Contacts of the strand formed by residues 177 - 182 (chain C) in PDB entry 3AP3


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 LYS 177 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70C  LEU      2.6    14.7    +      -       -      +
     71C  ILE*     3.5     4.5    -      -       +      +
     72C  PHE*     3.0    26.9    +      -       -      +
    175C  ASN      4.6     6.1    -      -       -      +
    176C  SER*     1.3    76.5    -      -       -      +
    178C  PHE*     1.3    65.4    +      -       -      +
    231C  GLU*     3.2    28.5    -      -       -      +
    232C  LYS*     3.6    10.3    -      -       +      +
    255C  PHE*     2.9    41.4    +      -       +      -
    256C  LEU*     3.6    37.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 178 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72C  PHE*     3.4    38.8    -      +       +      -
    163C  LEU*     4.3    11.9    -      -       +      -
    166C  SER*     3.6    25.4    -      -       -      -
    169C  LEU*     3.3    37.7    -      -       +      -
    170C  SER*     3.6    22.9    -      -       -      -
    176C  SER*     3.4    21.3    -      -       -      -
    177C  LYS*     1.3    76.6    -      -       -      +
    179C  LEU*     1.3    63.6    +      -       -      +
    180C  LEU      4.0     0.2    -      -       -      -
    228C  VAL*     4.8     6.3    -      -       +      -
    232C  LYS*     2.8    21.9    +      -       +      +
    233C  CYS*     3.4    17.3    -      -       -      -
    234C  LEU*     2.8    32.1    +      -       -      +
    255C  PHE*     4.2     1.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 179 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71C  ILE*     3.9    26.2    -      -       +      -
     72C  PHE      2.9    12.7    +      -       -      +
     73C  VAL*     3.3    15.4    -      -       +      +
     74C  GLY      2.9    27.0    +      -       -      +
     84C  MET*     4.6     9.2    -      -       +      -
     88C  LEU*     4.0    22.2    -      -       +      -
    163C  LEU*     4.2     2.5    -      -       -      -
    178C  PHE*     1.3    77.7    -      -       -      +
    180C  LEU*     1.3    59.6    +      -       -      +
    181C  MET*     3.9     0.9    -      -       -      -
    234C  LEU*     3.7    28.7    -      -       +      -
    236C  VAL*     3.9    17.9    -      -       +      -
    252C  ILE*     4.2    20.0    -      -       +      -
    255C  PHE*     4.1     9.9    -      -       +      -
    256C  LEU*     4.6     5.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 180 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74C  GLY      3.3     2.7    -      -       -      -
     75C  GLY*     3.6    26.2    -      -       -      +
    163C  LEU*     3.6    17.3    -      -       +      -
    178C  PHE      4.0     1.2    -      -       -      -
    179C  LEU*     1.3    70.2    -      -       -      +
    181C  MET*     1.3    65.8    +      -       -      +
    182C  VAL*     3.4    14.1    +      -       +      +
    218C  ILE*     4.7     6.7    -      -       +      -
    221C  MET*     3.3    50.0    -      -       +      +
    222C  TYR*     4.1    14.8    -      -       +      +
    225C  CYS*     3.9    16.4    -      -       +      -
    233C  CYS*     4.5     5.2    -      -       -      -
    234C  LEU      3.2    11.3    +      -       -      +
    235C  PRO*     3.7     2.9    -      -       +      +
    236C  VAL*     3.1    22.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with MET 181 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     73C  VAL*     4.2     5.8    -      -       +      -
     74C  GLY      2.7    12.3    +      -       -      +
     75C  GLY*     4.0    10.2    -      -       -      -
     76C  VAL      4.7     1.0    +      -       -      -
     79C  SER*     3.2    39.1    +      -       -      +
     80C  GLY*     3.7    14.4    -      -       -      +
     81C  THR*     3.6    33.9    -      -       +      -
     84C  MET*     3.5    29.4    -      -       +      +
    179C  LEU      3.7     1.1    +      -       -      +
    180C  LEU*     1.3    72.7    -      -       -      +
    182C  VAL*     1.3    62.5    +      -       -      +
    183C  ARG      4.1     0.4    -      -       -      -
    218C  ILE*     5.1     3.3    -      -       -      +
    236C  VAL*     3.5    22.7    -      -       +      +
    238C  TYR*     4.4    10.8    -      -       +      -
    241C  LEU*     3.9    24.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 182 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    180C  LEU*     3.7    18.8    -      -       +      +
    181C  MET*     1.3    77.4    -      -       -      +
    183C  ARG*     1.3    57.0    +      -       -      +
    218C  ILE*     4.1    20.2    -      -       +      -
    222C  TYR*     5.5     1.1    -      -       +      -
    235C  PRO*     4.8    12.8    -      -       +      -
    236C  VAL      2.7    13.4    +      -       -      +
    237C  TYR*     3.3    30.3    -      -       +      -
    238C  TYR*     2.9    12.4    +      -       -      +
    239C  GLU*     2.6    26.2    -      -       -      +
    323C  LEU*     3.8    24.9    -      -       +      -
    325C  TYR*     3.1    17.0    +      -       +      -
----------------------------------------------------------
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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