Contacts of the strand formed by residues 31 - 36 (chain A) in PDB entry 2DMZ


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 ILE 31 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21A  LEU*     3.8    14.4    -      -       +      -
     29A  LEU*     3.5    34.1    -      -       +      +
     30A  GLY*     1.3    77.1    -      -       -      +
     32A  ARG*     1.3    73.2    +      -       -      +
     33A  ILE*     3.9    13.7    +      -       +      +
     50A  VAL*     4.3    24.5    -      -       +      -
     52A  SER      4.1     2.2    -      -       -      -
     53A  VAL*     5.1     1.6    -      -       +      -
     54A  ILE*     4.0     1.4    -      -       -      +
     59A  ALA*     3.2    34.8    -      -       +      -
     65A  ILE*     4.0    17.0    -      -       +      -
     71A  ILE*     5.8     1.8    -      -       +      -
     91A  LEU*     4.7    11.6    -      -       +      +
    100A  LEU*     4.8     7.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 32 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31A  ILE*     1.3    74.4    -      -       -      +
     33A  ILE*     1.3    63.2    +      -       -      +
     50A  VAL*     3.3    10.6    -      -       -      +
     51A  LYS*     2.9    28.2    +      -       +      -
     52A  SER*     3.0    36.7    +      -       -      +
     54A  ILE*     3.4    33.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 33 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31A  ILE*     4.4    16.2    -      -       +      +
     32A  ARG*     1.3    80.5    -      -       -      +
     34A  VAL*     1.3    62.2    +      -       -      +
     48A  ILE*     3.8    21.8    -      -       +      -
     49A  TYR      3.4     5.4    -      -       -      +
     51A  LYS*     4.1     6.7    -      -       -      +
     71A  ILE*     4.9     8.3    -      -       +      -
     84A  ASN*     3.5    48.4    +      -       +      +
     87A  VAL*     3.9    23.6    -      -       +      -
     88A  VAL*     4.3    12.1    -      -       +      -
     91A  LEU*     4.8    10.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 34 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33A  ILE*     1.3    76.6    -      -       -      +
     35A  GLY*     1.3    65.4    +      -       -      +
     36A  TYR*     3.5    35.7    -      -       +      -
     47A  GLY      3.3    12.1    -      -       -      +
     48A  ILE*     3.3    12.5    -      -       -      +
     49A  TYR*     2.8    32.6    +      -       +      +
     51A  LYS*     4.1    29.8    -      -       +      +
     84A  ASN*     3.3     5.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 35 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34A  VAL*     1.3    78.6    -      -       -      +
     36A  TYR*     1.3    64.2    +      -       -      -
     37A  VAL*     4.2     5.8    +      -       -      +
     48A  ILE*     4.1     6.3    -      -       -      -
     84A  ASN*     2.9    31.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 36 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34A  VAL*     3.5    39.9    -      -       +      -
     35A  GLY*     1.3    75.5    -      -       -      +
     37A  VAL*     1.3    63.2    +      -       -      +
     38A  GLY      4.9     0.9    -      -       -      -
     44A  GLU*     3.4    28.3    +      -       +      -
     45A  ALA*     3.4    32.3    -      -       +      +
     46A  SER*     3.7     4.1    -      -       -      -
     47A  GLY*     3.2    33.3    +      -       -      +
     49A  TYR*     4.0    15.5    -      +       +      -
----------------------------------------------------------
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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