Contacts of the strand formed by residues 160 - 166 (chain A) in PDB entry 2VZ3


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 ARG 160 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    119A  ARG*     6.0     5.3    -      -       -      +
    154A  PRO*     3.4    33.9    -      -       +      +
    159A  GLY*     1.3    81.9    -      -       -      +
    161A  TRP*     1.3    76.0    +      -       -      +
    162A  GLY      4.7     0.5    -      -       -      +
    487A  ASN*     4.9     3.1    -      -       -      +
    527A  ILE      3.8     0.3    -      -       -      +
    528A  PHE*     3.5     7.9    -      -       -      -
    529A  THR*     2.8    33.3    +      -       -      -
    534A  TYR*     3.3    37.9    -      -       +      +
    538A  GLY      5.6     2.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with TRP 161 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117A  GLU*     3.6    31.8    -      -       +      +
    160A  ARG*     1.3    91.5    +      -       -      +
    162A  GLY*     1.3    58.9    +      -       -      +
    453A  PHE*     3.7    17.0    -      +       -      -
    455A  THR*     3.5    20.9    -      -       -      -
    473A  PRO*     3.7     7.6    -      -       +      +
    487A  ASN*     2.9    32.4    +      -       +      +
    488A  PRO      3.5    14.1    -      -       -      +
    489A  ASN*     3.5    20.1    -      -       +      +
    509A  ASN*     3.5    39.9    -      -       +      -
    526A  GLN*     3.7    27.1    -      -       +      +
    527A  ILE      3.4    16.6    -      -       -      -
    528A  PHE*     3.6    31.3    -      +       +      -
----------------------------------------------------------
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Residues in contact with GLY 162 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117A  GLU*     5.1     4.3    -      -       -      -
    160A  ARG*     4.7     0.5    -      -       -      +
    161A  TRP*     1.3    76.5    -      -       -      +
    163A  PRO*     1.3    77.9    -      -       -      +
    526A  GLN*     4.9     3.2    -      -       -      +
    527A  ILE*     2.7    24.3    +      -       -      +
    529A  THR*     4.5     7.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 163 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99A  PRO*     3.8    18.2    -      -       +      +
    100A  VAL*     3.5    16.4    -      -       -      +
    101A  ALA*     4.4     1.1    -      -       -      +
    102A  SER*     5.7     2.5    -      -       -      +
    162A  GLY*     1.3    85.8    -      -       -      +
    164A  THR*     1.3    65.7    +      -       -      +
    165A  ILE*     4.1    12.7    +      -       +      -
    207A  TRP*     6.2     0.4    -      -       +      -
    526A  GLN*     3.4     2.9    -      -       -      -
    527A  ILE*     3.1    41.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with THR 164 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    100A  VAL      2.9    14.4    +      -       -      -
    101A  ALA*     3.2     7.8    -      -       +      -
    102A  SER*     3.0    24.4    +      -       -      +
    115A  ASN      2.6    29.1    +      -       -      +
    116A  PHE*     3.4    11.8    -      -       -      +
    163A  PRO*     1.3    74.7    -      -       -      +
    165A  ILE*     1.3    71.0    +      -       -      +
    166A  ASP*     3.4    23.3    -      -       -      +
    524A  ASP*     3.9    11.2    -      -       +      +
    525A  ALA      3.4    11.9    -      -       -      +
    526A  GLN*     3.7    14.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 165 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102A  SER*     3.1    13.7    -      -       -      +
    163A  PRO*     4.4    15.7    -      -       +      -
    164A  THR*     1.3    82.6    -      -       -      +
    166A  ASP*     1.3    60.7    +      -       -      +
    167A  LEU*     3.7    11.1    -      -       +      +
    207A  TRP*     3.6    59.0    -      -       +      +
    214A  VAL*     3.7    15.9    -      -       +      -
    508A  PHE*     4.2    14.6    -      -       +      -
    524A  ASP*     3.2     6.1    -      -       -      +
    525A  ALA*     2.8    39.9    +      -       +      +
    527A  ILE*     4.5    11.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 166 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85A  HIS*     2.6    41.2    +      -       +      +
    101A  ALA*     4.2     5.7    -      -       -      +
    102A  SER      2.7    13.4    +      -       -      +
    103A  GLY*     3.2     4.3    -      -       -      -
    104A  SER      2.9    21.6    +      -       -      -
    105A  TRP*     3.6     5.9    +      -       +      +
    113A  TYR      3.8    14.1    -      -       -      +
    114A  SER*     2.6    28.4    +      -       -      -
    115A  ASN      4.6     0.3    +      -       -      -
    164A  THR*     3.4    20.0    -      -       -      +
    165A  ILE*     1.3    72.3    -      -       -      +
    167A  LEU*     1.3    66.0    +      -       -      +
    214A  VAL*     3.8     1.9    -      -       -      +
    523A  PHE      3.9     4.4    -      -       -      +
    524A  ASP*     4.2     4.9    -      -       -      +
----------------------------------------------------------
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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