Contacts of the strand formed by residues 127 - 131 (chain L) in PDB entry 4R2G


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 SER 127 (chain L).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    125L  SER      4.0     4.1    +      -       -      -
    126L  PRO*     1.3    75.8    +      -       -      +
    128L  VAL*     1.3    62.8    +      -       -      +
    129L  GLN*     4.9     1.3    -      -       -      +
    139L  GLN*     4.3    14.8    -      -       -      -
    140L  GLY      4.2     3.4    -      -       -      -
    141L  GLY*     5.1     0.9    -      -       -      -
    162L  LEU*     2.9    53.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 128 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    100L  LEU*     4.5    10.5    -      -       +      -
    118L  LEU*     3.6    31.4    -      -       +      -
    126L  PRO      4.8     3.4    -      -       -      +
    127L  SER*     1.3    78.7    -      -       -      +
    129L  GLN*     1.3    66.3    +      -       -      +
    130L  CYS*     4.2     7.6    -      -       -      -
    138L  ILE      3.6     0.4    -      -       -      +
    139L  GLN*     2.3    29.6    -      -       -      +
    140L  GLY      3.1    16.9    +      -       -      +
    142L  LYS      5.1     3.8    -      -       -      +
    144L  LEU*     3.4    30.5    -      -       +      -
    159L  CYS*     4.6     1.8    -      -       +      -
    160L  THR      3.7     6.3    -      -       -      +
    161L  VAL*     3.7    26.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 129 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127L  SER      4.9     1.6    -      -       -      +
    128L  VAL*     1.3    77.8    -      -       -      +
    130L  CYS*     1.3    62.5    +      -       -      +
    131L  ARG*     3.8    14.7    +      -       -      +
    137L  ASN*     3.5    33.0    +      -       +      +
    138L  ILE      3.5     4.3    -      -       -      -
    139L  GLN*     4.3    23.9    -      -       -      +
    158L  THR      4.0     1.0    -      -       -      +
    159L  CYS*     3.7     0.7    -      -       -      -
    160L  THR*     2.9    42.4    +      -       -      +
    162L  LEU*     4.9    16.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 130 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    100L  LEU*     4.5     0.9    -      -       -      -
    116L  LEU*     3.9    15.9    -      -       -      -
    128L  VAL*     4.6     2.7    -      -       -      -
    129L  GLN*     1.3    73.1    -      -       -      +
    131L  ARG*     1.3    61.0    +      -       -      +
    132L  SER      3.9     1.2    +      -       -      -
    137L  ASN*     3.2     3.8    -      -       -      -
    138L  ILE*     2.9    42.3    +      -       +      +
    144L  LEU*     3.6    24.0    -      -       +      +
    157L  TRP*     4.3    13.4    -      -       +      -
    159L  CYS*     2.0    53.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 131 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129L  GLN*     3.8    13.3    +      -       -      +
    130L  CYS*     1.3    74.5    -      -       -      +
    132L  SER*     1.3    66.9    +      -       -      +
    136L  LYS      3.2    17.3    -      -       -      +
    137L  ASN*     4.1    12.4    -      -       +      +
    157L  TRP*     3.6     5.9    -      -       -      -
    158L  THR*     2.9    45.2    +      -       -      +
    160L  THR*     5.3     9.8    +      -       -      -
    167L  LYS*     5.9     2.4    -      -       -      +
    169L  GLU*     5.8     1.8    +      -       -      -
----------------------------------------------------------
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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