Contacts of the strand formed by residues 75 - 82 (chain M) in PDB entry 2ZJR


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 GLU 75 (chain M).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9H  ASP*     4.9     5.0    -      -       -      +
     76H  ARG*     2.7    44.4    +      -       -      +
     91H  PHE*     4.9     3.2    -      -       +      +
     92H  ASP*     4.9     1.0    +      -       -      +
     93H  ARG*     3.7    39.5    +      -       -      +
     95H  ALA*     4.3     5.4    -      -       -      +
    112H  GLY*     5.1     1.3    -      -       -      -
    113H  PRO*     4.2    12.3    -      -       +      -
     71M  ILE*     4.1     2.6    -      -       -      +
     72M  SER      3.0    26.8    +      -       -      +
     73M  PHE      3.2     7.3    +      -       -      +
     74M  GLY*     1.3    85.1    -      -       -      +
     76M  GLY*     1.3    68.2    +      -       -      +
     77M  VAL*     3.1     9.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 76 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91H  PHE*     3.6     3.5    -      -       -      +
     92H  ASP*     2.8    47.0    +      -       -      +
     69M  ARG*     3.3    17.7    -      -       -      -
     70M  LYS      3.6     4.7    -      -       -      -
     71M  ILE*     3.8    10.8    -      -       -      +
     74M  GLY      4.4     0.2    -      -       -      -
     75M  GLU*     1.3    73.0    -      -       -      +
     77M  VAL*     1.3    59.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 77 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     89H  ILE*     4.0    12.6    -      -       +      -
     90H  ARG      4.0     5.4    -      -       -      +
     91H  PHE*     3.9    34.1    -      -       +      +
     92H  ASP*     3.6     1.5    +      -       -      -
    113H  PRO*     4.5     2.7    -      -       +      -
    134H  LEU*     3.9    21.3    -      -       +      -
     50M  PHE*     3.9    16.6    -      -       +      -
     69M  ARG*     3.4     2.7    -      -       -      +
     70M  LYS*     2.4    58.3    +      -       -      +
     72M  SER*     4.3     5.6    -      -       -      +
     75M  GLU      3.1    18.6    -      -       -      +
     76M  GLY*     1.3    70.8    -      -       -      +
     78M  GLU*     1.3    72.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 78 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88H  THR      3.8     0.7    -      -       -      +
     89H  ILE*     3.6     5.5    -      -       -      +
     90H  ARG*     2.4    76.5    +      -       -      +
     92H  ASP*     5.6     0.2    -      -       -      -
     50M  PHE*     4.7     0.4    -      -       -      -
     55M  ILE*     3.7    17.7    -      -       +      +
     67M  THR*     3.9     3.5    -      -       +      +
     68M  VAL      3.3     3.8    -      -       -      +
     69M  ARG*     3.4    42.7    +      -       +      +
     77M  VAL*     1.3    76.0    -      -       -      +
     79M  ARG*     1.3    64.1    +      -       -      +
    108M  ARG*     2.9    38.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 79 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     83H  ARG*     3.7    21.2    -      -       -      +
     87H  SER*     4.3    12.2    +      -       -      -
     88H  THR      3.3    15.5    -      -       -      -
     89H  ILE*     3.7    27.4    -      -       +      +
    134H  LEU*     4.4    12.9    +      -       -      +
     36M  ASP*     3.6    22.0    +      -       -      -
     48M  GLN*     3.9    14.1    -      -       -      +
     50M  PHE*     3.1    44.9    -      -       +      +
     66M  PHE      3.9     0.3    -      -       -      +
     67M  THR*     3.2     8.1    -      -       -      +
     68M  VAL*     2.8    32.0    +      -       +      +
     78M  GLU*     1.3    76.2    -      -       -      +
     80M  VAL*     1.3    64.2    +      -       -      +
     81M  PHE*     3.6    33.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 80 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86H  GLY      5.1     3.1    -      -       -      +
     87H  SER*     3.2    29.5    -      -       -      -
     88H  THR*     2.9    36.6    +      -       +      +
     90H  ARG*     3.9    20.6    -      -       -      +
     65M  SER*     4.5    11.9    -      -       -      +
     66M  PHE      3.7     2.7    -      -       -      +
     67M  THR*     3.3    21.8    -      -       +      +
     79M  ARG*     1.3    75.3    -      -       -      +
     81M  PHE*     1.3    63.7    +      -       -      +
     82M  PRO*     4.9     3.6    -      -       +      -
   2663X    U      4.1    26.7    -      -       -      +
   2664X    G      4.0     8.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 81 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85H  ASP*     5.3     2.0    -      -       -      -
     87H  SER*     4.7     9.2    -      -       -      -
     34M  ARG*     2.7    56.8    -      -       +      +
     36M  ASP*     3.8    14.8    -      -       +      -
     50M  PHE*     4.5     4.5    -      -       +      -
     65M  SER*     2.9    10.7    -      -       -      -
     66M  PHE*     2.8    52.4    +      +       +      -
     68M  VAL*     4.2    15.5    -      -       +      -
     79M  ARG*     3.6    52.0    -      -       +      -
     80M  VAL*     1.3    78.7    -      -       -      +
     82M  PRO*     1.3    60.7    -      -       +      +
     87M  LEU*     5.5     3.1    -      -       +      -
     88M  VAL*     3.4    14.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 82 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13B  GLN*     4.5    10.3    -      -       -      +
     15B  TRP*     3.9    20.6    -      -       +      -
     86H  GLY*     3.6    24.9    -      -       -      +
     87H  SER*     4.2     5.4    -      -       -      -
     34M  ARG*     4.4     3.6    +      -       -      -
     63M  ARG      5.7     0.4    -      -       -      +
     64M  LYS      3.5    11.4    -      -       -      +
     65M  SER*     3.9     4.9    -      -       -      -
     80M  VAL*     3.5    11.0    -      -       +      +
     81M  PHE*     1.3    83.1    -      -       +      +
     83M  PHE*     1.3    58.3    +      -       -      +
     84M  ALA      2.8     2.0    -      -       -      -
     85M  SER*     2.4    57.6    +      -       -      +
----------------------------------------------------------
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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