Contacts of the strand formed by residues 303 - 307 (chain A) in PDB entry 5X61


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 303 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    260A  VAL*     3.9    28.3    -      -       +      -
    261A  VAL      3.6     5.8    -      -       -      +
    262A  ALA*     3.8    16.2    -      -       +      -
    263A  PRO*     3.8     9.9    -      -       +      -
    267A  PRO*     4.0     9.4    -      -       +      -
    270A  ALA*     4.8     1.3    -      -       +      -
    271A  ALA      3.1    14.6    +      -       -      +
    272A  VAL*     3.3     9.8    -      -       +      +
    273A  MET      2.9    25.2    +      -       -      -
    302A  VAL*     1.3    68.3    -      -       -      +
    304A  VAL*     1.3    62.1    +      -       -      +
    305A  VAL*     4.2     2.7    -      -       +      -
    344A  ILE*     4.0    18.4    -      -       +      -
    347A  PHE*     3.4    25.1    -      -       +      +
    348A  GLY      3.8    20.2    -      -       -      +
    349A  GLY*     3.9     9.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 304 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    259A  ASN      4.0     0.5    -      -       -      +
    260A  VAL*     3.8     0.7    -      -       -      -
    261A  VAL*     2.9    37.3    +      -       +      +
    273A  MET*     3.4    11.0    -      -       +      +
    275A  TRP*     5.5     0.7    -      -       +      -
    293A  HIS*     3.9    42.3    -      -       +      +
    296A  LEU*     3.8    27.8    -      -       +      -
    297A  ALA*     3.7    27.8    -      -       +      +
    302A  VAL*     3.2    12.1    +      -       +      +
    303A  ILE*     1.3    72.2    -      -       -      +
    305A  VAL*     1.3    65.4    +      -       -      +
    357A  PHE*     5.2     2.9    -      -       +      -
    608A  PHE*     4.8     5.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 305 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    258A  ILE*     3.7    19.3    -      -       +      -
    259A  ASN      3.3     9.6    -      -       -      +
    260A  VAL*     4.2     8.7    -      -       +      -
    272A  VAL*     3.9    15.0    -      -       +      -
    273A  MET      2.9     8.2    +      -       -      +
    274A  LEU*     3.2    22.4    -      -       +      -
    275A  TRP*     2.6    34.8    +      -       -      +
    293A  HIS*     4.6     1.6    -      -       -      -
    303A  ILE*     4.2     4.9    -      -       +      -
    304A  VAL*     1.3    80.0    -      -       -      +
    306A  SER*     1.3    60.6    +      -       -      +
    307A  LEU*     5.9     0.4    -      -       +      -
    340A  VAL*     4.0    13.5    -      -       +      -
    344A  ILE*     3.6    29.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 306 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    257A  TYR      4.4     0.2    -      -       -      +
    258A  ILE*     3.4     6.4    -      -       -      +
    259A  ASN*     2.9    51.8    +      -       -      +
    274A  LEU*     5.0     0.9    -      -       -      -
    275A  TRP*     3.6    17.7    -      -       -      -
    286A  ALA*     3.7    13.3    -      -       -      +
    293A  HIS*     2.6    37.0    +      -       -      -
    305A  VAL*     1.3    76.0    -      -       -      +
    307A  LEU*     1.3    60.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 307 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    196A  TYR*     4.2     4.0    -      -       +      +
    257A  TYR      3.8     4.5    -      -       -      -
    258A  ILE*     4.2     8.1    -      -       +      -
    259A  ASN*     5.8     0.2    -      -       -      +
    274A  LEU*     3.6    28.3    -      -       +      -
    275A  TRP      3.8     6.6    +      -       -      +
    276A  ILE*     4.2    15.3    -      -       +      -
    277A  PHE*     3.6    14.4    +      -       -      -
    286A  ALA*     3.5    13.5    -      -       -      +
    305A  VAL*     5.9     0.4    -      -       +      -
    306A  SER*     1.3    75.8    -      -       -      +
    308A  GLN*     1.3    79.9    +      -       -      +
    309A  TYR*     3.8    19.9    -      -       +      +
    333A  GLN*     3.9    26.9    -      -       +      +
    336A  ALA*     3.8    26.0    -      -       +      -
    337A  LEU*     4.8     3.6    -      -       +      -
----------------------------------------------------------
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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