Contacts of the strand formed by residues 500 - 504 (chain B) in PDB entry 1G88


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 ILE 500 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    366A  GLN*     4.0     1.3    -      -       +      +
    368A  SER*     4.2     2.0    -      -       -      +
    410B  GLN*     4.2    10.7    -      -       -      +
    412B  TYR*     4.9     3.8    +      -       -      -
    496B  ARG*     3.1    50.3    -      -       +      +
    497B  ARG*     3.4    22.4    +      -       -      +
    498B  LEU      3.4     1.1    -      -       -      -
    499B  CYS*     1.3    86.3    -      -       +      +
    501B  LEU*     1.3    69.8    +      -       -      +
    502B  ARG*     4.7     4.5    -      -       +      +
    526B  GLU*     3.5    32.3    -      -       +      +
    527B  ILE      3.2    10.8    -      -       -      +
    528B  HIS*     3.2    31.6    -      -       +      +
    533B  LEU*     5.2     1.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 501 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    389B  LEU*     6.4     1.3    -      -       +      -
    397B  VAL*     3.9    26.0    -      -       +      -
    399B  VAL*     6.1     0.7    -      -       +      -
    409B  VAL*     4.9     4.3    -      -       +      -
    410B  GLN      4.1     2.5    -      -       -      +
    411B  SER*     3.7    24.0    -      -       -      +
    412B  TYR      5.3     0.7    -      -       -      +
    437B  VAL*     3.6    33.9    -      -       +      +
    438B  PHE*     4.2     8.7    -      -       +      -
    499B  CYS      4.4     0.2    +      -       -      -
    500B  ILE*     1.3    77.8    -      -       -      +
    502B  ARG*     1.3    69.3    +      -       -      +
    526B  GLU*     3.5     0.9    -      -       -      -
    527B  ILE*     2.7    51.6    +      -       +      +
    529B  LEU*     3.8    28.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 502 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    368A  SER*     5.0     5.5    +      -       -      -
    370A  VAL*     5.1     7.7    -      -       -      +
    409B  VAL*     3.4     4.9    -      -       -      +
    410B  GLN*     2.8    61.9    +      -       +      +
    496B  ARG*     6.1     0.8    -      -       -      +
    497B  ARG*     5.7    10.9    -      -       -      +
    500B  ILE*     4.7     3.7    -      -       +      +
    501B  LEU*     1.3    86.7    -      -       -      +
    503B  MET*     1.3    65.3    +      -       -      +
    518B  ILE*     4.1    21.5    -      -       +      +
    519B  LYS*     5.8     5.1    -      -       -      +
    524B  TRP*     3.8    26.0    -      -       +      -
    525B  ILE      3.3    13.0    -      -       -      +
    526B  GLU*     3.2    32.7    +      -       +      -
    527B  ILE*     4.1     2.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with MET 503 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    387B  VAL*     3.9    24.9    -      -       -      -
    389B  LEU*     3.9    12.3    -      -       +      -
    399B  VAL*     3.5    36.1    -      -       +      -
    407B  VAL*     3.2    24.9    -      -       +      -
    408B  PHE      3.3    10.1    -      -       -      +
    409B  VAL*     4.1    15.7    -      -       +      -
    502B  ARG*     1.3    78.2    -      -       -      +
    504B  SER*     1.3    60.8    +      -       -      +
    505B  PHE*     4.0     7.5    +      -       +      -
    518B  ILE*     4.0     2.4    -      -       -      +
    524B  TRP*     3.3     4.3    -      -       -      -
    525B  ILE*     3.0    48.8    +      -       +      +
    527B  ILE*     5.1     4.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 504 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    407B  VAL*     3.6     4.0    -      -       -      +
    408B  PHE*     2.9    30.7    +      -       -      -
    503B  MET*     1.3    74.0    -      -       -      +
    505B  PHE*     1.3    66.1    +      -       -      +
    507B  LYS      2.7    26.3    +      -       -      +
    509B  TRP*     3.6    22.2    -      -       -      -
    518B  ILE*     4.0     1.1    -      -       -      +
    521B  THR*     3.4    27.6    +      -       -      -
    523B  CYS      4.0     2.6    +      -       -      -
    524B  TRP*     3.6     9.2    -      -       -      -
----------------------------------------------------------
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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