Contacts of the strand formed by residues 630 - 635 (chain G) in PDB entry 6MZL


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 VAL 630 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    589G  TRP*     3.4    19.2    -      -       -      +
    603G  GLY*     3.7    22.7    -      -       -      +
    604G  GLY      2.9    26.2    +      -       -      +
    607G  ARG*     4.5     7.6    -      -       -      +
    608G  VAL      3.3    23.8    -      -       -      +
    626G  HIS*     4.6     5.8    -      -       -      +
    628G  ALA      3.2     7.7    +      -       -      +
    629G  ASP*     1.3    72.6    -      -       -      +
    631G  ASN*     1.3    65.4    +      -       -      +
    632G  CYS      3.8    11.2    -      -       -      +
    633G  THR*     4.5     1.1    -      -       +      -
    644G  THR*     3.7    31.9    -      -       +      -
    646G  SER*     3.6     9.4    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ASN 631 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    589G  TRP*     4.0    10.8    -      -       -      +
    590G  ASP*     3.3    18.2    -      -       -      +
    629G  ASP*     3.5     7.4    +      -       -      +
    630G  VAL*     1.3    78.6    -      -       -      +
    632G  CYS*     1.3    61.4    +      -       +      +
    645G  GLY      2.8    14.2    +      -       -      +
    646G  SER      3.0    25.4    +      -       -      -
    647G  ALA*     3.6     8.1    -      -       -      +
    671G  PRO*     4.3     5.5    -      -       -      +
    672G  ILE      2.5    33.0    +      -       -      +
    673G  HIS*     4.8     1.8    +      -       -      -
     60I  MET*     3.3    35.2    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with CYS 632 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    590G  ASP*     3.3     8.1    -      -       -      +
    630G  VAL*     3.8     0.9    -      -       -      +
    631G  ASN*     1.3    78.0    -      -       +      +
    633G  THR*     1.3    67.6    +      -       -      +
    634G  ARG*     5.5     7.0    -      -       +      -
    644G  THR*     3.4     3.5    -      -       -      +
    645G  GLY*     2.9    47.2    +      -       -      +
    672G  ILE*     4.4     7.0    -      -       -      -
    673G  HIS      4.8    11.2    -      -       -      +
    674G  SER*     4.3     6.7    -      -       -      +
    675G  LEU*     3.6    36.6    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 633 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    590G  ASP*     2.4    48.6    +      -       +      +
    592G  GLN*     3.4    13.5    -      -       -      +
    601G  VAL*     3.7    21.8    -      -       +      +
    602G  SER      4.3     1.6    -      -       -      -
    603G  GLY*     3.4    34.5    -      -       -      +
    609G  ALA*     4.9     4.2    -      -       -      +
    630G  VAL*     4.5     1.1    -      -       +      -
    632G  CYS*     1.3    74.6    -      -       -      +
    634G  ARG*     1.3    64.5    +      -       -      +
    642G  VAL*     4.7     3.8    -      -       -      +
    643G  ALA      3.1     8.7    +      -       -      -
    644G  THR*     3.2    22.2    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 634 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    590G  ASP*     4.4     5.4    -      -       -      +
    592G  GLN*     3.4    37.3    +      -       +      +
    601G  VAL*     4.8     0.2    -      -       -      -
    632G  CYS*     5.5     6.2    -      -       +      -
    633G  THR*     1.3    81.9    +      -       -      +
    635G  PHE*     1.3    70.1    +      -       -      +
    642G  VAL*     3.4     5.1    -      -       -      -
    643G  ALA*     2.9    35.0    +      -       -      +
    675G  LEU*     3.6    22.9    +      -       +      +
    676G  THR*     3.4    31.4    -      -       -      +
    677G  PHE*     3.7    12.2    -      -       +      +
    718G  ARG*     3.2    33.7    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 635 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    592G  GLN*     3.1    26.9    -      -       +      +
    593G  PHE      3.1    16.8    -      -       -      +
    594G  SER*     3.1    35.2    -      -       -      -
    595G  PRO*     3.7     9.0    -      -       +      -
    599G  TYR*     4.9     2.0    -      -       +      -
    600G  PHE*     3.7     9.9    -      -       -      -
    601G  VAL*     3.5    28.5    -      -       +      -
    611G  LEU*     4.1    11.4    -      -       +      -
    634G  ARG*     1.3    82.9    +      -       -      +
    636G  HIS*     1.3    70.2    +      -       -      +
    637G  PRO*     4.0     1.2    -      -       -      +
    639G  SER*     3.6    32.5    -      -       -      -
    641G  TYR      3.3     3.4    -      -       -      -
    642G  VAL*     3.7    13.5    -      -       +      -
    677G  PHE*     3.2    17.3    -      -       -      +
----------------------------------------------------------
 Back to top of page


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