Contacts of the strand formed by residues 232 - 238 (chain 6) 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 TYR 232 (chain 6).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    2196  THR*     4.3     1.6    -      -       -      -
    2206  SER*     2.8    43.0    +      -       -      +
    2236  GLY*     5.2     1.8    -      -       -      -
    2246  HIS*     3.3    49.5    +      -       +      -
    2256  LEU*     4.3     3.6    -      -       +      +
    2266  LEU*     4.3    12.5    +      -       +      +
    2306  ALA*     5.7     2.0    -      -       +      -
    2316  GLU*     1.3    82.5    -      -       -      +
    2336  LEU*     1.3    59.7    +      -       -      +
    2346  HIS*     3.2    16.2    +      -       +      -
    2586  PHE*     3.5    24.0    -      +       +      -
    2936  LEU*     3.1    46.5    +      -       +      +
    2966  ARG*     3.9     5.6    -      -       +      -
    2976  THR*     3.7    32.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 233 (chain 6). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    2176  LEU*     5.8     0.4    -      -       +      -
    2186  LEU      3.5     7.2    -      -       -      +
    2196  THR*     3.5    11.3    -      -       +      +
    2316  GLU      4.0     1.0    +      -       -      -
    2326  TYR*     1.3    74.7    -      -       -      +
    2346  HIS*     1.3    57.9    +      -       -      +
    2356  TRP      3.8     9.4    -      -       -      +
    2366  LEU*     3.7    23.6    -      -       +      -
    2526  CYS*     3.8    25.4    -      -       +      -
    2556  LEU*     4.8     1.9    -      -       -      +
    2586  PHE*     5.9     0.2    -      -       -      -
    2956  GLN      5.3     0.4    -      -       -      +
    2966  ARG*     2.7    80.4    +      -       +      +
    2986  PHE*     3.5    35.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 234 (chain 6). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    2186  LEU*     2.8    24.1    +      -       +      +
    2206  SER*     3.9    22.0    +      -       -      -
    2246  HIS*     5.5     1.6    -      +       -      -
    2326  TYR*     3.2    21.8    +      -       +      -
    2336  LEU*     1.3    75.0    +      -       -      +
    2356  TRP*     1.3    52.2    +      -       -      +
    2536  PRO      2.7    24.9    -      -       -      +
    2546  TYR*     3.2     8.6    -      +       +      -
    2556  LEU*     3.0    34.7    +      -       +      +
    2566  PRO      3.3    31.1    +      -       -      -
    2576  PRO*     3.6    14.0    -      -       +      +
    2586  PHE*     3.5    24.7    +      +       -      -
    2686  LEU*     4.3    13.8    -      -       +      +
    2966  ARG*     3.5     7.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 235 (chain 6). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    2016  ALA*     3.4    19.3    -      -       +      -
    2026  PRO*     3.8    33.4    -      -       +      -
    2046  VAL*     4.7     7.2    -      -       +      -
    2166  LEU*     3.3    26.6    -      -       +      +
    2176  LEU*     4.3     2.0    -      -       -      +
    2186  LEU*     3.5    42.7    +      -       +      +
    2336  LEU*     3.8     8.8    -      -       -      +
    2346  HIS*     1.3    78.9    -      -       -      +
    2366  LEU*     1.3    68.5    +      -       -      +
    2376  LEU*     3.5    42.1    -      -       +      +
    2456  VAL*     4.7     8.3    -      -       +      -
    2506  VAL*     5.6     1.6    -      -       +      -
    2526  CYS*     3.2    20.6    -      -       -      +
    2536  PRO*     3.8     7.6    -      -       +      -
    2546  TYR*     3.8    22.7    -      +       +      +
    2706  PHE*     4.7     3.4    -      +       -      -
----------------------------------------------------------
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Residues in contact with LEU 236 (chain 6). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    2156  THR*     6.0     1.8    -      -       -      -
    2166  LEU      4.0     4.5    -      -       -      +
    2176  LEU*     4.4    16.8    -      -       +      +
    2336  LEU*     3.7    23.1    -      -       +      -
    2356  TRP*     1.3    78.1    -      -       -      +
    2376  LEU*     1.3    69.2    +      -       -      +
    2386  THR*     3.3    32.9    +      -       +      +
    2506  VAL*     3.6     2.6    -      -       -      +
    2516  THR*     3.2    42.2    +      -       -      +
    2526  CYS*     2.8    14.0    +      -       +      -
    2816  PHE*     5.0    11.4    -      -       +      -
    2986  PHE*     4.5     4.7    -      -       +      -
    3036  PHE*     4.4    20.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 237 (chain 6). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    2156  THR*     3.5     4.3    -      -       -      -
    2166  LEU*     2.8    50.8    +      -       +      +
    2356  TRP*     3.5    45.5    -      -       +      -
    2366  LEU*     1.3    74.2    -      -       -      +
    2386  THR*     1.3    62.7    +      -       -      +
    2406  ILE*     3.8    15.5    -      -       +      -
    2456  VAL*     3.4    38.8    -      -       +      +
    2486  GLY      6.0     0.2    -      -       -      -
    2496  GLN      3.4     4.9    -      -       -      +
    2506  VAL*     3.5    35.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 238 (chain 6). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    2156  THR*     4.2     5.4    -      -       +      -
    2366  LEU*     3.3    34.5    +      -       +      +
    2376  LEU*     1.3    73.6    -      -       -      +
    2396  ASN*     1.3    69.6    +      -       -      +
    2406  ILE*     3.2     5.5    +      -       -      +
    2486  GLY*     3.6     1.0    -      -       -      -
    2496  GLN*     2.8    60.3    +      -       -      +
    2506  VAL      4.1     0.9    +      -       -      -
    2516  THR*     4.3    10.2    -      -       +      +
    2816  PHE*     3.2    40.7    -      -       +      -
----------------------------------------------------------
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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