Contacts of the strand formed by residues 255 - 259 (chain C) in PDB entry 3CB4


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 VAL 255 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6C  ASN*     3.7    19.5    -      -       -      +
     58C  SER*     4.8     5.4    -      -       -      +
     60C  THR*     3.6    12.1    +      -       -      +
     74C  ASN*     3.9    21.3    -      -       +      +
     75C  PHE      5.9     0.4    -      -       -      +
     76C  ILE*     4.2    25.1    -      -       +      -
    196C  ILE*     4.3     6.5    -      -       +      -
    209C  LEU*     4.3    16.6    -      -       +      -
    210C  ILE      3.3    10.3    -      -       -      +
    211C  ARG*     3.7    21.3    -      -       +      -
    239C  ILE*     3.5    18.4    -      -       -      +
    240C  PHE      5.5     0.2    +      -       -      -
    250C  LEU*     4.4     3.8    -      -       -      +
    254C  GLU*     1.3    80.6    -      -       -      +
    256C  GLY*     1.3    61.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 256 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    209C  LEU*     3.2    13.2    -      -       -      +
    210C  ILE*     2.8    38.8    +      -       -      -
    238C  GLY      3.1    14.6    -      -       -      -
    239C  ILE*     4.3     4.3    -      -       -      -
    240C  PHE*     5.3     1.3    -      -       -      -
    250C  LEU*     4.0    14.9    -      -       -      +
    255C  VAL*     1.3    76.5    -      -       -      +
    257C  TRP*     1.3    59.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with TRP 257 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    199C  TRP*     4.8     0.9    -      -       +      -
    204C  LEU*     5.1     0.2    -      -       +      -
    207C  VAL*     3.9    10.3    -      -       +      -
    208C  SER      3.2     9.0    -      -       -      +
    210C  ILE*     5.4     0.7    -      -       -      -
    236C  ARG*     3.8    12.1    -      -       +      -
    237C  LEU*     3.3    31.1    -      -       -      +
    238C  GLY      2.8    42.7    +      -       -      +
    239C  ILE      3.0    28.2    +      -       -      +
    240C  PHE*     3.4    37.7    -      +       +      -
    244C  GLN*     3.6    27.6    -      -       +      +
    245C  VAL      3.6    12.1    -      -       -      -
    246C  ASP*     3.4    32.3    -      -       -      -
    250C  LEU*     4.0     4.5    -      -       -      +
    256C  GLY*     1.3    75.0    -      -       -      -
    258C  LEU*     1.3    62.1    +      -       -      +
    259C  VAL*     3.6    32.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 258 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    206C  VAL      4.0     1.0    -      -       -      +
    207C  VAL*     3.6     5.5    -      -       -      -
    208C  SER*     2.9    33.8    +      -       -      +
    210C  ILE*     3.6    18.8    -      -       +      -
    217C  LEU*     4.0    15.3    -      -       +      -
    223C  VAL*     4.7     5.6    -      -       +      -
    234C  ALA*     3.7    28.7    -      -       +      -
    236C  ARG      3.6    15.5    -      -       -      +
    237C  LEU*     3.9    11.9    -      -       +      -
    250C  LEU*     5.8     0.4    -      -       +      -
    257C  TRP*     1.3    75.9    -      -       -      +
    259C  VAL*     1.3    62.9    +      -       -      +
    260C  CYS*     3.7    25.1    +      -       -      -
    262C  ILE*     6.1     0.2    -      -       +      -
    274C  LEU*     3.5    32.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 259 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    204C  LEU*     3.8    48.7    -      -       +      +
    206C  VAL      4.3     6.5    -      -       -      +
    207C  VAL*     3.9    12.8    -      -       +      -
    235C  ASP*     3.4    10.4    +      -       +      +
    236C  ARG*     2.7    50.9    +      -       +      +
    257C  TRP*     3.6    26.2    -      -       +      -
    258C  LEU*     1.3    74.1    -      -       -      +
    260C  CYS*     1.3    63.7    -      -       -      +
    261C  ALA*     5.3     1.3    -      -       -      +
----------------------------------------------------------
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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