Contacts of the strand formed by residues 117 - 122 (chain G) in PDB entry 1P8Z


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 VAL 117 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    166A  TYR*     5.7     5.2    -      -       -      +
    167A  GLU*     3.6     5.8    -      -       -      +
     83G  TYR      3.2     9.0    +      -       -      +
     84G  ASP*     3.4    13.4    -      -       -      +
     85G  LEU      3.0    23.1    +      -       -      +
    115G  ARG      4.8     4.3    -      -       -      +
    116G  ALA*     1.3    75.3    -      -       -      +
    118G  GLN*     1.3    63.9    +      -       -      +
    119G  HIS*     3.4    32.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 118 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    148A  THR*     2.9    48.2    +      -       -      +
    149A  THR*     5.9     0.2    -      -       -      +
    167A  GLU*     2.9    46.2    +      -       +      +
     85G  LEU*     3.3     7.6    -      -       +      -
     87G  TYR*     5.1     1.6    -      -       +      -
    105G  THR*     3.5    24.5    -      -       +      +
    106G  VAL*     3.8     8.0    -      -       -      +
    109G  ASP*     2.5    37.2    -      -       +      +
    117G  VAL*     1.3    76.6    -      -       -      +
    119G  HIS*     1.3    70.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 119 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84G  ASP*     2.8    22.3    +      -       -      -
     85G  LEU      2.7    10.0    +      -       -      +
     86G  HIS*     3.2    32.6    +      +       -      +
     87G  TYR*     3.0    33.6    +      -       -      -
    117G  VAL*     3.4    32.8    -      -       +      +
    118G  GLN*     1.3    74.6    +      -       -      +
    120G  ARG*     1.3    60.1    +      -       -      +
    121G  GLU*     3.4    19.1    +      -       -      +
    127G  SER*     5.7     0.9    -      -       -      -
    129G  THR*     6.0     3.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 120 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    145A  SER      4.1     3.6    +      -       -      -
    146A  GLY      2.7    25.7    +      -       -      -
    147A  ARG*     3.4    46.9    -      -       -      +
    296A  ASN*     4.9     3.6    +      -       -      -
     87G  TYR*     3.5    32.6    -      -       +      +
     89G  LEU*     3.4    24.5    -      -       +      +
    119G  HIS*     1.3    70.9    -      -       -      +
    121G  GLU*     1.3    63.7    +      -       -      +
    122G  VAL*     3.3    27.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 121 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86G  HIS*     2.6    47.5    +      -       +      -
     87G  TYR      2.9    14.2    +      -       -      +
     88G  TRP*     3.2    18.8    -      -       +      -
     89G  LEU*     2.8    28.1    +      -       -      +
    119G  HIS*     3.4    10.4    -      -       -      +
    120G  ARG*     1.3    77.3    -      -       -      +
    122G  VAL*     1.3    63.5    +      -       -      +
    123G  GLN      4.2     0.2    +      -       -      -
    125G  PHE      5.6     0.2    -      -       -      -
    126G  GLU*     3.5     5.9    -      -       +      +
    127G  SER*     2.9    41.8    +      -       -      -
    130G  PHE*     3.5    19.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 122 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88G  TRP*     4.7     0.2    -      -       -      -
     89G  LEU*     4.0    12.8    -      -       +      +
     91G  ASN*     4.9     7.9    -      -       -      +
    120G  ARG*     3.3    42.0    +      -       +      +
    121G  GLU*     1.3    77.5    -      -       -      +
    123G  GLN*     1.3    75.5    +      -       -      +
    124G  GLY      3.3     0.2    +      -       -      -
    125G  PHE*     2.8    34.1    +      -       +      -
    126G  GLU*     3.5    10.7    +      -       -      +
----------------------------------------------------------
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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