Contacts of the strand formed by residues 1490 - 1493 (chain C) in PDB entry 5ZCJ


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 ARG1490 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1488C  GLY      3.8     1.2    +      -       -      +
   1489C  LEU*     1.3    73.3    -      -       -      +
   1491C  VAL*     1.3    64.1    +      -       -      +
   1503C  SER*     4.3     1.6    -      -       -      -
   1504C  GLY      3.4    19.8    +      -       -      +
   1505C  LYS*     3.6    35.9    -      -       +      +
   1520C  ASP*     2.6    45.9    +      -       -      -
   1534C  LEU*     3.5    15.9    -      -       -      +
   1535C  CYS      4.6     1.4    +      -       -      +
   1536C  ASP*     3.5    41.5    -      -       +      +
   1583C  ARG*     3.5    38.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL1491 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1489C  LEU      3.7    10.5    -      -       -      +
   1490C  ARG*     1.3    81.0    +      -       -      +
   1492C  VAL*     1.3    68.4    +      -       -      +
   1493C  ALA*     4.4     1.6    -      -       +      -
   1503C  SER*     3.5     4.5    -      -       -      -
   1504C  GLY      2.8    40.0    +      -       -      +
   1505C  LYS*     4.4     1.1    -      -       -      +
   1506C  ILE*     3.7    24.7    -      -       +      -
   1517C  LEU*     3.5    33.0    -      -       +      -
   1532C  ILE*     3.8    15.9    -      -       +      -
   1533C  LEU      3.3    14.1    -      -       -      +
   1534C  LEU*     4.3    10.5    -      -       +      -
   1535C  CYS      4.7     2.5    -      -       -      -
   1536C  ASP*     6.1     0.2    -      -       -      -
   1602C  LEU*     5.4     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL1492 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1491C  VAL*     1.3    77.3    -      -       -      +
   1493C  ALA*     1.3    65.2    +      -       -      +
   1501C  PHE*     3.6    30.1    -      -       +      +
   1502C  TYR      3.3    12.6    -      -       -      +
   1503C  SER*     4.3    10.5    -      -       -      +
   1533C  LEU*     2.8    44.4    +      -       +      +
   1535C  CYS*     3.9    20.0    -      -       -      +
   1538C  ILE*     4.2    24.2    -      -       +      -
   1586C  VAL      5.9     0.9    -      -       -      +
   1587C  ILE*     5.7     1.1    -      -       -      -
   1588C  LEU*     3.8    18.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA1493 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1491C  VAL*     4.3     1.5    -      -       +      -
   1492C  VAL*     1.3    77.5    -      -       -      +
   1494C  LYS*     1.3    62.8    +      -       -      +
   1500C  TYR      3.9     0.2    -      -       -      +
   1501C  PHE*     3.6     5.2    -      -       -      -
   1502C  TYR*     2.6    38.1    +      -       -      +
   1517C  LEU*     3.6    31.0    -      -       +      -
   1519C  PHE*     3.2    13.5    -      -       +      -
   1527C  VAL*     4.5     0.7    -      -       +      -
   1531C  ASP      3.2    14.6    -      -       -      +
   1532C  ILE*     3.9    11.2    -      -       +      -
----------------------------------------------------------
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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