Contacts of the strand formed by residues 154 - 165 (chain S) 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 VAL 154 (chain S).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129S  ARG*     3.6     4.0    +      -       -      -
    133S  VAL*     4.0    22.6    -      -       +      +
    136S  VAL*     3.6    43.3    -      -       +      -
    143S  LEU*     5.0     0.4    -      -       +      -
    149S  LEU*     4.2     6.5    -      -       +      -
    150S  GLY      3.6     5.6    +      -       -      +
    151S  LYS*     3.1    19.0    -      -       -      +
    153S  LEU*     1.3   100.8    -      -       +      +
    155S  ARG*     1.3    70.5    +      -       -      +
    198S  ILE*     4.0    16.2    -      -       +      -
    199S  GLU      3.5    13.0    -      -       -      +
    200S  ILE*     4.1     5.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 155 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129S  ARG*     3.3    50.3    -      -       +      +
    130S  LEU      5.0     1.8    -      -       -      -
    133S  VAL*     5.4     1.8    -      -       -      -
    151S  LYS      4.7     0.2    -      -       -      +
    154S  VAL*     1.3    80.0    -      -       -      +
    156S  VAL*     1.3    66.6    +      -       -      +
    157S  GLU*     2.7    40.0    +      -       -      +
    197S  SER      3.8     0.7    -      -       -      +
    198S  ILE*     3.6     1.7    -      -       -      -
    199S  GLU*     3.0    74.8    +      -       -      +
     52j  ALA*     4.5    12.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 156 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97S  ALA*     3.9    17.0    -      -       +      -
     99S  VAL*     4.0     6.1    -      -       +      -
    108S  VAL*     5.5     1.1    -      -       +      -
    129S  ARG*     3.4     4.9    -      -       -      +
    130S  LEU*     2.8    63.2    +      -       +      +
    133S  VAL*     3.4    28.0    -      -       +      -
    154S  VAL*     4.8     1.1    -      -       +      -
    155S  ARG*     1.3    76.5    -      -       -      +
    157S  GLU*     1.3    65.3    +      -       -      +
    195S  ILE*     3.9    27.1    -      -       +      -
    197S  SER      3.5     4.3    -      -       -      +
    198S  ILE*     4.2    14.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 157 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127S  ARG*     3.0    42.4    +      -       -      +
    128S  ILE      3.2     6.7    -      -       -      -
    129S  ARG*     3.9     9.5    -      -       -      +
    155S  ARG*     2.7    47.5    +      -       -      +
    156S  VAL*     1.3    74.2    -      -       -      +
    158S  ALA*     1.3    60.4    +      -       -      +
    195S  ILE*     3.4     7.6    -      -       -      +
    196S  ASN*     2.8    23.8    +      -       -      -
    197S  SER*     2.8    27.4    +      -       -      +
    199S  GLU*     5.4     0.4    -      -       -      +
     52j  ALA*     3.3    26.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 158 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127S  ARG*     3.6     0.6    -      -       -      -
    128S  ILE*     2.8    45.1    +      -       +      +
    130S  LEU*     4.1    22.7    -      -       +      -
    157S  GLU*     1.3    76.2    -      -       -      +
    159S  THR*     1.3    59.5    +      -       -      +
    193S  LEU*     4.1    18.6    -      -       +      -
    194S  ARG      3.3    11.2    -      -       -      +
    195S  ILE*     4.1    15.3    -      -       +      -
    196S  ASN*     3.6     3.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 159 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    125S  GLY*     4.4    10.5    -      -       -      +
    126S  GLU      3.5     7.0    -      -       -      +
    127S  ARG*     3.7    29.8    -      -       +      +
    158S  ALA*     1.3    71.7    -      -       -      +
    160S  VAL*     1.3    64.8    +      -       -      +
    161S  ILE*     3.3     0.9    +      -       -      +
    193S  LEU*     3.6     2.1    -      -       -      -
    194S  ARG*     2.8    39.0    +      -       -      +
    196S  ASN*     3.0    35.5    +      -       -      +
     18b  GLY*     3.2    22.6    +      -       -      +
     22b  TYR*     6.1     2.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 160 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120S  LEU*     4.7     1.8    -      -       +      -
    122S  LEU*     3.9    24.2    -      -       +      +
    123S  ALA      4.2    10.3    -      -       -      +
    124S  CYS*     3.4    19.2    -      -       -      +
    125S  GLY*     2.8    29.5    +      -       -      -
    126S  GLU      3.2    12.1    +      -       -      +
    128S  ILE*     3.6    19.1    -      -       +      -
    159S  THR*     1.3    71.3    -      -       -      +
    161S  ILE*     1.3    61.1    -      -       -      +
    162S  GLU      4.3     7.6    -      -       -      +
    163S  LYS*     4.6     8.3    -      -       +      -
    191S  THR*     4.8     7.4    -      -       +      -
    192S  VAL      3.7    10.1    -      -       -      +
    193S  LEU*     3.6    22.7    -      -       +      -
     22b  TYR*     4.6     1.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 161 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113S  LEU*     3.4    22.4    -      -       +      -
    124S  CYS*     3.2     7.1    -      -       -      -
    159S  THR      3.3     0.6    +      -       -      +
    160S  VAL*     1.3    72.4    -      -       -      +
    162S  GLU*     1.3    76.2    +      -       +      +
    192S  VAL*     2.8    19.6    +      -       +      +
    194S  ARG*     3.7    25.8    -      -       +      -
     13b  SER*     3.1    33.7    -      -       -      +
     17b  ASN*     4.1    24.7    -      -       +      +
     18b  GLY*     4.0    15.0    -      -       -      +
     22b  TYR*     3.0    33.8    +      -       -      -
     25b  GLN*     6.2     0.2    -      -       +      -
    106b  ASP      4.4     0.2    -      -       -      +
    108b  SER*     5.6     3.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 162 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124S  CYS*     3.5     6.0    -      -       -      -
    160S  VAL*     4.3     1.3    -      -       -      +
    161S  ILE*     1.3    89.3    -      -       +      +
    163S  LYS*     1.3    63.1    +      -       -      +
    164S  THR*     3.2    17.9    +      -       +      +
    191S  THR*     3.4     2.9    -      -       -      -
    192S  VAL*     2.8    58.6    +      -       +      +
      9b  ARG*     4.8     9.4    +      -       -      -
     11b  LEU*     5.3     1.0    -      -       -      +
     12b  ALA      4.2    13.7    -      -       -      +
     13b  SER*     4.8     2.8    +      -       -      -
    106b  ASP*     3.9    12.6    -      -       -      +
    107b  GLN*     4.2     0.7    -      -       -      -
    108b  SER*     3.1    39.9    +      -       -      +
    110b  LEU*     5.2     0.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 163 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    119S  GLU*     3.5    31.7    +      -       +      -
    120S  LEU*     5.7     0.2    -      -       -      -
    121S  ASP*     3.7    23.9    +      -       -      +
    122S  LEU      3.4    27.3    +      -       -      +
    123S  ALA*     5.4     0.2    -      -       -      -
    124S  CYS*     3.8     7.0    -      -       -      -
    160S  VAL*     4.6     2.2    -      -       +      -
    162S  GLU*     1.3    73.9    -      -       -      +
    164S  THR*     1.3    65.7    +      -       -      +
    190S  GLN      3.4     8.7    -      -       -      +
    191S  THR*     4.0    20.6    -      -       +      -
    102b  GLN*     6.0     0.2    -      -       -      +
    103b  LYS*     4.4     4.7    -      -       -      +
    106b  ASP*     3.1    36.7    +      -       +      +
    107b  GLN*     3.5    18.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 164 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    162S  GLU*     3.2    33.9    -      -       +      +
    163S  LYS*     1.3    81.3    -      -       -      +
    165S  GLU*     1.3    67.3    +      -       -      +
    189S  PRO*     3.4     6.9    -      -       -      +
    190S  GLN*     2.8    55.4    +      -       -      +
    192S  VAL*     5.3     4.5    -      -       +      +
    103b  LYS*     5.4     5.4    -      -       -      -
    107b  GLN*     3.7    21.1    -      -       +      +
    112b  VAL*     6.1     1.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 165 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    164S  THR*     1.3    88.3    +      -       -      +
    166S  SER*     1.3    69.1    +      -       -      +
    187S  THR*     3.3    35.3    +      -       -      +
    188S  THR      3.9     2.9    -      -       -      -
    189S  PRO*     4.3     6.1    -      -       +      -
    190S  GLN*     4.7     1.9    -      -       -      +
    103b  LYS*     2.8    42.3    +      -       +      +
    107b  GLN*     4.9     3.4    -      -       -      +
    112b  VAL*     4.7    14.6    -      -       +      +
----------------------------------------------------------
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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