Contacts of the strand formed by residues 30 - 35 (chain A) in PDB entry 2A1A


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 GLY 30 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26A  ILE*     4.8     0.4    -      -       -      -
     27A  ALA*     2.7    39.9    +      -       -      +
     28A  GLU      3.1     4.2    +      -       -      -
     29A  MET*     1.3    81.5    -      -       -      +
     31A  ALA*     1.3    58.2    +      -       -      -
     32A  TYR*     4.2     2.8    +      -       -      -
     44A  MET*     4.4     9.9    -      -       -      -
     45A  ILE      3.2    12.1    -      -       -      -
     47A  LEU*     3.7    15.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 31 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23A  VAL*     4.1    18.6    -      -       +      -
     25A  GLN      3.3     8.5    -      -       -      +
     26A  ILE*     4.2    13.9    -      -       +      +
     30A  GLY*     1.3    72.2    -      -       -      -
     32A  TYR*     1.3    63.7    +      -       -      +
     33A  VAL*     3.7     4.9    +      -       +      +
     44A  MET*     3.3     2.5    -      -       -      +
     45A  ILE*     2.7    48.6    +      -       +      +
     47A  LEU*     4.7     8.0    -      -       +      +
     62A  ILE*     4.9    11.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 32 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23A  VAL*     3.7     0.7    -      -       -      +
     24A  GLN*     2.7    37.4    +      -       +      +
     25A  GLN*     2.7    47.7    +      -       +      +
     27A  ALA*     3.9    24.1    -      -       +      +
     30A  GLY      4.5     1.6    -      -       -      -
     31A  ALA*     1.3    72.2    -      -       -      +
     33A  VAL*     1.3    56.2    +      -       -      +
     42A  GLU*     5.3     5.8    -      -       +      +
     43A  GLY      3.5     5.6    -      -       -      +
     44A  MET*     3.7    29.6    -      -       +      -
    489B  PHE*     3.5    31.4    -      +       -      -
    492B  SER*     3.1    28.1    +      -       -      -
    493B  LYS*     4.0    19.3    +      -       -      -
    496B  THR*     5.5     1.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 33 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21A  VAL*     3.7    21.5    -      -       +      -
     22A  ASN      3.3     9.0    -      -       -      +
     23A  VAL*     3.8    23.6    -      -       +      -
     24A  GLN*     4.3     2.9    -      -       -      +
     31A  ALA      3.8     6.3    -      -       -      +
     32A  TYR*     1.3    79.5    -      -       -      +
     34A  LYS*     1.3    62.2    +      -       -      +
     35A  LEU*     4.3     1.1    -      -       +      -
     42A  GLU*     3.5     7.3    -      -       -      +
     43A  GLY*     2.8    38.9    +      -       -      +
     45A  ILE*     3.7    27.4    -      -       +      -
     84A  LEU*     3.6    30.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 34 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21A  VAL*     3.2     4.7    -      -       -      -
     22A  ASN*     2.9    36.0    +      -       +      +
     24A  GLN*     3.0    49.9    +      -       +      +
     33A  VAL*     1.3    74.1    -      -       -      +
     35A  LEU*     1.3    64.7    +      -       -      +
     36A  LEU*     3.3     2.0    +      -       +      +
     40A  ASN*     3.4    45.6    -      -       +      +
     41A  ILE      3.5     3.8    -      -       -      -
     42A  GLU*     4.4    19.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 35 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13A  PRO*     3.7    30.7    -      -       +      -
     19A  VAL*     4.0    18.2    -      -       +      -
     20A  MET      3.9     5.6    -      -       -      +
     21A  VAL*     3.8     9.9    -      -       +      -
     33A  VAL*     4.3     0.9    -      -       +      -
     34A  LYS*     1.3    71.7    -      -       -      +
     36A  LEU*     1.3    64.5    +      -       -      +
     37A  GLU      3.2     2.1    +      -       -      +
     38A  TYR*     3.2    26.7    +      -       +      -
     40A  ASN*     3.1    22.2    +      -       -      -
     41A  ILE*     2.9    27.4    +      -       +      +
     42A  GLU      4.5     0.7    -      -       -      -
     43A  GLY*     4.3    11.4    -      -       -      +
     82A  ILE*     4.0    13.5    -      -       +      -
     84A  LEU*     3.7    27.8    -      -       +      -
----------------------------------------------------------
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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