Contacts of the strand formed by residues 144 - 151 (chain C) in PDB entry 2GH0


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 LEU 144 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    167A  MET*     3.3    42.4    -      -       +      +
    170A  THR*     3.9     6.9    +      -       -      +
    179A  ARG*     5.6     0.5    +      -       -      -
    129C  LEU*     3.8    35.4    -      -       +      -
    130C  VAL*     3.2     9.2    -      -       -      +
    131C  PRO*     3.7    31.6    -      -       +      -
    142C  ASP      5.0     4.0    -      -       -      +
    143C  GLU*     1.3    78.6    -      -       -      +
    145C  VAL*     1.3    66.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 145 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    170A  THR*     4.6     2.7    -      -       -      -
    179A  ARG*     6.2     1.1    -      -       -      +
    180A  LYS*     4.4     6.7    -      -       -      +
    129C  LEU*     3.4     6.7    -      -       -      -
    130C  VAL*     2.8    42.3    +      -       +      +
    132C  VAL*     3.7    18.8    -      -       +      -
    135C  LEU*     3.9    27.8    -      -       +      -
    143C  GLU*     5.3     1.1    -      -       -      +
    144C  LEU*     1.3    79.9    -      -       -      +
    146C  ARG*     1.3    68.5    +      -       -      +
    147C  PHE*     3.4     3.1    +      -       +      -
    196C  VAL*     3.8    25.6    -      -       +      -
    197C  SER      4.0    15.3    -      -       -      +
    198C  PHE*     4.3     4.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 146 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    170A  THR*     2.9    30.2    +      -       +      +
    171A  LEU*     3.3    11.9    +      -       -      +
    172A  ASN      3.4     0.4    +      -       -      -
    173A  ASP*     2.8    56.8    +      -       -      +
    176A  ASP*     3.7    19.4    +      -       -      +
    180A  LYS*     3.0    24.2    +      -       -      +
    127C  SER*     4.1    16.1    +      -       -      +
    128C  GLN      3.6     5.4    -      -       -      +
    129C  LEU*     3.8    19.0    -      -       +      +
    145C  VAL*     1.3    77.3    -      -       -      +
    147C  PHE*     1.3    58.7    +      -       -      +
    148C  ARG*     3.7    32.5    +      -       -      +
    196C  VAL*     4.5     2.6    -      -       -      +
    212C  SER*     4.2     4.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 147 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126C  ARG      4.2     0.2    -      -       -      +
    127C  SER*     3.6     0.3    -      -       -      -
    128C  GLN*     2.8    32.5    +      -       -      +
    130C  VAL*     3.8    21.8    -      -       +      -
    135C  LEU*     3.8    16.8    -      -       +      -
    145C  VAL*     3.4     2.4    +      -       +      -
    146C  ARG*     1.3    75.0    -      -       -      +
    148C  ARG*     1.3    68.7    +      -       -      +
    149C  PHE*     4.1    13.7    -      +       +      -
    196C  VAL*     5.0     4.5    -      -       +      -
    211C  LEU*     3.1    47.1    -      -       +      -
    212C  SER*     3.9     7.0    -      -       -      -
    161D  HIS*     3.6    17.9    -      +       -      -
    164D  SER*     4.3     0.2    -      -       -      -
    165D  LEU*     4.1    27.8    -      -       +      -
    168D  LEU*     3.5    25.8    -      -       +      -
    174D  LEU*     4.8     2.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 148 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    176A  ASP*     4.8     5.7    +      -       -      -
    177A  ARG*     4.4    29.7    -      -       -      +
    180A  LYS*     5.0     5.1    -      -       -      +
    125C  LEU*     3.9    23.3    -      -       +      +
    126C  ARG      3.0    11.7    -      -       -      +
    127C  SER*     3.7    25.1    +      -       -      +
    146C  ARG*     3.7    44.1    +      -       -      +
    147C  PHE*     1.3    75.7    -      -       -      +
    149C  PHE*     1.3    61.8    +      -       -      +
    194C  GLU*     3.6    21.1    +      -       -      -
    212C  SER*     3.0    12.7    +      -       -      +
    213C  ALA*     3.0    43.8    +      -       -      +
    214C  THR*     5.4     1.6    -      -       -      +
    161D  HIS*     3.3     9.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 149 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    125C  LEU*     3.6     3.1    -      -       -      -
    126C  ARG*     2.9    59.3    +      -       +      +
    127C  SER      4.7     0.4    -      -       -      -
    128C  GLN*     4.7     7.2    -      -       +      -
    147C  PHE*     4.1    19.5    -      +       +      -
    148C  ARG*     1.3    79.3    -      -       -      +
    150C  CYS*     1.3    67.1    +      -       -      +
    151C  SER*     4.2     1.3    -      -       -      -
    213C  ALA*     4.0     4.2    -      -       -      +
    216C  CYS*     4.4     0.4    -      -       -      -
    161D  HIS*     3.9    18.6    -      -       +      +
    165D  LEU*     4.0    16.4    -      -       +      -
    174D  LEU*     3.8    30.3    -      -       +      -
    175D  ARG      5.0     3.4    -      -       -      -
    177D  PRO*     3.6    30.7    -      -       +      -
    182D  PRO*     3.8    29.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 150 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124C  ARG      3.5     0.7    -      -       -      -
    149C  PHE*     1.3    78.0    -      -       -      +
    151C  SER*     1.3    65.4    +      -       -      +
    188C  CYS*     3.8    17.3    -      -       -      +
    189C  ARG*     3.8    14.1    -      -       -      +
    190C  PRO*     3.4    32.9    -      -       +      +
    213C  ALA*     4.1     4.0    -      -       -      -
    215C  ALA      3.7     2.0    -      -       -      -
    216C  CYS*     2.0    52.0    -      -       +      -
    161D  HIS*     5.0     0.8    -      -       -      -
    165D  LEU*     5.3     1.6    -      -       -      +
    182D  PRO*     3.6    15.6    -      -       -      +
    183D  VAL      4.8     1.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 151 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124C  ARG      3.1    20.4    +      -       -      -
    126C  ARG*     2.8    39.9    +      -       -      +
    149C  PHE*     4.2     2.9    +      -       -      -
    150C  CYS*     1.3    76.1    -      -       -      +
    152C  GLY*     1.3    58.8    +      -       -      +
    188C  CYS*     3.3    12.7    -      -       -      -
    177D  PRO*     3.5    18.7    -      -       -      +
    180D  SER      3.9     6.1    +      -       -      -
    182D  PRO*     3.8    31.4    -      -       -      -
----------------------------------------------------------
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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