Contacts of the strand formed by residues 95 - 102 (chain W) 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 GLY 95 (chain W).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60W  TYR*     3.5    19.8    -      -       -      -
     61W  VAL*     2.8    34.8    +      -       -      +
     93W  GLU      3.5     0.2    +      -       -      -
     94W  GLU*     1.3    76.0    -      -       -      +
     96W  ILE*     1.3    60.9    +      -       -      -
    133W  VAL*     3.6     8.5    -      -       -      -
    134W  VAL      3.5    11.0    -      -       -      -
    136W  ALA*     3.9     8.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 96 (chain W). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     58W  GLY*     3.5    28.7    -      -       -      +
     59W  HIS      3.5     3.8    -      -       -      +
     60W  TYR*     4.4    15.7    -      -       +      -
     95W  GLY*     1.3    77.1    -      -       -      +
     97W  VAL*     1.3    76.9    -      -       -      +
     98W  ARG*     3.6    23.7    +      -       -      +
    133W  VAL*     3.3     3.7    -      -       -      +
    134W  VAL*     2.8    47.5    +      -       +      +
    136W  ALA*     5.4     5.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 97 (chain W). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55W  LYS*     4.2     9.2    -      -       +      +
     56W  MET      3.8    15.0    -      -       -      +
     58W  GLY      2.8    25.2    +      -       -      -
     59W  HIS      3.2     6.0    +      -       -      +
     61W  VAL*     3.2    35.2    -      -       +      -
     67W  ILE*     4.2    19.1    -      -       +      -
     96W  ILE*     1.3    72.5    -      -       -      +
     98W  ARG*     1.3    70.1    +      -       -      +
     99W  TYR*     3.3    31.9    -      -       +      -
    131W  VAL*     3.7    15.0    -      -       +      -
    132W  HIS      3.3     4.7    -      -       -      -
    133W  VAL*     4.5     3.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 98 (chain W). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     776  TYR*     3.5    47.8    +      -       +      -
   2062A    A      5.5     4.0    +      -       -      +
     57W  GLU*     3.7    27.1    +      -       -      +
     58W  GLY*     4.1    10.1    -      -       -      -
     96W  ILE*     3.9    28.4    -      -       -      +
     97W  VAL*     1.3    77.8    +      -       -      +
     99W  TYR*     1.3    64.9    +      -       -      +
    131W  VAL*     3.5     2.9    -      -       -      +
    132W  HIS*     2.8    40.9    +      -       +      +
    134W  VAL*     3.8    27.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 99 (chain W). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     726  ARG      3.5     8.5    -      -       -      +
     776  TYR*     3.9     3.1    +      -       -      -
   2063A    G      3.3    38.7    -      -       -      +
   2064A    A      3.4    18.6    -      -       -      +
     53W  ILE*     3.3    28.3    -      -       +      +
     55W  LYS      3.1    17.5    +      -       -      -
     56W  MET*     4.3     0.9    -      -       -      -
     57W  GLU*     2.7    31.7    +      -       +      +
     67W  ILE*     3.9     9.7    -      -       -      +
     68W  ALA*     4.5     1.7    -      -       -      +
     75W  TRP*     3.7    21.1    -      +       -      -
     97W  VAL*     3.3    24.2    -      -       +      -
     98W  ARG*     1.3    78.3    -      -       -      +
    100W  THR*     1.3    70.3    +      -       -      +
    129W  THR*     5.6     2.7    -      -       -      -
    130W  PHE      3.4     5.2    -      -       -      -
    131W  VAL*     3.5    28.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 100 (chain W). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     726  ARG      3.6     2.2    -      -       -      +
     736  THR*     3.2    43.1    -      -       -      +
     746  TYR*     4.8     0.2    -      -       -      -
     776  TYR*     3.7     9.9    -      -       +      -
   2064A    A      5.2     1.7    +      -       -      -
     99W  TYR*     1.3    81.0    -      -       -      +
    101W  LYS*     1.3    64.4    +      -       -      +
    102W  GLU*     3.4    10.2    +      -       -      +
    129W  THR*     3.4     3.0    -      -       -      -
    130W  PHE*     2.8    31.5    +      -       -      +
    132W  HIS*     2.3    47.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 101 (chain W). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     716  TRP*     3.1    40.1    +      -       +      +
     726  ARG      4.8     0.4    +      -       -      -
     736  THR*     4.0     5.5    +      -       -      +
   2064A    A      3.3    25.1    -      -       -      +
   2065A    A      3.8     3.4    +      -       -      -
   2066A    C      4.0    14.5    +      -       -      -
    100W  THR*     1.3    75.7    -      -       -      +
    102W  GLU*     1.3    67.4    +      -       -      +
    127W  TYR*     3.9     6.5    -      -       +      -
    128W  LYS      3.4     6.7    -      -       -      +
    129W  THR*     3.5    22.2    -      -       +      +
     48f  TYR      3.5    15.0    -      -       -      +
     53f  THR*     3.1    41.4    +      -       +      +
     54f  HIS      4.0     0.6    +      -       -      -
     56f  ILE*     3.4    30.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 102 (chain W). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     696  HIS*     6.0     0.9    -      -       -      -
     736  THR*     3.8    10.9    +      -       -      -
     746  TYR*     2.6    53.0    +      -       -      +
     67P  TRP*     4.3    20.9    -      -       +      -
    100W  THR*     3.4    21.4    +      -       -      +
    101W  LYS*     1.3    81.8    -      -       -      +
    103W  VAL*     1.3    70.8    +      -       -      +
    104W  TYR      3.4     0.2    +      -       -      -
    127W  TYR*     3.9     3.5    -      -       -      -
    128W  LYS      2.8    28.1    +      -       -      +
    130W  PHE*     3.6    20.6    -      -       +      -
    132W  HIS*     4.4     0.4    +      -       -      +
----------------------------------------------------------
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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