Contacts of the strand formed by residues 237 - 244 (chain A) in PDB entry 3CJR


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 ARG 237 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    211A  GLY*     5.0     6.1    +      -       -      -
    213A  ARG*     6.0     1.6    -      -       -      +
    235A  GLY      4.6     5.8    +      -       -      +
    236A  PHE*     1.3    74.7    -      -       -      +
    238A  PRO*     1.4    73.3    -      -       +      +
    239A  LEU*     4.0    18.1    -      -       -      +
    252A  TYR*     3.3     4.9    -      -       -      -
    253A  GLY*     2.7    55.1    +      -       -      +
    254A  ARG*     2.9    31.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 238 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    232A  ALA*     6.4     1.1    -      -       +      -
    236A  PHE      4.2     4.3    -      -       -      +
    237A  ARG*     1.4    87.6    +      -       +      +
    239A  LEU*     1.3    65.8    +      -       -      +
    240A  GLU      5.3     0.9    -      -       -      +
    241A  GLU*     6.0     3.6    -      -       +      +
    251A  ALA      3.9     1.1    -      -       -      +
    252A  TYR*     3.8    22.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 239 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117A  HIS*     4.3     7.2    -      -       +      -
    213A  ARG*     3.7    44.2    -      -       +      +
    237A  ARG*     4.2    19.5    -      -       -      +
    238A  PRO*     1.3    80.6    -      -       -      +
    240A  GLU*     1.3    68.4    +      -       +      +
    251A  ALA*     2.9    15.8    +      -       +      +
    252A  TYR      3.5    24.9    -      -       -      +
    253A  GLY*     3.6    17.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 240 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113A  ALA*     5.0     0.2    -      -       -      +
    116A  ARG*     2.8    40.2    +      -       -      -
    117A  HIS*     2.7    30.5    +      -       +      +
    238A  PRO*     5.3     0.8    -      -       -      +
    239A  LEU*     1.3    80.3    -      -       -      +
    241A  GLU*     1.3    72.5    +      -       -      +
    249A  LEU*     5.1     1.6    -      -       +      +
    251A  ALA*     3.0    41.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 241 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    228A  ARG*     2.8    45.7    +      -       -      +
    238A  PRO*     6.0     3.4    -      -       +      +
    240A  GLU*     1.3    85.7    -      -       -      +
    242A  ALA*     1.3    62.8    +      -       -      +
    248A  VAL*     5.6     3.4    -      -       +      +
    249A  LEU*     3.4     8.3    -      -       -      +
    250A  LEU*     3.4    22.9    -      -       +      +
    252A  TYR*     5.2     1.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 242 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109A  LEU*     3.9    18.2    -      -       +      +
    116A  ARG*     4.2    24.2    -      -       -      +
    240A  GLU*     6.1     0.2    -      -       -      -
    241A  GLU*     1.3    76.3    -      -       -      +
    243A  ALA*     1.3    61.1    +      -       -      +
    248A  VAL*     3.3     5.6    -      -       -      +
    249A  LEU*     2.7    41.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 243 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109A  LEU*     3.8     7.7    -      -       -      +
    221A  LYS*     3.6    30.1    -      -       -      +
    242A  ALA*     1.3    76.6    -      -       -      +
    244A  GLU*     1.3    64.7    +      -       -      +
    245A  GLY      5.4     0.4    -      -       -      +
    247A  TRP      3.4     9.9    -      -       -      +
    248A  VAL*     4.1     2.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 244 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    105A  GLU*     3.7    25.9    -      -       +      +
    108A  ARG*     2.7    49.7    +      -       -      +
    109A  LEU*     4.1    15.0    +      -       +      +
    112A  LYS*     4.8     7.6    +      -       -      +
    243A  ALA*     1.3    75.3    -      -       -      +
    245A  GLY*     1.3    67.6    +      -       -      +
    246A  GLU      3.4     0.5    +      -       -      -
    247A  TRP*     3.0    30.0    +      -       -      +
----------------------------------------------------------
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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