Contacts of the strand formed by residues 430 - 437 (chain C) in PDB entry 6VSB


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 THR 430 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    380C  TYR*     2.7    38.3    +      -       -      +
    382C  VAL*     5.2     0.2    -      -       -      -
    412C  PRO*     5.3     3.5    -      -       -      +
    425C  LEU*     4.3    21.9    -      -       +      +
    426C  PRO*     4.6    11.4    +      -       -      +
    428C  ASP      3.6     7.5    +      -       -      -
    429C  PHE*     1.3    81.6    +      -       -      +
    431C  GLY*     1.3    70.3    +      -       -      +
    432C  CYS*     3.6     2.9    -      -       -      +
    433C  VAL*     6.0     2.2    -      -       +      -
    464C  PHE*     4.8     4.8    -      -       +      -
    512C  VAL*     4.0    20.2    -      -       +      -
    513C  LEU      4.1     1.8    -      -       -      +
    514C  SER*     3.8    23.3    -      -       -      +
    515C  PHE      5.3     1.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 431 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    379C  CYS*     3.0    13.5    -      -       -      +
    380C  TYR      3.2     1.6    +      -       -      -
    382C  VAL*     4.2     7.6    -      -       -      +
    430C  THR*     1.3    74.8    -      -       -      +
    432C  CYS*     1.3    73.2    +      -       -      +
    513C  LEU      3.0    21.7    +      -       -      -
    515C  PHE*     3.4    35.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 432 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    377C  PHE*     4.4     3.8    -      -       +      -
    378C  LYS      3.3     6.7    -      -       -      +
    379C  CYS*     2.0    43.5    -      -       -      +
    380C  TYR      4.6     0.7    -      -       -      +
    382C  VAL*     5.4     0.4    -      -       -      -
    387C  LEU*     4.1    19.3    -      -       -      -
    430C  THR*     3.6     2.6    +      -       -      +
    431C  GLY*     1.3    83.4    -      -       -      +
    433C  VAL*     1.3    65.4    +      -       -      +
    434C  ILE*     3.8    18.8    -      -       +      +
    511C  VAL      4.0     1.0    -      -       -      +
    512C  VAL*     3.8     6.7    -      -       -      +
    513C  LEU*     3.3    35.7    +      -       +      +
    515C  PHE*     4.8     7.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 433 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    376C  THR*     3.8     6.8    -      -       +      +
    378C  LYS*     2.6    45.3    +      -       +      +
    380C  TYR*     3.5    30.3    -      -       +      -
    407C  VAL      5.3     2.5    -      -       -      +
    410C  ILE*     3.4    45.5    -      -       +      +
    411C  ALA*     5.0     1.8    -      -       -      -
    425C  LEU*     5.2     7.4    -      -       +      -
    430C  THR*     6.0     2.7    -      -       +      -
    432C  CYS*     1.3    75.2    -      -       -      +
    434C  ILE*     1.3    71.3    +      -       -      +
    435C  ALA*     6.1     0.7    -      -       +      -
    510C  VAL*     4.7     2.0    -      -       +      -
    511C  VAL      4.4     0.9    -      -       -      -
    512C  VAL*     4.6     7.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 434 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    342C  PHE*     4.5    12.3    -      -       +      -
    368C  LEU*     5.7     1.3    -      -       +      -
    374C  PHE*     3.5    27.6    -      -       +      -
    376C  THR*     3.5     4.0    -      -       -      +
    377C  PHE*     3.4    33.7    -      -       +      -
    432C  CYS*     3.8    20.9    -      -       +      +
    433C  VAL*     1.3    87.1    -      -       -      +
    435C  ALA*     1.3    68.0    +      -       -      +
    436C  TRP*     4.6     4.5    -      -       +      -
    510C  VAL*     3.2    25.6    -      -       -      +
    511C  VAL*     3.3    38.4    +      -       +      +
    513C  LEU*     5.2    10.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 435 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    374C  PHE*     3.7     1.2    -      -       -      -
    375C  SER*     2.7    31.0    +      -       -      -
    376C  THR*     3.1    24.3    +      -       +      +
    407C  VAL*     5.1    10.3    -      -       +      -
    433C  VAL*     6.1     0.7    -      -       +      -
    434C  ILE*     1.3    81.9    -      -       -      +
    436C  TRP*     1.3    57.6    +      -       -      +
    508C  TYR*     4.4    13.7    -      -       +      -
    509C  ARG      3.3     8.3    -      -       -      +
    510C  VAL*     3.6    18.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 436 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    341C  VAL      4.3     0.4    -      -       -      -
    342C  PHE*     3.3    65.3    +      +       +      -
    344C  ALA      5.5     0.2    -      -       -      -
    347C  PHE*     3.6    19.3    -      +       -      -
    373C  SER*     3.2    29.8    -      -       -      +
    374C  PHE*     5.0     1.1    -      -       +      -
    375C  SER*     3.8    10.1    -      -       -      +
    434C  ILE*     4.6     6.3    -      -       +      -
    435C  ALA*     1.3    78.9    -      -       -      +
    437C  ASN*     1.3    85.7    +      -       -      +
    438C  SER*     4.9     3.2    -      -       -      -
    508C  TYR*     3.2     9.6    -      -       -      -
    509C  ARG*     3.0    61.7    +      -       +      +
    511C  VAL*     3.8    17.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 437 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    375C  SER*     3.8     7.7    +      -       -      +
    436C  TRP*     1.3    91.8    -      -       -      +
    438C  SER*     1.3    71.0    +      -       -      +
    439C  ASN*     3.0    28.7    +      -       -      +
    440C  ASN*     4.6     3.6    +      -       -      +
    503C  VAL*     3.5    10.3    -      -       -      +
    506C  GLN*     3.3    23.1    -      -       -      +
    507C  PRO      3.9     1.1    -      -       -      -
    508C  TYR*     3.2    45.5    +      -       +      +
----------------------------------------------------------
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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