Contacts of the strand formed by residues 257 - 261 (chain c) in PDB entry 3J7Y


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 LEU 257 (chain c).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    142b  GLY*     6.0     1.4    -      -       -      -
    255c  SER      4.1     0.4    +      -       -      +
    256c  ARG*     1.3    75.0    -      -       -      +
    258c  THR*     1.3    64.6    +      -       -      +
    259c  ARG      3.5    26.0    -      -       -      +
    260c  GLN*     3.4    29.8    -      -       +      +
    270c  TYR*     4.5    11.0    -      -       +      -
    271c  PHE      3.5    11.9    -      -       -      +
    272c  VAL*     3.5    21.8    -      -       +      +
    289c  VAL*     5.2    11.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 258 (chain c). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    138b  THR*     5.6     4.8    -      -       -      +
    142b  GLY*     5.3     8.7    -      -       -      -
    256c  ARG*     5.2     0.4    -      -       +      -
    257c  LEU*     1.3    74.9    -      -       -      +
    259c  ARG*     1.3    78.0    +      -       -      +
    271c  PHE*     2.5    37.0    +      -       -      +
    273c  GLY*     3.8    23.8    -      -       -      +
    275c  TYR*     4.1    21.5    -      -       +      +
    280c  LEU*     5.1     3.6    -      -       +      -
    283c  GLU*     4.1    17.2    +      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 259 (chain c). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    142K  VAL*     5.9     1.8    -      -       -      -
    133b  PHE*     3.2    63.1    +      -       +      +
    136b  LYS*     3.2    25.2    +      -       -      +
    137b  PRO      5.0     4.4    +      -       -      -
    138b  THR*     3.2    31.9    -      -       +      +
    257c  LEU*     3.5     4.2    -      -       -      +
    258c  THR*     1.3    94.4    +      -       -      +
    260c  GLN*     1.3    66.3    +      -       -      +
    269c  LEU      4.1     0.4    -      -       -      -
    271c  PHE*     2.6    48.8    +      -       +      +
    283c  GLU*     5.0     7.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 260 (chain c). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    139K  LYS      4.8     5.5    +      -       -      +
    140K  ASN      4.4     2.8    -      -       -      +
    141K  LEU      5.0     0.7    -      -       -      +
    142K  VAL*     3.6    13.9    -      -       -      +
    133b  PHE*     4.7     1.5    -      -       -      -
    144b  ARG*     4.3    27.0    -      -       -      +
    257c  LEU*     3.4    25.5    -      -       +      +
    259c  ARG*     1.3    81.2    -      -       -      +
    261c  SER*     1.3    61.7    +      -       -      +
    262c  GLY      4.2     8.1    +      -       -      +
    263c  GLY*     6.1     0.4    -      -       -      -
    269c  LEU      3.4     7.0    -      -       -      -
    270c  TYR*     3.4    37.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 261 (chain c). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15K  ALA*     4.9     0.2    -      -       -      +
     16K  ARG      3.8     8.7    +      -       -      -
     17K  ILE*     3.7    36.8    -      -       -      +
     18K  TRP      4.5     1.1    -      -       -      -
    140K  ASN      4.2     0.2    -      -       -      -
    142K  VAL*     3.6    20.9    -      -       -      -
    133b  PHE*     3.9     8.0    -      -       -      -
    260c  GLN*     1.3    72.3    -      -       -      +
    262c  GLY*     1.3    62.7    +      -       -      +
    267c  LEU      5.3     0.8    +      -       -      -
    268c  PRO*     3.3     3.3    -      -       -      +
    269c  LEU*     2.8    48.8    +      -       -      +
----------------------------------------------------------
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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