Contacts of the strand formed by residues 162 - 169 (chain G) in PDB entry 6H25


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 162 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7A  SER*     4.6    14.5    +      -       -      +
      9A  CYS*     4.7     6.7    -      -       +      -
    118G  ILE*     3.8    18.4    -      -       +      -
    119G  GLY      3.2    12.6    -      -       -      +
    120G  ILE*     4.6     6.0    -      -       +      +
    160G  GLY      4.3     0.2    +      -       -      -
    161G  ASP*     1.3    75.7    -      -       +      +
    163G  ILE*     1.3    62.5    +      -       -      +
    192G  VAL*     4.0     6.2    -      -       -      +
    193G  ILE*     3.6    37.9    +      -       +      -
    194G  GLY      3.4    25.8    -      -       -      +
    199G  LEU*     3.8    28.3    -      -       +      -
    238G  TRP*     3.9    26.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 163 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117G  VAL      3.5     2.6    -      -       -      +
    118G  ILE*     3.5     4.0    -      -       -      -
    119G  GLY*     2.9    35.4    +      -       -      +
    121G  VAL*     3.7    24.0    -      -       +      -
    129G  PHE*     4.4     0.4    -      -       +      -
    131G  VAL*     5.5     3.1    -      -       +      -
    141G  LEU*     4.1    21.3    -      -       +      -
    146G  PHE*     3.9    19.1    -      -       +      -
    157G  VAL*     4.2    15.0    -      -       +      -
    161G  ASP*     4.0     6.5    -      -       +      +
    162G  LEU*     1.3    79.8    -      -       -      +
    164G  TYR*     1.3    62.0    +      -       -      +
    165G  GLY      4.0     0.2    +      -       -      -
    178G  MET*     4.5     7.2    -      -       +      +
    180G  CYS*     3.6    27.4    -      -       -      -
    191G  GLY      3.6    10.3    -      -       -      +
    192G  VAL*     4.5     9.9    -      -       +      -
    193G  ILE*     4.9     2.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 164 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    116G  HIS*     3.3    45.8    +      +       +      +
    117G  VAL      4.0     4.9    -      -       -      -
    118G  ILE*     4.1    11.9    -      -       +      +
    163G  ILE*     1.3    73.1    -      -       -      +
    165G  GLY*     1.3    59.7    +      -       -      +
    180G  CYS*     3.4     7.7    -      -       -      -
    188G  ASN      5.5     2.9    -      -       -      -
    189G  GLY      4.2    17.0    -      -       -      -
    190G  MET*     3.6    18.3    -      -       +      +
    191G  GLY      3.0    31.0    +      -       -      +
    193G  ILE*     3.7    25.7    -      -       +      +
    230G  VAL*     3.8    18.6    -      -       +      -
    231G  PHE      3.5    21.5    +      -       -      -
     72K  TYR      4.9     0.3    +      -       -      -
     73K  GLY*     3.7    20.8    -      -       -      -
     74K  ARG*     3.9    15.6    +      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 165 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    116G  HIS*     3.5     7.0    +      -       -      -
    117G  VAL      3.2    29.1    +      -       -      -
    164G  TYR*     1.3    78.0    -      -       -      +
    166G  GLN*     1.3    64.5    +      -       -      +
    178G  MET*     3.7    14.6    -      -       -      +
    179G  VAL      3.3    13.0    -      -       -      -
    180G  CYS*     3.9     1.8    -      -       -      -
    190G  MET*     4.4    11.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 166 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114G  GLY*     4.9     9.2    -      -       -      -
    115G  ASP      3.3    19.5    -      -       -      +
    116G  HIS*     3.6    20.3    +      -       -      +
    117G  VAL*     5.1     0.4    -      -       -      +
    165G  GLY*     1.3    75.4    -      -       -      +
    167G  PHE*     1.3    67.1    -      -       -      +
    168G  VAL*     5.5     2.9    -      -       +      +
    178G  MET*     3.7     6.6    -      -       -      +
    179G  VAL*     2.8    42.6    +      -       +      +
    181G  ILE      3.9    12.1    +      -       -      -
    182G  ASP*     4.9     5.7    -      -       -      +
    183G  SER      5.5     1.0    -      -       -      +
    190G  MET*     3.8    23.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 167 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109G  TYR*     4.0    14.4    -      +       -      -
    111G  PRO*     5.4     4.9    -      -       +      -
    112G  VAL      3.9    18.4    -      -       -      +
    113G  LYS*     4.5     0.9    -      -       -      +
    114G  GLY*     3.2    31.0    +      -       -      +
    115G  ASP      3.8    11.7    +      -       -      +
    117G  VAL*     3.6    29.2    -      -       +      -
    133G  VAL*     3.6    29.8    -      -       +      -
    139G  ALA*     3.9    23.3    -      -       +      -
    166G  GLN*     1.3    76.6    -      -       -      +
    168G  VAL*     1.3    61.7    +      -       -      +
    170G  ALA*     4.4    12.6    -      -       +      -
    176G  PRO*     4.2    17.5    -      -       +      -
    177G  GLU      3.6    12.3    -      -       -      +
    178G  MET*     3.7    20.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 168 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113G  LYS*     3.4    29.3    -      -       -      +
    166G  GLN*     3.6     4.6    +      -       +      +
    167G  PHE*     1.3    76.2    -      -       -      +
    169G  VAL*     1.3    77.8    +      -       +      +
    177G  GLU*     2.9    17.2    +      -       +      +
    178G  MET      4.6     0.2    -      -       -      -
    179G  VAL*     3.7    44.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 169 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113G  LYS*     5.4     0.9    -      -       -      -
    167G  PHE*     4.5     0.5    -      -       -      +
    168G  VAL*     1.3    89.3    +      -       +      +
    170G  ALA*     1.3    64.0    +      -       -      +
    171G  ASN*     5.3     4.5    -      -       -      +
    175G  GLU      5.2     2.2    -      -       -      +
    176G  PRO*     3.4     5.4    -      -       +      +
    177G  GLU*     3.1    61.4    +      -       +      +
----------------------------------------------------------
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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