Contacts of the strand formed by residues 1624 - 1630 (chain B) 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 PRO1624 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1538B  PHE*     4.1    21.5    -      -       +      -
   1539B  THR      4.9     3.1    -      -       -      +
   1540B  ALA*     3.9    25.2    -      -       +      +
   1541B  ALA      4.9     0.9    +      -       -      -
   1550B  MET*     4.2    23.6    -      -       -      -
   1610B  ILE*     5.7     3.4    -      -       +      -
   1623B  ARG*     1.4    93.8    -      -       +      +
   1625B  MET*     1.3    61.6    +      -       -      +
   1638B  PHE*     5.2     3.6    -      -       +      -
   1639B  SER      3.8     7.4    -      -       -      +
   1640B  TRP*     3.5    44.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET1625 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1540B  ALA*     5.1     1.6    -      -       -      +
   1541B  ALA      5.8     1.6    -      -       -      +
   1621B  THR*     5.4     5.8    -      -       -      +
   1623B  ARG      3.8     9.4    -      -       -      +
   1624B  PRO*     1.3    79.5    -      -       -      +
   1626B  LEU*     1.3    67.4    +      -       -      +
   1627B  ILE*     3.6     3.1    +      -       +      +
   1638B  PHE*     3.3    18.7    -      -       -      -
   1639B  SER      3.1    27.2    +      -       -      +
   1700B  PRO*     3.7    46.7    -      -       +      +
   1701B  MET      5.4     2.5    -      -       -      +
   1919B  ILE*     4.1    35.2    -      -       +      -
   1923B  ALA      3.5    23.6    -      -       -      +
   1924B  LYS*     5.4     1.6    -      -       -      -
   1925B  LEU*     5.4     7.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU1626 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1540B  ALA*     5.2     2.5    -      -       +      +
   1541B  ALA      4.3    18.4    +      -       -      +
   1542B  TYR*     3.8    27.8    -      -       +      -
   1543B  SER      5.5     0.2    -      -       -      +
   1548B  VAL*     5.4     3.4    -      -       +      -
   1625B  MET*     1.3    76.2    -      -       -      +
   1627B  ILE*     1.3    68.6    +      -       -      +
   1628B  SER*     4.5     8.7    -      -       -      +
   1629B  LEU*     3.9    25.6    -      -       +      -
   1636B  LEU*     4.7     1.3    -      -       +      -
   1637B  PHE      4.2     6.5    -      -       -      +
   1638B  PHE*     3.8    31.7    -      -       +      -
   1701B  MET      4.9     1.6    -      -       -      +
   1702B  HIS*     4.8     9.4    -      -       -      -
   1923B  ALA*     5.6     5.0    -      -       +      +
     19C  PHE*     4.1    17.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE1627 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1625B  MET*     4.4     4.7    -      -       +      +
   1626B  LEU*     1.3    78.3    -      -       -      +
   1628B  SER*     1.3    64.9    +      -       -      +
   1637B  PHE*     3.4    22.3    +      -       +      +
   1638B  PHE      4.3     1.3    -      -       -      -
   1639B  SER*     3.4    35.4    -      -       -      +
   1700B  PRO*     3.6    33.7    -      -       +      -
   1701B  MET      4.2    12.1    -      -       -      +
   1702B  HIS*     4.1     5.4    +      -       -      -
   1703B  ALA*     3.1    21.5    +      -       -      -
   1704B  VAL      3.8    22.7    -      -       -      +
   1705B  PRO*     3.8    16.8    -      -       +      -
   1706B  CYS      4.9     4.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER1628 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1626B  LEU*     3.7     6.4    -      -       -      +
   1627B  ILE*     1.3    84.2    -      -       -      +
   1629B  LEU*     1.3    85.3    +      -       -      +
   1637B  PHE*     3.3    26.1    +      -       -      +
   1703B  ALA*     3.9    19.5    +      -       -      +
   1705B  PRO*     3.8    27.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU1629 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1606B  TYR*     5.5     5.4    -      -       +      -
   1626B  LEU*     3.9    20.6    -      -       +      -
   1628B  SER*     1.3    96.3    +      -       -      +
   1630B  ASP*     1.3    64.6    +      -       -      +
   1631B  LYS*     3.7    11.8    +      -       +      +
   1634B  CYS*     5.5     2.0    -      -       -      -
   1635B  THR      3.4    20.9    -      -       -      +
   1636B  LEU*     3.5    30.1    -      -       +      -
   1637B  PHE*     4.3     3.4    -      -       -      -
   1705B  PRO*     5.6     2.1    -      -       -      +
     19C  PHE*     3.5    34.3    -      -       +      -
     53C  LEU*     5.9     6.5    -      -       +      -
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Residues in contact with ASP1630 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1629B  LEU*     1.3    73.2    -      -       -      +
   1631B  LYS*     1.3    64.6    +      -       -      +
   1632B  GLN*     3.4    21.0    +      -       -      +
   1633B  THR*     3.3    29.9    +      -       +      +
   1634B  CYS*     3.4    16.3    +      -       -      -
   1635B  THR*     3.5    14.2    +      -       -      +
   1637B  PHE*     3.6    24.4    -      -       +      -
----------------------------------------------------------
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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