Contacts of the strand formed by residues 462 - 467 (chain V) in PDB entry 5IY8


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 CYS 462 (chain V).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    332V  ARG*     4.2    15.3    -      -       -      +
    357V  VAL*     4.3    16.8    -      -       +      -
    359V  LYS*     4.4     6.7    -      -       +      -
    436V  GLY      3.4     8.5    +      -       -      +
    437V  LEU*     3.6    23.0    -      -       +      +
    438V  MET*     2.8    26.9    +      -       -      +
    461V  HIS*     1.3   109.7    -      -       -      +
    463V  LYS*     1.3    65.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 463 (chain V). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    282V  LYS*     5.0    10.7    +      -       -      +
    285V  ILE*     4.3    10.4    -      -       -      +
    332V  ARG*     3.3    20.7    +      -       -      +
    335V  SER      5.0     0.2    -      -       -      -
    336V  GLY*     3.5    20.4    -      -       -      +
    437V  LEU*     5.4     1.1    -      -       -      -
    438V  MET*     3.4    14.4    -      -       +      +
    440V  LEU*     5.1     1.1    -      -       +      -
    455V  LEU*     3.7    30.3    +      -       +      +
    458V  VAL      5.4     1.4    +      -       -      -
    459V  GLN      4.7     3.8    +      -       -      -
    460V  ALA*     3.2    42.6    +      -       +      +
    462V  CYS*     1.3    78.7    -      -       -      +
    464V  LEU*     1.3    61.3    +      -       -      +
    482V  PHE      4.7     2.4    +      -       -      -
    483V  LEU      2.9    23.8    +      -       -      +
    484V  ILE*     3.5    21.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 464 (chain V). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    327V  MET*     4.1    23.3    -      -       +      -
    335V  SER*     6.5     0.2    -      -       -      -
    336V  GLY*     3.5    14.6    -      -       -      +
    338V  ILE*     4.1    25.6    -      -       +      -
    349V  VAL*     5.0     1.6    -      -       +      +
    353V  ALA*     3.5    32.3    -      -       +      -
    437V  LEU*     5.2     1.1    -      -       +      +
    438V  MET      2.8    10.6    +      -       -      +
    439V  ILE*     3.4    18.4    -      -       +      +
    440V  LEU*     2.9    26.5    +      -       -      +
    463V  LYS*     1.3    74.2    -      -       -      +
    465V  GLY*     1.4    73.4    +      -       -      +
    466V  LEU*     4.0    20.8    -      -       +      +
    484V  ILE*     4.0     4.5    -      -       -      -
    488V  LEU*     6.0     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 465 (chain V). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    336V  GLY      3.0    14.0    +      -       -      -
    337V  VAL*     3.5     3.7    -      -       -      -
    338V  ILE      2.9    26.4    +      -       -      -
    440V  LEU*     3.4     7.0    -      -       -      -
    443V  VAL*     3.9    27.4    -      -       -      -
    464V  LEU*     1.4    72.5    -      -       -      +
    466V  LEU*     1.3    67.5    -      -       -      +
    484V  ILE*     3.7     2.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 466 (chain V). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    338V  ILE*     3.4    20.2    -      -       +      +
    340V  LEU*     5.0     3.6    -      -       +      -
    346V  LYS*     3.9    27.6    -      -       +      +
    349V  VAL*     3.6    23.8    -      -       +      -
    350V  GLY*     3.7    35.4    -      -       -      +
    374V  TRP*     4.9     6.7    -      -       +      -
    439V  ILE*     4.5    10.8    -      -       +      -
    440V  LEU      2.9    12.2    +      -       -      +
    441V  ASP*     4.4     2.5    -      -       -      +
    442V  GLU      2.9    12.8    +      -       -      -
    443V  VAL*     2.9    21.5    +      -       -      +
    464V  LEU*     4.0    15.9    -      -       +      +
    465V  GLY*     1.3    81.6    -      -       -      +
    467V  THR*     1.3    58.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 467 (chain V). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    337V  VAL*     5.1     0.7    -      -       +      -
    338V  ILE      3.4     5.3    +      -       -      +
    339V  VAL*     3.2    17.0    -      -       +      +
    340V  LEU*     3.0    28.1    +      -       -      +
    346V  LYS*     4.0    10.2    -      -       -      +
    442V  GLU*     4.3     2.5    -      -       -      +
    443V  VAL*     3.6    24.0    -      -       +      +
    444V  HIS*     3.0    23.2    +      -       -      -
    466V  LEU*     1.3    73.3    -      -       -      +
    468V  ALA*     1.3    65.1    +      -       -      +
    469V  THR      3.2     1.2    +      -       -      -
    470V  LEU*     3.1    45.7    +      -       +      -
----------------------------------------------------------
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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