Contacts of the strand formed by residues 1607 - 1614 (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 LYS1607 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1574B  VAL      3.7     1.3    -      -       -      -
   1591B  VAL*     5.4     8.1    -      -       +      -
   1592B  TYR      3.3    13.7    -      -       -      +
   1593B  LYS*     4.8     5.2    -      -       -      -
   1594B  ASP      5.3     0.9    -      -       -      +
   1604B  LEU*     6.1     4.4    -      -       -      +
   1605B  SER      4.3     6.3    -      -       -      +
   1606B  TYR*     1.3    76.8    -      -       -      +
   1608B  SER*     1.3    57.7    +      -       -      +
   1609B  VAL*     6.2     1.1    -      -       +      -
   1633B  THR*     3.3    33.8    +      -       -      -
   1634B  CYS      3.0    11.2    +      -       -      +
   1635B  THR*     3.2    20.6    -      -       +      +
   1636B  LEU*     2.8    31.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER1608 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1565B  ALA*     5.4     1.1    -      -       -      -
   1574B  VAL*     2.7    37.5    +      -       -      +
   1590B  LEU      3.7     0.9    -      -       -      +
   1591B  VAL*     3.3     4.9    -      -       -      +
   1592B  TYR*     2.7    55.3    +      -       -      +
   1607B  LYS*     1.3    71.7    -      -       -      +
   1609B  VAL*     1.3    62.4    +      -       -      +
   1610B  ILE*     3.8     3.4    +      -       -      -
   1636B  LEU*     3.5    20.3    -      -       -      +
   1638B  PHE*     4.1    11.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL1609 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1589B  GLN*     4.8    16.4    -      -       -      +
   1590B  LEU      3.3     5.4    -      -       -      +
   1591B  VAL*     3.8    29.6    -      -       +      -
   1607B  LYS*     5.7     1.6    -      -       +      -
   1608B  SER*     1.3    74.7    -      -       -      +
   1610B  ILE*     1.3    63.9    +      -       -      +
   1611B  SER*     3.5     8.1    +      -       -      -
   1635B  THR*     3.7    15.9    -      -       +      -
   1636B  LEU      2.7    21.4    +      -       -      +
   1637B  PHE*     3.4    30.9    -      -       +      -
   1638B  PHE      3.2    14.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE1610 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1550B  MET*     3.7    29.4    -      -       +      -
   1552B  ILE*     3.8    18.6    -      -       +      -
   1565B  ALA*     5.7     1.1    -      -       +      -
   1588B  LEU      3.9     0.9    -      -       -      +
   1589B  GLN*     3.5     1.7    -      -       -      +
   1590B  LEU*     2.6    46.9    +      -       +      +
   1592B  TYR*     3.5    36.8    -      -       +      -
   1608B  SER*     3.8     3.5    -      -       -      -
   1609B  VAL*     1.3    70.3    -      -       -      +
   1611B  SER*     1.3    64.1    +      -       -      +
   1612B  PHE*     4.5    13.6    -      -       +      -
   1624B  PRO*     5.7     2.0    -      -       +      -
   1638B  PHE*     3.6    35.0    -      -       +      -
   1639B  SER      5.2     0.2    -      -       -      +
   1640B  TRP*     5.1     9.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER1611 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1587B  VAL*     3.6    12.6    -      -       -      -
   1588B  LEU      3.7     4.0    -      -       -      -
   1589B  GLN*     3.3    25.5    +      -       -      +
   1609B  VAL      3.5     9.0    +      -       -      -
   1610B  ILE*     1.3    76.2    -      -       -      +
   1612B  PHE*     1.3    63.9    +      -       -      +
   1613B  VAL*     3.6     2.6    +      -       -      +
   1638B  PHE      3.1    10.4    +      -       -      -
   1639B  SER*     3.4     4.3    -      -       -      -
   1640B  TRP      3.0    23.2    +      -       -      -
   1708B  ALA*     3.5    28.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE1612 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1529B  LEU*     3.6    30.1    -      -       +      -
   1532B  LEU*     4.0    12.1    -      -       +      -
   1552B  ILE*     3.6    33.2    -      -       +      -
   1581B  LEU*     4.7     0.7    -      -       +      -
   1586B  GLN      4.2     0.5    -      -       -      +
   1587B  VAL*     3.4     7.6    -      -       -      +
   1588B  LEU*     2.9    58.2    +      -       +      +
   1590B  LEU*     3.6    26.2    -      -       +      -
   1610B  ILE*     4.5     7.6    -      -       +      -
   1611B  SER*     1.3    71.6    -      -       -      +
   1613B  VAL*     1.3    61.5    +      -       -      +
   1640B  TRP*     3.5    44.6    -      +       +      -
   1642B  THR*     4.3     5.8    -      -       -      -
   1645B  ALA*     3.8    18.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL1613 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1586B  GLN      4.8     3.4    -      -       -      +
   1587B  VAL*     4.7     3.8    -      -       +      -
   1611B  SER      3.9    11.9    -      -       -      +
   1612B  PHE*     1.3    76.1    -      -       -      +
   1614B  CYS*     1.3    65.0    +      -       -      +
   1639B  SER*     4.5     3.6    -      -       -      -
   1640B  TRP      3.1     5.2    +      -       -      +
   1641B  HIS*     3.3    42.0    -      -       +      +
   1642B  THR      3.0    27.7    +      -       -      +
   1645B  ALA*     3.6     3.9    -      -       -      +
   1697B  PRO*     3.6    27.4    -      -       +      -
   1708B  ALA*     4.0    23.6    -      -       +      -
   1709B  GLY*     3.8    15.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS1614 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1586B  GLN*     4.5    16.6    +      -       +      +
   1613B  VAL*     1.3    78.9    -      -       -      +
   1615B  ARG*     1.3    61.1    +      -       -      +
   1616B  PRO*     4.2     8.7    -      -       -      -
   1641B  HIS*     4.2     3.3    -      -       -      -
   1642B  THR      3.7     1.1    -      -       -      -
   1645B  ALA      3.3    15.9    +      -       -      +
   1646B  CYS*     2.0    50.3    -      -       -      -
   1647B  GLU      4.9     1.3    -      -       -      -
   1648B  GLN      5.2     3.4    -      -       -      -
   1649B  ALA      5.8     2.5    -      -       -      -
   1696B  GLN*     5.1     0.5    -      -       -      +
   1697B  PRO*     3.4    33.9    -      -       +      +
----------------------------------------------------------
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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