Contacts of the strand formed by residues 266 - 275 (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 HIS 266 (chain 6).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    2226  ASP*     2.6    25.4    +      -       -      +
    2246  HIS*     3.1    42.5    +      +       +      +
    2596  PRO*     3.0    29.4    -      -       +      +
    2606  ALA      4.4     0.7    -      -       -      -
    2636  SER*     2.7    29.9    +      -       -      -
    2646  GLY      4.4     1.8    -      -       -      -
    2656  ILE*     1.3    82.7    -      -       -      +
    2676  ARG*     1.3    61.0    -      -       -      +
    2686  LEU*     4.0     6.7    -      -       +      -
    3196  PHE      3.8     0.2    -      -       -      +
    3206  GLN*     3.1     6.4    -      -       -      -
    3216  CYS*     2.8    44.7    +      -       +      +
     47P  PHE*     3.7    17.7    -      +       -      -
     49P  ASN*     5.3     0.7    -      -       -      -
     51P  ASN*     5.1     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 267 (chain 6). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1556  TYR*     2.9    34.0    +      -       +      -
    1566  GLY*     3.3    16.0    +      -       -      -
    1576  LEU*     4.8     3.6    -      -       +      +
    1596  ARG*     5.6     1.4    -      -       -      +
    1606  ASP*     3.1    22.6    +      -       -      +
    2206  SER*     4.8     0.2    -      -       -      -
    2216  LEU*     3.1    60.1    +      -       +      +
    2226  ASP*     3.4    19.5    +      -       -      +
    2666  HIS*     1.3    73.8    -      -       -      +
    2686  LEU*     1.3    65.6    +      -       -      +
    3186  PHE*     5.5     5.2    -      -       +      -
    3196  PHE      3.6     6.5    -      -       -      +
    3206  GLN*     4.6     5.4    -      -       +      +
     50P  ARG*     3.3    35.3    +      -       -      +
     51P  ASN*     3.3    29.6    -      -       +      +
     52P  PRO*     5.1     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 268 (chain 6). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1776  TYR*     5.8     0.7    -      -       -      +
    2186  LEU*     3.8    21.8    -      -       +      -
    2196  THR      3.4     3.6    -      -       -      -
    2206  SER*     3.2    33.9    -      -       -      +
    2246  HIS*     5.4     1.3    -      -       +      -
    2346  HIS*     4.3    15.5    -      -       +      +
    2546  TYR*     5.9     0.4    -      -       +      +
    2576  PRO*     3.9    18.6    -      -       +      -
    2666  HIS*     5.2     6.3    -      -       +      -
    2676  ARG*     1.3    76.3    -      -       -      +
    2696  ALA*     1.3    58.1    +      -       -      +
    2706  PHE*     5.9     0.4    -      -       -      -
    3186  PHE*     3.2     6.9    -      -       -      +
    3196  PHE*     2.8    67.4    +      -       +      +
    3216  CYS*     3.7    20.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 269 (chain 6). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1576  LEU*     3.6    18.4    -      -       +      -
    1616  LEU*     4.3     2.2    -      -       +      -
    2186  LEU*     3.2     5.9    -      -       -      -
    2196  THR*     2.8    39.6    +      -       -      +
    2216  LEU*     3.4    22.2    -      -       +      -
    2686  LEU*     1.3    77.4    -      -       -      +
    2706  PHE*     1.3    62.3    +      -       -      +
    2716  LEU*     3.9    17.5    +      -       +      +
    3166  LEU*     6.0     0.4    -      -       +      -
    3176  SER      3.7     5.8    -      -       -      +
    3186  PHE*     4.2     0.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 270 (chain 6). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1736  LEU*     4.2    11.2    -      -       +      -
    1756  VAL*     3.6    36.8    -      -       +      -
    1776  TYR*     4.0    15.3    -      +       -      -
    1876  VAL*     3.8    22.7    -      -       +      -
    2026  PRO*     4.2     6.3    -      -       +      -
    2046  VAL*     5.3     0.7    -      -       +      -
    2166  LEU*     3.8    24.0    -      -       +      -
    2176  LEU      3.2     6.3    -      -       -      +
    2186  LEU*     3.4    35.9    -      -       +      +
    2356  TRP*     4.7     3.1    -      +       -      -
    2696  ALA*     1.3    73.0    -      -       -      +
    2716  LEU*     1.3    67.7    +      -       -      +
    3166  LEU*     3.6     5.6    -      -       -      +
    3176  SER*     2.8    52.9    +      -       -      +
    3196  PHE*     4.8     9.9    -      +       +      -
----------------------------------------------------------
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Residues in contact with LEU 271 (chain 6). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1616  LEU*     3.4    35.4    -      -       +      -
    1626  PHE*     4.7     9.0    -      -       +      -
    1736  LEU*     4.8     1.1    -      -       -      -
    2156  THR      3.5     2.1    -      -       -      +
    2166  LEU*     3.3     7.4    -      -       -      +
    2176  LEU*     2.8    64.8    +      -       +      +
    2196  THR*     4.4     0.9    -      -       -      +
    2696  ALA*     4.1    10.8    -      -       +      +
    2706  PHE*     1.3    86.0    -      -       -      +
    2726  LEU*     1.3    61.9    +      -       -      +
    2736  PHE*     4.1    24.2    -      -       +      -
    3006  THR*     4.3    15.5    -      -       +      -
    3036  PHE*     6.4     0.2    -      -       +      -
    3136  PRO*     6.1     1.3    -      -       +      -
    3156  GLY      3.6     4.5    -      -       -      -
    3166  LEU*     3.5    15.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 272 (chain 6). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1716  VAL*     5.3     8.1    -      -       +      -
    1736  LEU*     3.9    14.6    -      -       +      -
    2066  TYR*     3.8    24.5    -      -       +      -
    2146  TRP*     3.5    40.4    -      -       +      -
    2156  THR      3.7     2.0    -      -       -      -
    2166  LEU*     3.7    39.9    -      -       +      +
    2406  ILE*     5.7     0.2    -      -       +      -
    2716  LEU*     1.3    73.8    -      -       -      +
    2736  PHE*     1.3    61.9    +      -       -      +
    3136  PRO*     3.4     6.1    -      -       -      +
    3146  ALA*     2.8    27.4    +      -       +      -
    3156  GLY*     2.8    30.8    +      -       -      +
    3166  LEU*     5.0     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 273 (chain 6). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1626  PHE*     5.0     4.3    -      +       -      -
    2146  TRP*     3.2    34.5    -      -       -      -
    2156  THR*     3.2    30.0    +      -       -      +
    2176  LEU*     4.6    12.3    -      -       +      -
    2716  LEU*     4.1    35.0    -      -       +      -
    2726  LEU*     1.3    76.0    -      -       -      +
    2746  LYS*     1.3    60.5    +      -       -      +
    3036  PHE*     4.4    10.1    -      +       -      -
    3046  TYR*     3.7    28.3    -      +       -      -
    3086  GLN*     3.7    24.9    -      -       -      -
    3116  MET*     3.4    17.5    -      -       +      -
    3126  THR*     3.3    10.8    -      -       -      +
    3136  PRO*     3.6    28.3    -      -       +      -
    3146  ALA      4.0     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 274 (chain 6). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1706  ARG*     5.1    13.2    -      -       -      +
    1716  VAL*     5.4     3.4    -      -       +      -
    2146  TRP*     3.9    19.3    -      -       +      -
    2736  PHE*     1.3    70.8    -      -       -      +
    2756  GLN*     1.3    61.8    +      -       -      +
    2766  ASP*     3.8     2.2    +      -       -      +
    3106  THR      4.2     0.2    -      -       -      +
    3116  MET*     3.1    27.2    -      -       -      +
    3126  THR*     2.8    37.0    +      -       -      +
    3136  PRO      5.0     1.8    -      -       -      -
    3146  ALA*     3.5    30.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 275 (chain 6). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    2136  LEU*     2.8    58.8    +      -       +      +
    2146  TRP      3.5     5.5    -      -       -      +
    2156  THR*     3.1    27.8    -      -       +      +
    2396  ASN*     3.0    40.8    +      -       -      +
    2736  PHE      3.8     0.2    +      -       -      -
    2746  LYS*     1.3    71.0    -      -       -      +
    2766  ASP*     1.3    65.6    +      -       -      +
    2776  GLN      3.9    15.0    +      -       -      +
    2786  PRO*     4.9     3.6    -      -       -      -
    2796  ILE*     4.5     2.8    -      -       -      +
    2816  PHE*     4.1     7.5    -      -       -      -
    3116  MET*     3.7    25.2    -      -       +      +
----------------------------------------------------------
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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