Contacts of the strand formed by residues 510 - 515 (chain A) in PDB entry 2P2M


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 TYR 510 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    423A  ILE*     4.0    29.6    -      -       +      -
    436A  SER*     2.9    17.8    +      -       -      -
    437A  ALA*     3.2    13.7    +      -       -      +
    438A  THR      2.9    19.6    +      -       -      +
    440A  PRO*     4.3    10.5    -      -       +      -
    446A  PRO*     3.6    44.4    +      -       +      +
    447A  ALA      4.2     0.8    +      -       -      -
    448A  LEU*     4.0    31.9    -      -       +      -
    464A  LEU*     4.5     2.7    -      -       +      -
    502A  ALA*     4.5     5.8    -      -       +      -
    503A  ARG      3.3    10.5    -      -       -      -
    504A  ARG*     3.1    34.4    +      -       +      -
    508A  GLY      3.6    16.6    -      -       -      -
    509A  TYR*     1.3    72.8    -      -       -      +
    511A  TRP*     1.3    60.3    +      -       -      +
    512A  ILE*     4.0     8.2    +      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 511 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    392A  PRO*     5.2     4.7    -      -       +      -
    433A  LYS*     3.7    35.4    -      -       +      -
    434A  ALA      3.3    28.0    -      -       -      -
    435A  GLY*     3.6    22.2    -      -       -      +
    436A  SER*     3.6    16.7    +      -       -      -
    502A  ALA*     3.2     2.5    -      -       -      -
    503A  ARG*     2.7    89.2    +      -       +      +
    505A  ASP*     3.0    26.7    +      -       +      +
    509A  TYR      3.4    14.9    +      -       -      -
    510A  TYR*     1.3    72.9    -      -       -      +
    512A  ILE*     1.3    63.3    +      -       -      +
    513A  THR*     3.5     4.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 512 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    389A  PRO*     3.9    17.8    -      -       -      +
    413A  TRP*     3.7    39.5    -      -       +      +
    423A  ILE*     4.5     8.1    -      -       +      -
    435A  GLY      5.2     4.4    +      -       -      +
    437A  ALA*     4.0    17.9    -      -       +      +
    464A  LEU*     4.0    16.6    -      -       +      -
    500A  ASP*     4.3     9.0    -      -       -      +
    501A  GLY      3.7     8.7    -      -       -      +
    502A  ALA*     4.1     2.5    -      -       +      -
    510A  TYR*     4.1    18.2    -      -       +      -
    511A  TRP*     1.3    72.7    -      -       -      +
    513A  THR*     1.3    63.0    +      -       -      +
    514A  GLY      3.8     9.9    -      -       -      +
    998A  PRX      3.6    31.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 513 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    389A  PRO*     4.2    10.8    -      -       -      +
    461A  GLU*     6.0     2.0    -      -       -      +
    501A  GLY*     3.1    23.7    +      -       -      -
    502A  ALA*     3.7     2.3    +      -       -      -
    503A  ARG*     3.9    28.5    -      -       +      +
    511A  TRP*     3.9     6.5    -      -       +      +
    512A  ILE*     1.3    76.2    -      -       -      +
    514A  GLY*     1.3    57.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 514 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    389A  PRO*     4.6     9.2    -      -       -      -
    500A  ASP*     3.2    10.8    -      -       -      -
    501A  GLY*     2.8    25.1    +      -       -      -
    512A  ILE*     3.5     9.7    +      -       -      +
    513A  THR*     1.3    81.0    +      -       -      +
    515A  ARG*     1.3    66.1    +      -       -      +
    516A  VAL*     4.2     1.7    -      -       -      +
    998A  PRX      4.6     4.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 515 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    266A  GLY*     5.7     0.4    -      -       -      -
    267A  SER      5.6     0.2    -      -       -      +
    415A  GLN*     3.5     9.5    -      -       -      +
    488A  TYR*     6.2     1.8    -      -       -      -
    498A  SER      3.5    16.5    +      -       -      -
    499A  GLY*     3.3     6.5    +      -       -      -
    500A  ASP*     3.2    15.7    +      -       -      -
    514A  GLY*     1.3    73.6    -      -       -      +
    516A  VAL*     1.3    61.1    +      -       -      +
    517A  ASP*     2.8    46.9    +      -       -      +
    519A  VAL*     3.5    45.1    -      -       +      +
    520A  LEU      5.2     3.8    -      -       -      +
    521A  ASN*     5.7     4.5    -      -       +      +
    526A  ARG*     3.7    33.5    -      -       -      +
    998A  PRX      3.0    32.3    +      -       -      +
----------------------------------------------------------
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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