Contacts of the strand formed by residues 251 - 258 (chain C) in PDB entry 1GZH


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 251 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    161C  ALA*     4.2    10.1    -      -       +      -
    162C  ILE      3.2    11.4    -      -       -      +
    163C  TYR*     3.4    35.7    -      -       +      -
    164C  LYS      4.0     0.9    -      -       -      +
    173C  VAL*     3.9    11.2    -      -       +      -
    194C  LEU*     3.7    17.3    -      -       +      -
    236C  TYR*     4.6    10.3    -      -       +      -
    240C  SER*     5.5     1.1    -      -       -      +
    246C  MET*     3.4    30.3    -      -       +      -
    249C  ARG      4.9     0.2    -      -       -      +
    250C  PRO*     1.3    72.1    -      -       -      +
    252C  LEU*     1.3    78.4    +      -       -      +
    253C  THR*     5.2     0.9    -      -       -      +
    271C  GLU*     3.5     2.8    -      -       -      +
    272C  VAL*     3.1    47.2    +      -       +      +
    274C  VAL*     5.3     1.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 252 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    100C  GLN*     3.4    35.4    -      -       +      +
    160C  MET      3.6     0.5    -      -       -      +
    161C  ALA*     3.1     5.9    -      -       -      -
    162C  ILE*     2.8    44.2    +      -       +      +
    164C  LYS*     3.8    34.3    -      -       +      +
    251C  ILE*     1.3    88.8    -      -       -      +
    253C  THR*     1.3    64.6    +      -       -      +
    254C  ILE*     3.8     4.4    +      -       +      -
    269C  SER*     4.7    12.3    -      -       -      +
    270C  PHE      3.5    10.1    -      -       -      +
    271C  GLU*     3.5    22.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 253 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    159C  ALA*     4.6     5.4    -      -       +      -
    160C  MET      3.5     4.7    -      -       -      +
    161C  ALA*     4.4     2.3    -      -       -      +
    195C  ILE*     4.2    17.6    -      -       +      +
    234C  TYR*     5.9     1.3    -      -       +      -
    236C  TYR*     2.7    33.2    +      -       -      +
    251C  ILE*     5.2     0.5    -      -       -      +
    252C  LEU*     1.3    73.9    -      -       -      +
    254C  ILE*     1.3    61.1    +      -       -      +
    255C  ILE*     3.9    16.5    +      -       +      -
    269C  SER*     3.1    24.3    -      -       -      -
    270C  PHE*     2.9    38.2    +      -       +      -
    272C  VAL*     3.2    11.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 254 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98C  PRO*     4.6     7.0    -      -       +      -
     99C  SER      3.6    26.5    -      -       -      +
    100C  GLN*     4.1     9.0    -      -       +      -
    158C  ARG*     3.6     1.2    -      -       -      +
    159C  ALA*     3.6     3.5    -      -       -      -
    160C  MET*     2.6    41.8    +      -       +      +
    162C  ILE*     3.4    45.8    -      -       +      -
    252C  LEU*     4.4     5.4    -      -       +      +
    253C  THR*     1.3    74.3    -      -       -      +
    255C  ILE*     1.3    61.2    +      -       -      +
    256C  THR*     3.9    22.6    +      -       +      +
    267C  ARG*     4.0    11.7    -      -       +      -
    268C  ASN      3.6     4.7    -      -       -      +
    269C  SER*     4.0     9.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 255 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109C  PHE*     3.8    22.8    -      -       +      -
    111C  LEU*     4.2    17.7    -      -       +      -
    143C  VAL*     4.6     2.2    -      -       +      -
    145C  LEU*     4.1     7.9    -      -       +      -
    157C  VAL*     3.9    17.9    -      -       +      -
    158C  ARG      3.3     5.6    -      -       -      +
    159C  ALA*     3.9     9.6    -      -       +      -
    234C  TYR*     3.7    30.1    -      -       +      +
    253C  THR*     3.9    20.4    +      -       +      -
    254C  ILE*     1.3    71.0    -      -       -      +
    256C  THR*     1.3    64.4    +      -       -      +
    267C  ARG*     3.3     2.9    -      -       -      -
    268C  ASN      2.8    40.8    +      -       -      +
    270C  PHE*     4.0    21.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 256 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109C  PHE*     4.7     1.1    -      -       -      -
    156C  ARG      3.7     0.5    -      -       -      +
    157C  VAL*     3.5     5.7    -      -       -      +
    158C  ARG*     2.9    56.9    +      -       -      +
    254C  ILE*     3.9    21.7    +      -       +      +
    255C  ILE*     1.3    79.9    -      -       -      +
    257C  LEU*     1.3    64.3    +      -       -      +
    258C  GLU*     3.9     8.9    +      -       -      -
    264C  LEU*     4.3    12.1    -      -       +      -
    266C  GLY      3.3     5.8    -      -       -      +
    267C  ARG*     3.9    19.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 257 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    107C  TYR*     4.9    11.2    -      -       +      -
    109C  PHE*     3.9    43.7    -      -       +      -
    145C  LEU*     4.7     2.0    -      -       +      -
    147C  VAL*     4.2    15.0    -      -       +      -
    151C  PRO*     4.6    14.1    -      -       +      -
    155C  THR*     4.0    12.3    -      -       +      -
    156C  ARG      3.5     3.6    -      -       -      +
    157C  VAL*     3.7    29.2    -      -       +      -
    220C  TYR*     4.3    11.9    -      -       +      -
    256C  THR*     1.3    72.6    -      -       -      +
    258C  GLU*     1.3    53.6    +      -       -      +
    264C  LEU*     3.8     1.6    -      -       -      +
    265C  LEU*     2.7    35.5    +      -       +      +
    266C  GLY*     2.7    23.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 258 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    155C  THR*     3.0     5.5    -      -       -      +
    156C  ARG*     2.7    54.5    +      -       +      +
    158C  ARG*     2.8    50.8    +      -       -      -
    217C  VAL*     4.3     5.9    -      -       -      +
    256C  THR*     3.9    11.2    +      -       -      +
    257C  LEU*     1.3    74.4    -      -       -      +
    259C  ASP*     1.3    67.0    +      -       -      +
    262C  GLY*     3.9    23.3    -      -       -      +
    263C  ASN      3.1    16.2    -      -       -      +
    264C  LEU*     4.7     1.6    -      -       +      +
    265C  LEU*     3.2     6.3    -      -       -      +
----------------------------------------------------------
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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