Contacts of the strand formed by residues 764 - 767 (chain M) in PDB entry 2W4G


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 764 (chain M).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    502M  GLU*     2.8    36.3    +      -       -      -
    506M  GLU*     2.5    37.1    +      -       +      +
    714M  ARG*     4.4    19.3    -      -       +      +
    715M  VAL      2.8    24.7    -      -       -      +
    716M  LEU*     3.8    17.8    -      -       +      +
    717M  TYR*     3.7    10.8    -      -       -      -
    761M  GLY      2.9    26.4    +      -       -      +
    763M  THR*     1.3    87.4    -      -       -      +
    765M  VAL*     1.3    61.1    +      -       -      +
    766M  PHE*     3.7     8.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 765 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96C  LYS*     5.3     3.6    -      -       -      -
    714M  ARG*     3.2     8.8    -      -       -      +
    715M  VAL*     3.0    31.1    +      -       +      +
    717M  TYR*     3.4    32.5    -      -       +      +
    720M  PHE*     5.5     0.4    -      -       +      -
    744M  SER*     4.9     4.9    -      -       -      -
    748M  LEU*     5.2     3.4    -      -       +      -
    758M  TYR*     3.8    14.8    -      -       +      -
    759M  ARG      3.1    10.8    -      -       -      +
    760M  PHE*     3.8    14.6    -      -       +      +
    764M  LYS*     1.3    76.3    -      -       -      +
    766M  PHE*     1.3    88.6    +      -       -      +
    767M  PHE*     3.5    29.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 766 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    502M  GLU*     3.0    33.2    -      -       +      -
    503M  TYR*     3.4    24.9    -      +       -      -
    506M  GLU*     2.9    31.9    -      -       +      -
    508M  ILE*     2.6    31.9    -      -       +      -
    711M  PHE*     3.5    18.6    -      -       +      -
    713M  SER      4.0     1.3    -      -       -      -
    714M  ARG*     3.3    37.0    -      -       +      -
    758M  TYR*     2.9     9.6    -      -       -      +
    759M  ARG*     2.3    39.8    +      -       +      +
    764M  LYS*     3.7    12.6    -      -       +      -
    765M  VAL*     1.3    81.9    -      -       -      +
    767M  PHE*     1.3    62.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 767 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    711M  PHE*     3.6     5.9    -      -       -      +
    712M  PRO*     3.5    16.3    -      -       -      +
    713M  SER*     2.9    25.4    +      -       -      +
    715M  VAL*     3.8    16.2    -      -       +      -
    720M  PHE*     3.6    38.8    -      +       -      -
    748M  LEU*     4.3    11.0    -      -       +      -
    757M  GLN      3.5     3.8    -      -       -      -
    758M  TYR*     3.6    18.8    -      +       +      -
    765M  VAL*     3.5    30.7    -      -       +      -
    766M  PHE*     1.3    74.0    -      -       -      +
    768M  LYS*     1.3    67.5    +      -       -      +
    771M  LEU*     3.0    36.3    -      -       +      -
    772M  LEU*     3.3    26.7    -      -       +      -
    775M  LEU*     4.2     3.6    -      -       +      -
----------------------------------------------------------
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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