Contacts of the strand formed by residues 383 - 387 (chain B) in PDB entry 2G4C


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 383 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    381B  ILE      2.7     9.2    +      -       -      -
    382B  LYS*     1.3    78.9    -      -       -      +
    384B  ALA*     1.3    76.2    +      -       -      +
    406B  LEU*     4.7     3.4    -      -       +      -
    411B  ILE*     3.9    24.9    -      -       +      -
    412B  SER      3.3     3.9    +      -       -      +
    413B  VAL*     3.3    12.9    -      -       +      +
    414B  TRP*     3.0    20.7    +      -       -      -
    437B  ILE*     3.5     3.1    -      -       -      -
    439B  PHE*     3.4    26.5    -      -       +      +
    441B  VAL*     4.0    21.8    -      -       +      -
    475B  LEU*     4.0    15.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 384 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    383B  VAL*     1.3    92.7    -      -       -      +
    385B  LEU*     1.3    70.7    +      -       -      +
    414B  TRP*     3.4    20.9    -      -       +      -
    432B  TYR*     3.2    34.3    -      -       +      -
    437B  ILE*     3.5    20.5    -      -       +      +
    439B  PHE      3.3     5.6    +      -       -      -
    440B  THR*     4.4     2.9    -      -       +      -
    441B  VAL      3.6     7.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 385 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    384B  ALA*     1.3    81.8    -      -       -      +
    386B  ASP*     1.3    66.1    -      -       -      +
    399B  CYS*     4.2    21.1    -      -       +      +
    402B  LEU*     4.1    22.0    -      -       +      -
    403B  PHE      4.7     0.2    -      -       -      +
    406B  LEU*     5.4     2.2    -      -       +      -
    413B  VAL*     3.6    21.5    -      -       +      -
    414B  TRP      3.4    14.4    +      -       -      +
    415B  PRO*     3.7     0.2    -      -       +      -
    416B  GLY      3.3     3.5    +      -       -      +
    417B  TYR*     3.3    40.9    +      -       +      -
    432B  TYR*     4.8     1.2    -      -       -      -
    440B  THR*     5.1     1.3    -      -       -      -
    441B  VAL*     2.8    34.8    -      -       +      +
    443B  VAL*     5.5     2.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 386 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    385B  LEU*     1.3    76.8    -      -       -      +
    387B  VAL*     1.3    75.7    +      -       +      +
    399B  CYS*     4.3     2.8    -      -       -      -
    416B  GLY*     2.7    35.7    -      -       -      +
    417B  TYR*     3.8     6.5    -      -       -      -
    428B  LEU*     3.2    28.7    -      -       +      +
    432B  TYR*     3.1    25.6    +      -       -      -
    440B  THR*     5.1     3.0    -      -       -      +
    441B  VAL      3.4     5.5    +      -       -      -
    442B  LEU*     3.8    10.2    -      -       +      +
    443B  VAL*     3.1    24.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 387 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    386B  ASP*     1.3    81.7    -      -       +      +
    388B  GLY*     1.3    60.2    +      -       -      +
    392B  THR*     6.0     2.9    -      -       -      +
    395B  LEU*     3.4    21.3    -      -       +      -
    396B  ARG*     4.0    18.8    -      -       +      +
    399B  CYS*     3.3    33.2    -      -       -      -
    417B  TYR*     3.7    18.8    -      -       +      +
    422B  GLN*     6.0     1.9    -      -       -      -
    442B  LEU*     4.0     5.1    -      -       -      +
    443B  VAL      3.2     5.6    -      -       -      -
----------------------------------------------------------
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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