Contacts of the strand formed by residues 1572 - 1576 (chain A) in PDB entry 2V5P


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 ILE1572 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1566A  CYS*     3.2     2.6    -      -       -      -
   1567A  PHE*     3.0    53.3    +      -       +      +
   1570A  THR*     3.0    32.6    +      -       -      +
   1571A  ARG*     1.3    69.8    -      -       -      +
   1573A  SER*     1.3    64.4    +      -       -      +
   1574A  VAL      3.7     0.2    +      -       -      -
   1596A  SER*     3.3    22.0    -      -       -      +
   1606A  TYR*     4.3    12.1    -      -       +      -
     12D  GLU*     4.0    35.7    -      -       +      +
     15D  ASP*     4.2    10.5    -      -       +      -
     16D  THR*     4.1     9.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER1573 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1560A  PRO*     6.0     0.2    -      -       -      -
   1563A  VAL*     3.3    36.2    -      -       -      +
   1565A  ALA      3.6     6.3    -      -       -      -
   1566A  CYS*     4.3     0.7    -      -       -      +
   1571A  ARG      3.3     7.5    +      -       -      -
   1572A  ILE*     1.3    73.7    -      -       -      +
   1574A  VAL*     1.3    62.2    +      -       -      +
   1575A  GLY      3.2    14.4    +      -       -      -
   1576A  LYS*     5.2     0.7    -      -       -      +
   1594A  ASP      5.1     0.2    +      -       -      -
   1595A  GLY*     3.7     7.2    -      -       -      -
   1596A  SER*     3.3    33.7    +      -       -      -
   1606A  TYR*     3.5    13.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL1574 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1548A  VAL*     4.9     6.5    -      -       +      -
   1565A  ALA*     3.0    34.8    +      -       +      +
   1566A  CYS*     4.2     3.4    -      -       -      +
   1567A  PHE*     3.5    35.2    -      -       +      -
   1573A  SER*     1.3    74.1    -      -       -      +
   1575A  GLY*     1.3    56.5    +      -       -      +
   1592A  TYR*     4.9     0.4    -      -       -      -
   1606A  TYR*     3.7    18.8    -      -       +      -
   1607A  LYS      3.3     1.2    -      -       -      -
   1608A  SER*     2.7    50.1    +      -       -      +
   1636A  LEU*     3.8    30.1    -      -       +      -
   1638A  PHE*     5.4     0.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY1575 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1563A  VAL*     3.8     2.6    -      -       -      +
   1564A  GLY*     3.3    19.1    +      -       -      -
   1565A  ALA      3.8     4.3    +      -       -      -
   1573A  SER*     3.2    16.4    +      -       -      -
   1574A  VAL*     1.3    80.8    -      -       -      +
   1576A  LYS*     1.3    61.6    +      -       -      -
   1592A  TYR*     3.6    18.5    -      -       -      +
   1593A  LYS      3.6    11.4    -      -       -      -
   1595A  GLY*     3.9     7.7    -      -       -      -
   1606A  TYR      4.3     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS1576 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1562A  GLY*     3.4    18.2    -      -       -      +
   1563A  VAL*     4.3     8.3    -      -       +      +
   1573A  SER*     5.3     0.7    -      -       -      +
   1575A  GLY*     1.3    74.5    -      -       -      -
   1577A  ALA*     1.3    63.6    +      -       -      +
   1578A  ASN*     3.6     7.0    +      -       -      +
   1592A  TYR*     3.1    23.9    -      -       -      -
   1593A  LYS*     2.7    16.3    +      -       +      +
   1594A  ASP*     3.4    33.5    +      -       +      +
----------------------------------------------------------
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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