Contacts of the strand formed by residues 241 - 244 (chain A) in PDB entry 1JYF


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 ALA 241 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    174A  LEU*     3.4    35.7    -      -       +      -
    179A  HIS*     3.6    16.6    -      -       +      +
    181A  GLN      3.4     3.8    +      -       -      +
    182A  ILE*     3.5     5.7    -      -       +      -
    183A  ALA      3.1    22.1    +      -       -      -
    239A  PRO*     3.3     9.7    -      -       -      +
    240A  THR*     1.3    84.1    -      -       -      +
    242A  MET*     1.3    62.9    +      -       -      +
    268A  ILE*     4.4     0.4    -      -       -      -
    269A  SER*     3.1    12.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with MET 242 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    174A  LEU*     4.1     5.1    -      -       -      +
    182A  ILE*     4.9     0.4    -      -       -      -
    183A  ALA*     3.3    13.2    -      -       +      +
    184A  LEU      5.4     0.4    -      -       -      -
    185A  LEU*     4.2    24.9    -      -       +      +
    229A  THR*     3.5    35.0    -      -       -      +
    232A  MET*     3.8    25.1    -      -       +      -
    239A  PRO*     3.9    13.5    -      -       +      -
    241A  ALA*     1.3    79.2    -      -       -      +
    243A  LEU*     1.3    63.5    +      -       -      +
    244A  VAL*     4.0     7.4    -      -       +      -
    253A  ALA*     4.4     8.7    -      -       +      -
    257A  ILE*     4.3     7.6    -      -       -      -
    268A  ILE*     4.1    13.5    -      -       +      -
    269A  SER      2.9     9.8    +      -       -      +
    270A  VAL*     3.7     5.4    -      -       +      -
    271A  VAL*     3.0    27.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 243 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    170A  GLY*     3.9    19.1    -      -       -      -
    171A  VAL*     3.7    20.0    -      -       +      -
    174A  LEU*     3.6    29.8    -      -       +      -
    182A  ILE*     4.4     7.6    -      -       +      -
    183A  ALA      2.9     6.9    +      -       -      -
    184A  LEU*     3.6    24.7    -      -       +      -
    185A  LEU      2.9    23.4    +      -       -      -
    201A  TRP*     3.4    42.7    -      -       +      +
    205A  LEU*     4.8     2.5    -      -       +      -
    242A  MET*     1.3    70.9    -      -       -      +
    244A  VAL*     1.3    62.0    +      -       -      +
    271A  VAL*     3.9    17.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 244 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    185A  LEU*     3.5    23.8    -      -       +      +
    201A  TRP*     3.3    12.6    -      -       -      -
    242A  MET*     4.5    10.1    -      -       +      -
    243A  LEU*     1.3    74.4    -      -       -      +
    245A  ALA*     1.3    62.3    +      -       -      +
    246A  ASN      3.1     9.9    +      -       -      +
    249A  MET*     3.5    18.2    -      -       +      -
    250A  ALA*     3.5    40.8    -      -       +      +
    253A  ALA*     4.4    10.5    -      -       +      -
    270A  VAL*     4.3    16.8    -      -       +      -
    271A  VAL      2.9    18.3    +      -       -      +
    272A  GLY      3.7     1.4    -      -       -      +
    273A  TYR*     3.6    10.7    -      -       -      +
----------------------------------------------------------
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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