Contacts of the strand formed by residues 404 - 411 (chain A) in PDB entry 2CVP


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 404 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    337A  ALA*     3.4     8.3    -      -       -      -
    339A  LEU*     3.9    21.5    -      -       +      -
    395A  ILE*     4.2    20.0    -      -       -      -
    402A  ILE*     3.3    27.5    +      -       -      -
    403A  PRO*     1.3    75.0    -      -       -      +
    405A  ASP*     1.3    63.9    +      -       -      +
    406A  PHE*     3.6    23.6    -      -       +      -
    436A  LEU*     5.2     0.2    -      -       -      -
    473A  PRO      3.7     5.3    +      -       -      -
    474A  THR*     3.2    12.7    -      -       +      +
    475A  ASN      2.8    24.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 405 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    320A  LEU*     4.9     3.6    -      -       -      +
    336A  HIS*     3.1    30.7    +      -       -      -
    337A  ALA      2.9     8.5    +      -       -      -
    338A  LEU*     3.9     9.9    -      -       +      -
    339A  LEU*     2.8    29.3    +      -       -      +
    404A  CYS*     1.3    72.2    -      -       -      +
    406A  PHE*     1.3    60.9    +      -       -      +
    407A  LEU*     3.5     6.5    -      -       +      +
    475A  ASN*     3.0    35.5    -      -       +      +
    477A  ILE*     4.3     6.1    -      -       +      +
    494A  TYR*     2.7    35.8    +      -       -      +
    497A  LYS*     4.6     1.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 406 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    339A  LEU*     3.5    18.8    -      -       +      -
    341A  TYR*     3.5    39.9    -      +       -      -
    392A  TYR*     3.6    14.6    -      +       -      -
    395A  ILE*     6.2     0.4    -      -       +      -
    404A  CYS*     3.6    29.8    -      -       +      -
    405A  ASP*     1.3    73.6    -      -       -      +
    407A  LEU*     1.3    54.2    +      -       -      +
    429A  PHE*     3.4    23.6    -      +       +      -
    432A  GLN*     3.7    14.6    -      -       +      -
    433A  THR*     3.6    21.1    -      -       +      -
    436A  LEU*     4.0    17.3    -      -       +      -
    474A  THR*     3.8    17.7    -      -       +      -
    475A  ASN      2.8    12.6    +      -       -      +
    476A  SER*     3.4     1.3    -      -       -      +
    477A  ILE*     2.7    33.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 407 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    338A  LEU*     4.8     2.7    -      -       +      -
    339A  LEU      3.2     9.1    +      -       -      +
    340A  PRO*     4.0    25.8    -      -       +      -
    341A  TYR*     2.5    35.2    +      -       -      +
    345A  MET*     4.7     5.2    -      -       +      -
    348A  PHE*     4.3    19.7    -      -       +      -
    405A  ASP*     3.5    20.9    -      -       +      +
    406A  PHE*     1.3    76.5    -      -       -      +
    408A  ILE*     1.3    59.0    +      -       -      +
    429A  PHE*     3.5     2.6    -      -       -      -
    477A  ILE*     3.1    28.7    -      -       +      +
    479A  PHE*     4.1    13.5    -      -       +      -
    490A  LEU*     4.9     5.4    -      -       +      -
    494A  TYR*     3.9    33.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 408 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    341A  TYR*     3.5    27.6    -      -       +      +
    407A  LEU*     1.3    75.1    -      -       -      +
    409A  PRO*     1.3    81.1    -      -       +      +
    422A  HIS*     4.4     2.2    -      -       +      -
    425A  LEU*     4.1    11.7    -      -       +      -
    426A  LEU*     3.7    36.8    -      -       +      -
    429A  PHE*     3.6    43.5    -      -       +      -
    477A  ILE      3.1     6.9    +      -       -      -
    478A  VAL*     3.3    17.4    -      -       +      +
    479A  PHE*     3.2    28.7    +      -       -      -
    549B  ILE*     5.8     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 409 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    341A  TYR      4.1     5.8    -      -       -      +
    342A  ASP*     3.6    30.1    -      -       +      +
    345A  MET*     5.2     0.2    -      -       -      -
    408A  ILE*     1.3    97.9    -      -       +      +
    410A  VAL*     1.3    59.8    +      -       -      +
    411A  GLN      3.6    17.7    -      -       -      +
    412A  THR*     5.4     2.0    -      -       -      -
    422A  HIS*     3.0    28.9    +      -       +      -
    426A  LEU*     4.3     0.3    -      -       -      +
    479A  PHE*     3.2    29.1    -      -       +      +
    481A  LYS*     4.0     1.8    -      -       -      -
    482A  LEU*     3.8    18.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 410 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    409A  PRO*     1.3    71.4    -      -       -      +
    411A  GLN*     1.3    57.3    +      -       -      +
    422A  HIS*     2.9    23.3    +      -       -      -
    426A  LEU*     4.3    10.0    -      -       -      +
    478A  VAL*     3.6    22.7    -      -       +      -
    479A  PHE      2.8    18.6    +      -       -      +
    480A  THR      3.5     7.9    -      -       -      +
    704A  GOL      5.3     2.0    +      -       -      +
    548B  PHE*     3.9    18.6    -      -       +      -
    549B  ILE*     3.4    39.0    -      -       +      +
    552B  GLN*     3.9     7.9    -      -       +      -
    553B  ARG*     3.6    27.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 411 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    409A  PRO*     3.6    17.8    -      -       -      +
    410A  VAL*     1.3    78.1    -      -       -      +
    412A  THR*     1.3    64.6    +      -       -      +
    413A  GLN*     4.0     1.0    +      -       -      +
    422A  HIS*     4.2     1.8    -      -       -      -
    480A  THR*     2.9    29.1    +      -       -      +
    481A  LYS*     3.8    37.3    +      -       +      +
    482A  LEU      4.6     0.2    +      -       -      -
    552B  GLN      2.9    21.8    +      -       -      +
    553B  ARG*     3.6    25.6    +      -       +      +
    555B  THR      2.7    29.5    +      -       -      +
    557B  LEU*     5.3     3.3    +      -       -      +
----------------------------------------------------------
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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