    -      -       +      +
   1073A  GLY*     3.5    11.7    +      -       -      -
   1074A  THR*     4.7     0.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE1062 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1015A  ILE*     3.9    26.0    -      -       +      -
   1016A  GLY      5.7     0.4    -      -       -      +
   1038A  LEU*     4.2    13.2    -      -       +      -
   1039A  PRO*     3.8    41.7    -      -       +      +
   1059A  TYR*     3.8    27.4    -      -       +      +
   1060A  ASP      3.7    14.6    -      -       -      +
   1061A  GLN*     1.3    78.3    -      -       -      +
   1063A  LEU*     1.3    75.3    +      -       -      +
   1064A  ILE*     3.7     3.3    +      -       -      +
   1071A  ALA      3.7     0.7    -      -       -      +
   1072A  ILE*     3.2     4.4    -      -       -      -
   1073A  GLY      2.9    30.2    +      -       -      +
   1075A  VAL*     3.9    10.0    -      -       +      +
   1089A  LEU*     5.3     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU1063 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    907A  PGR      3.7    14.8    -      -       +      +
   1014A  LYS      4.3     0.2    -      -       -      +
   1015A  ILE*     3.9    12.5    -      -       -      +
   1016A  GLY      4.7     1.9    +      -       -      -
   1061A  GLN      4.1     2.0    +      -       -      -
   1062A  ILE*     1.3    82.6    -      -       -      +
   1064A  ILE*     1.3    62.9    +      -       -      +
   1070A  LYS*     4.6    24.2    -      -       +      +
   1071A  ALA      3.4     7.2    -      -       -      +
   1072A  ILE*     3.5    28.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE1064 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1013A  ILE*     4.0    15.9    -      -       +      -
   1014A  LYS      3.5    11.2    -      -       -      +
   1015A  ILE*     4.1    20.2    -      -       +      -
   1031A  THR*     5.2     0.9    -      -       +      -
   1033A  LEU*     4.9     3.1    -      -       +      -
   1062A  ILE*     4.8     2.5    -      -       +      +
   1063A  LEU*     1.3    78.7    -      -       -      +
   1065A  GLU*     1.3    66.0    +      -       -      +
   1066A  ILE*     3.6    35.7    -      -       +      -
   1070A  LYS*     3.3     4.4    -      -       -      +
   1071A  ALA*     2.9    47.3    +      -       +      +
   1075A  VAL*     5.2     1.3    -      -       +      -
   1085A  ILE*     4.0    20.6    -      -       +      -
   1089A  LEU*     4.1    22.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU1065 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1012A  THR      4.0     0.3    -      -       -      +
   1013A  ILE*     3.2     6.2    -      -       -      +
   1014A  LYS*     2.9    72.9    +      -       +      +
   1064A  ILE*     1.3    73.0    -      -       -      +
   1066A  ILE*     1.3    61.3    +      -       -      +
   1067A  CYS      3.7     1.0    +      -       -      -
   1068A  GLY*     3.8    36.0    +      -       -      +
   1069A  HIS      3.4     2.7    -      -       -      +
   1070A  LYS*     3.4    32.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE1066 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1011A  VAL*     4.1     9.4    -      -       +      -
   1013A  ILE*     4.2     9.4    -      -       +      -
   1024A  LEU*     3.9    29.2    -      -       +      -
   1064A  ILE*     3.6    37.0    -      -       +      -
   1065A  GLU*     1.3    72.4    -      -       -      +
   1067A  CYS*     1.3    78.7    +      -       +      +
   1068A  GLY      3.0     0.9    +      -       -      -
   1069A  HIS*     2.8    26.3    +      -       -      +
   1071A  ALA*     4.8     0.2    -      -       +      -
   1085A  ILE*     3.9    22.2    -      -       +      -
   1089A  LEU*     4.0    12.8    -      -       +      -
   1093A  ILE*     4.0    33.6    -      -       +      +
----------------------------------------------------------
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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