Contacts of the strand formed by residues 176 - 183 (chain B) in PDB entry 2PI8


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 ASN 176 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    166B  TYR*     4.1     1.1    -      -       -      -
    167B  ILE      2.8    37.5    +      -       -      +
    169B  PHE*     4.4    14.9    -      -       +      -
    174B  PRO      3.4     4.5    +      -       -      +
    175B  LEU*     1.3    71.0    -      -       -      +
    177B  PHE*     1.3    60.9    +      -       -      +
    178B  PHE*     3.4    18.6    +      -       +      -
    238B  PRO*     3.2    22.0    -      -       -      +
    239B  GLN      3.2     9.2    +      -       -      -
    240B  SER*     2.9    38.8    +      -       -      +
    241B  PHE      3.7     4.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 177 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103B  THR*     4.1     2.9    -      -       +      -
    164B  SER*     3.4    36.1    -      -       -      -
    165B  GLY      4.0    12.1    -      -       -      -
    166B  TYR*     3.6    22.0    -      +       +      -
    175B  LEU      3.7     3.6    +      -       -      -
    176B  ASN*     1.3    71.7    +      -       -      +
    178B  PHE*     1.3    61.1    +      -       -      +
    179B  SER*     3.3    25.0    +      -       -      -
    237B  LYS      3.4     0.2    -      -       -      +
    239B  GLN*     2.7    46.0    +      -       +      +
    240B  SER      4.2     0.4    -      -       -      +
    241B  PHE      3.8     4.4    -      -       -      +
    242B  ALA      3.5    24.2    -      -       -      +
    243B  PRO      4.0     9.4    -      -       -      -
    244B  VAL*     3.8    26.9    -      -       +      -
    245B  LYS*     3.8    25.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 178 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120B  ILE*     3.8    27.1    -      -       +      -
    147B  LEU*     3.7    39.3    -      -       +      -
    148B  ALA*     4.7     3.4    -      -       +      -
    159B  MSE      5.0     3.1    -      -       -      -
    164B  SER*     3.2    22.1    -      -       -      -
    165B  GLY      3.0    16.5    +      -       -      +
    167B  ILE*     3.6    33.4    -      -       +      -
    169B  PHE*     4.7     9.4    -      +       -      -
    176B  ASN*     3.6    33.2    -      -       +      -
    177B  PHE*     1.3    71.8    -      -       -      +
    179B  SER*     1.3    63.5    +      -       -      +
    236B  PHE*     3.3    22.1    -      +       +      -
    237B  LYS      3.7     4.3    -      -       -      -
    238B  PRO*     3.7    15.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 179 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    164B  SER*     4.1     1.8    -      -       -      -
    177B  PHE*     3.3    27.3    +      -       -      -
    178B  PHE*     1.3    75.4    -      -       -      +
    180B  TYR*     1.3    60.0    +      -       -      +
    181B  ALA      3.0     4.0    +      -       -      -
    236B  PHE*     3.2     7.3    -      -       -      -
    237B  LYS      2.9    30.2    +      -       -      -
    239B  GLN*     3.0    31.0    +      -       -      -
    245B  LYS*     5.5     1.8    -      -       -      -
    696B  PO4      4.7     0.6    +      -       -      -
      5F  NAG      4.0    10.8    -      -       -      -
      6F  NAG      3.7    11.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 180 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    163B  GLY*     3.3    33.9    +      -       -      +
    164B  SER*     4.2     2.0    -      -       -      -
    179B  SER*     1.3    70.1    -      -       -      +
    181B  ALA*     1.3    60.2    +      -       -      +
    182B  GLY*     4.0    20.2    -      -       -      -
    183B  LYS*     3.6    26.9    -      -       +      +
    234B  VAL*     3.7    28.0    -      -       +      -
    235B  PHE      4.2     2.7    -      -       -      -
    236B  PHE*     4.6     0.7    -      -       -      -
      3F  NAG      4.2    14.4    -      -       -      -
      4F  NAG      3.8    44.5    +      -       -      +
      5F  NAG      2.9    51.5    +      -       -      +
      6F  NAG      3.5     3.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 181 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    123B  MSE      3.6    35.6    -      -       +      +
    179B  SER      3.0     2.0    +      -       -      -
    180B  TYR*     1.3    76.4    -      -       -      +
    182B  GLY*     1.3    58.7    +      -       -      +
    235B  PHE      3.0    14.5    +      -       -      +
    236B  PHE      3.6    20.2    -      -       -      +
    237B  LYS*     3.7    15.5    -      -       +      -
      5F  NAG      5.4     0.8    +      -       -      -
      6F  NAG      3.4    20.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 182 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    123B  MSE      3.9    13.7    -      -       -      +
    180B  TYR*     3.6    14.9    -      -       -      -
    181B  ALA*     1.3    79.3    -      -       -      +
    183B  LYS*     1.3    62.0    +      -       -      +
    234B  VAL*     3.4    10.0    -      -       -      +
    235B  PHE*     2.9    28.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 183 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    123B  MSE      4.8     0.4    -      -       -      -
    129B  ARG*     4.2    13.5    -      -       -      +
    180B  TYR*     3.6    19.0    +      -       +      +
    182B  GLY*     1.3    74.3    -      -       -      +
    184B  ASN*     1.3    88.3    +      -       -      +
    185B  GLY      4.9     0.2    -      -       -      -
    186B  HIS      2.8    30.7    +      -       -      -
    187B  ALA*     4.8     1.6    -      -       -      +
    188B  TYR*     5.2     4.2    -      -       +      +
    232B  SER*     3.1    17.8    +      -       -      +
    233B  PHE      3.3    18.6    -      -       -      +
    234B  VAL*     4.1     8.7    -      -       +      -
    235B  PHE*     3.8    12.4    -      -       -      -
----------------------------------------------------------
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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