Contacts of the strand formed by residues 633 - 638 (chain A) in PDB entry 2EIE


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 SER 633 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    546A  ILE*     3.5    36.8    +      -       -      +
    549A  THR*     4.7    10.7    -      -       -      +
    619A  MET      3.7     0.7    -      -       -      -
    620A  LEU*     2.8    44.0    +      -       -      +
    631A  VAL      4.7     0.7    +      -       -      -
    632A  ALA*     1.3    74.4    +      -       -      +
    634A  THR*     1.3    63.5    +      -       -      +
    635A  ILE*     3.7     3.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 634 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    178A  PRO      3.9    14.4    +      -       -      +
    179A  THR*     5.6     1.1    -      -       -      -
    552A  GLN*     3.9    16.8    -      -       -      +
    576A  TYR*     2.7    35.0    +      -       +      +
    617A  TYR*     3.8    28.9    -      -       +      -
    618A  TRP      3.6     3.8    -      -       -      +
    632A  ALA      4.1     2.5    +      -       -      -
    633A  SER*     1.3    70.8    -      -       -      +
    635A  ILE*     1.3    70.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 635 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    549A  THR*     5.1     8.7    -      -       +      -
    551A  THR      3.7    21.5    -      -       -      +
    552A  GLN*     3.4    12.3    -      -       +      +
    554A  VAL*     3.9     9.2    -      -       +      -
    560A  ILE*     3.8    27.8    -      -       +      -
    573A  LEU*     4.7    11.9    -      -       +      -
    616A  GLY      3.9     0.2    -      -       -      +
    617A  TYR*     3.5     5.3    -      -       -      -
    618A  TRP*     2.7    44.9    +      -       +      +
    620A  LEU*     4.2    24.5    -      -       +      -
    633A  SER*     4.1    10.8    -      -       -      +
    634A  THR*     1.3    85.0    -      -       -      +
    636A  ARG*     1.3    72.0    +      -       -      +
    637A  VAL*     4.4     7.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 636 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    235A  GLY      3.9     7.5    +      -       -      -
    236A  ASN*     3.0    55.1    +      -       -      +
    552A  GLN      2.8    15.1    +      -       -      +
    553A  SER*     3.4    14.5    -      -       -      +
    554A  VAL*     2.9    30.3    +      -       -      +
    616A  GLY      3.5    10.8    -      -       -      +
    617A  TYR*     3.6    36.9    +      -       +      -
    635A  ILE*     1.3    72.3    -      -       -      +
    637A  VAL*     1.3    68.5    +      -       -      +
    638A  THR*     5.6     6.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 637 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    235A  GLY      4.4     2.9    -      -       -      +
    554A  VAL*     3.3    17.9    -      -       +      +
    556A  VAL*     3.8    27.1    -      -       +      +
    573A  LEU*     5.0     5.6    -      -       +      -
    606A  VAL*     4.3    18.4    -      -       +      -
    613A  ALA*     3.9    14.1    -      -       +      +
    615A  PRO*     3.3     4.6    -      -       +      +
    616A  GLY*     2.8    33.0    +      -       -      +
    618A  TRP*     3.6    34.3    -      -       +      +
    635A  ILE*     4.4     7.6    -      -       +      -
    636A  ARG*     1.3    81.4    +      -       -      +
    638A  THR*     1.3    65.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 638 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    235A  GLY      5.9     0.4    -      -       -      -
    553A  SER*     6.4     0.7    -      -       -      -
    554A  VAL      3.0    20.9    +      -       -      +
    555A  LYS*     3.4    16.2    -      -       +      -
    556A  VAL*     3.0    31.4    +      -       -      +
    615A  PRO*     4.5     1.8    -      -       -      -
    636A  ARG*     5.6     7.6    -      -       -      +
    637A  VAL*     1.3    74.8    -      -       -      +
    639A  GLN*     1.3    76.7    +      -       -      +
----------------------------------------------------------
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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