Contacts of the strand formed by residues 464 - 470 (chain B) in PDB entry 5ZRV


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 GLY 464 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    342B  TYR*     4.3     3.6    -      -       -      -
    343B  VAL      2.5    31.4    +      -       -      +
    354B  GLY      4.0    20.2    -      -       -      -
    358B  ALA*     6.5     0.7    -      -       -      -
    457B  ALA      3.5     8.7    -      -       -      -
    462B  GLY      3.5     1.6    +      -       -      -
    463B  GLN*     1.3    74.8    -      -       -      +
    465B  HIS*     1.3    57.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 465 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    341B  MET      4.3     5.8    -      -       -      -
    342B  TYR*     5.1     0.7    -      -       -      +
    354B  GLY      5.2     0.4    +      -       -      -
    355B  PRO*     5.0     5.4    -      -       -      +
    358B  ALA*     6.5     1.3    -      -       -      -
    455B  VAL      4.4     0.4    -      -       -      -
    456B  ALA*     2.9     4.9    -      -       -      -
    457B  ALA*     2.9    34.7    +      -       -      +
    464B  GLY*     1.3    74.8    -      -       -      -
    466B  ALA*     1.3    57.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 466 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    340B  PHE*     3.5     1.9    -      -       -      -
    341B  MET*     3.1    35.4    +      -       -      +
    358B  ALA      6.0     6.1    -      -       -      -
    359B  THR*     6.2     2.0    -      -       -      +
    362B  VAL*     6.0     1.2    -      -       -      -
    455B  VAL      3.2     9.6    -      -       -      -
    456B  ALA*     4.1     2.5    -      -       -      +
    465B  HIS*     1.3    75.2    -      -       -      +
    467B  MET*     1.3    58.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 467 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    339B  ASP      3.4    13.2    -      -       -      -
    340B  PHE*     4.2     2.0    -      -       -      +
    454B  LEU*     3.4     2.8    -      -       -      +
    455B  VAL*     2.9    30.9    +      -       -      +
    466B  ALA*     1.3    75.4    -      -       -      +
    468B  ILE*     1.3    63.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 468 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    337B  LEU*     4.4     1.7    -      -       -      -
    338B  ARG*     3.5    26.6    +      -       -      +
    339B  ASP      3.4     8.8    +      -       -      +
    453B  GLY      3.6     7.6    -      -       -      +
    454B  LEU*     4.1     4.7    -      -       -      +
    467B  MET*     1.3    74.4    -      -       -      +
    469B  VAL*     1.3    58.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 469 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    336B  TYR      4.3    10.3    -      -       -      -
    337B  LEU*     5.2     0.2    -      -       -      +
    338B  ARG      5.1     0.2    -      -       -      +
    452B  TYR*     3.5     1.7    -      -       -      -
    453B  GLY      2.8    37.3    +      -       -      +
    467B  MET      4.0     0.2    +      -       -      -
    468B  ILE*     1.3    73.7    -      -       -      +
    470B  GLU*     1.3    62.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 470 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    334B  LYS      4.6     0.2    -      -       -      +
    335B  ALA*     3.6    16.1    -      -       -      -
    336B  TYR*     4.0    13.3    +      -       -      +
    338B  ARG      5.5     0.8    -      -       -      +
    442B  ALA*     6.0     1.7    -      -       -      -
    451B  GLN      3.3     9.2    -      -       -      -
    452B  TYR*     4.5     2.5    -      -       -      +
    469B  VAL*     1.3    73.9    -      -       -      +
    471B  ALA*     1.3    67.3    +      -       -      +
----------------------------------------------------------
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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