Contacts of the strand formed by residues 116 - 122 (chain A) in PDB entry 3ZWG


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 TRP 116 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103A  LEU*     5.0     2.2    -      -       +      -
    104A  PHE*     3.5     1.4    -      -       -      -
    105A  SER*     2.7    45.9    +      -       -      +
    114A  SER*     2.9    41.2    +      -       -      +
    115A  ASN*     1.3    78.0    -      -       -      +
    117A  TRP*     1.3    62.0    +      -       -      +
    137A  TYR*     4.0    31.3    +      +       +      -
    142A  PRO*     3.5    41.5    -      -       +      -
    143A  PHE      3.3    23.3    -      -       -      -
    144A  ARG*     3.5    44.9    -      -       +      -
    145A  GLY      4.2     0.9    -      -       -      +
    164A  MET*     3.7     6.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 117 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103A  LEU*     3.2    15.3    -      -       -      +
    116A  TRP*     1.3    76.1    -      -       -      +
    118A  ASN*     1.3    69.4    +      -       -      +
    119A  VAL*     3.4    34.5    -      -       +      -
    142A  PRO*     3.2     4.6    -      -       -      +
    143A  PHE*     2.8    80.6    +      +       +      +
    144A  ARG      4.1     6.7    +      -       -      -
    150A  HIS*     3.7    17.3    -      +       +      -
    160A  SER*     4.9     3.1    -      -       -      -
    161A  ARG      4.5     0.4    -      -       -      -
    162A  GLY*     3.3    47.1    -      -       -      -
    164A  MET*     3.4    36.5    -      -       +      +
    172A  LEU*     3.7    22.2    -      -       +      -
    174A  ILE*     4.2    11.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 118 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101A  ALA      4.4     1.1    -      -       -      -
    102A  VAL*     3.3     5.5    -      -       -      +
    103A  LEU*     2.9    49.7    +      -       +      +
    117A  TRP*     1.3    78.0    -      -       -      +
    119A  VAL*     1.3    79.8    +      -       -      +
    120A  ARG*     4.9     0.4    -      -       -      -
    136A  LEU*     2.8    37.1    +      -       +      +
    140A  ARG*     3.8    17.6    +      -       -      +
    142A  PRO*     3.5    22.0    -      -       +      +
    143A  PHE*     4.6     2.5    -      -       -      -
    152A  ARG*     3.4    21.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 119 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    100A  LEU*     4.1    19.3    -      -       +      -
    101A  ALA      3.5     5.8    -      -       -      +
    102A  VAL*     4.3     7.2    -      -       +      -
    117A  TRP*     3.4    27.9    -      -       +      -
    118A  ASN*     1.3    91.3    +      -       -      +
    120A  ARG*     1.3    65.8    +      -       -      +
    143A  PHE*     5.1     3.1    -      -       +      -
    152A  ARG*     4.2    11.6    +      -       -      -
    154A  LEU*     3.3    18.5    -      -       +      +
    160A  SER*     3.6    27.6    +      -       -      +
    174A  ILE*     3.9    22.7    -      -       +      -
    176A  VAL*     4.7     5.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 120 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99A  THR      3.8     0.3    -      -       -      +
    100A  LEU*     3.9     2.6    -      -       -      +
    101A  ALA*     3.0    33.2    +      -       -      +
    118A  ASN*     4.4     1.2    +      -       -      -
    119A  VAL*     1.3    78.1    +      -       -      +
    121A  VAL*     1.3    75.3    +      -       -      +
    122A  TYR*     3.9    22.2    -      -       +      -
    136A  LEU*     3.5    22.6    -      -       +      +
    140A  ARG*     2.8    61.6    +      -       -      +
    152A  ARG*     2.5    45.0    -      -       -      +
    153A  GLY      4.9     5.9    +      -       -      -
    154A  LEU*     3.9    11.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 121 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94A  MET*     4.1    15.9    -      -       +      -
     98A  ASN*     4.2     1.3    -      -       +      -
     99A  THR      3.4     9.0    -      -       -      +
    100A  LEU*     3.9    13.2    -      -       +      -
    120A  ARG*     1.3    85.3    -      -       -      +
    122A  TYR*     1.3    71.6    +      -       -      +
    123A  LYS      4.3     0.2    +      -       -      -
    140A  ARG*     6.0     0.2    +      -       -      -
    154A  LEU*     3.7    42.1    +      -       +      +
    156A  TYR*     3.3    45.5    +      -       +      -
    158A  LEU*     4.4    11.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 122 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98A  ASN*     3.1     7.6    -      -       -      +
     99A  THR*     2.8    40.9    +      -       +      +
    101A  ALA*     3.9    28.9    -      -       +      -
    120A  ARG*     3.9    18.2    -      -       +      +
    121A  VAL*     1.3    79.8    -      -       -      +
    123A  LYS*     1.3    60.5    +      -       -      +
    124A  GLY      4.5     0.2    -      -       -      -
    126A  LYS*     3.9    31.0    -      -       +      -
    132A  MET*     4.0    20.3    -      -       +      +
    135A  GLU*     2.7    40.6    +      -       -      +
    136A  LEU*     3.8    13.6    -      -       +      +
    140A  ARG*     4.2    20.3    +      -       -      -
    156A  TYR*     4.6     1.1    -      -       -      -
----------------------------------------------------------
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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