Contacts of the strand formed by residues 95 - 101 (chain A) in PDB entry 3IMJ


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 PHE 95 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61A  PHE*     3.7    22.2    -      +       -      -
     85A  ILE*     4.0    18.6    -      -       +      -
     86A  ARG      3.2    15.3    -      -       -      +
     87A  GLU*     3.7    22.2    -      -       +      -
     93A  GLY      4.5     2.5    -      -       -      -
     94A  ASP*     1.3    77.0    -      -       -      +
     96A  SER*     1.3    66.4    +      -       -      +
    109A  LYS*     3.7     6.2    -      -       -      +
    110A  VAL*     3.1    42.5    +      -       +      +
    118A  TYR*     4.0    20.4    -      +       -      -
    128A  LEU*     4.0    12.6    -      -       +      -
     95B  PHE*     3.5    35.2    -      +       -      -
    112B  ARG*     5.5     1.3    -      -       -      -
    118B  TYR*     3.4    25.8    -      -       -      -
    128B  LEU*     4.1     4.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 96 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1A  AYI      3.1    28.3    +      -       -      -
     85A  ILE*     3.5     5.4    -      -       -      +
     86A  ARG*     2.8    65.3    +      -       -      +
     88A  SER*     3.6     8.0    -      -       -      -
     95A  PHE*     1.3    77.1    +      -       -      +
     97A  LEU*     1.3    60.0    +      -       -      +
    108A  PHE      3.4    12.1    -      -       -      -
    109A  LYS*     4.2     2.3    -      -       -      +
    110A  VAL*     4.1     4.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 97 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     83A  PHE*     3.6    26.0    -      -       +      -
     84A  LEU      3.4    16.4    -      -       -      +
     85A  ILE*     3.9    17.3    -      -       +      -
     96A  SER*     1.3    73.2    -      -       -      +
     98A  SER*     1.3    63.2    +      -       -      +
     99A  VAL*     3.8    20.4    -      -       +      -
    106A  GLN      3.6     1.2    -      -       -      +
    107A  HIS*     3.4     3.6    -      -       -      +
    108A  PHE*     2.8    56.7    +      -       +      +
    110A  VAL*     4.2     6.7    -      -       +      +
    120A  LEU*     4.1    14.4    -      -       +      -
    131A  LEU*     5.1     5.8    -      -       +      -
    140A  VAL*     3.9    27.6    -      -       +      -
    148A  LEU*     4.3     8.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 98 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70A  ALA*     3.9    10.2    -      -       -      +
     74A  LEU*     3.3    19.1    -      -       -      +
     83A  PHE*     3.2     5.5    -      -       -      +
     84A  LEU*     3.1    35.8    +      -       -      -
     86A  ARG*     2.8    24.0    +      -       -      -
     96A  SER      4.2     0.4    -      -       -      -
     97A  LEU*     1.3    70.3    -      -       -      +
     99A  VAL*     1.3    60.7    +      -       -      +
    105A  VAL*     4.3     0.7    -      -       -      -
    106A  GLN      3.3     4.7    -      -       -      -
    107A  HIS*     2.8    31.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 99 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74A  LEU*     4.1     0.4    -      -       -      +
     81A  GLY*     3.7    26.0    -      -       -      +
     82A  ALA      3.5     2.7    -      -       -      -
     83A  PHE*     4.3     0.2    -      -       +      -
     97A  LEU*     3.8    12.6    -      -       +      -
     98A  SER*     1.3    77.9    -      -       -      +
    100A  LYS*     1.3    75.2    +      -       -      +
    101A  PHE*     4.8     0.6    -      -       +      +
    105A  VAL*     3.3     6.0    -      -       -      +
    106A  GLN*     2.8    41.0    +      -       +      +
    108A  PHE*     3.8    26.7    -      -       +      -
    140A  VAL*     4.5     2.2    -      -       +      -
    146A  ILE*     3.8    17.9    -      -       +      -
    148A  LEU*     3.7    24.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 100 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74A  LEU*     3.4    25.6    -      -       +      +
     75A  SER*     3.3    19.8    +      -       -      +
     77A  GLN*     3.2    30.3    +      -       +      +
     78A  ARG      3.8    13.7    -      -       -      -
     79A  HIS      3.4    20.0    -      -       -      +
     80A  ASP*     4.0    10.3    -      -       -      -
     81A  GLY*     2.8    27.8    +      -       -      -
     82A  ALA*     2.8    19.3    +      -       +      +
     99A  VAL*     1.3    75.3    -      -       -      +
    101A  PHE*     1.3    62.9    +      -       -      +
    102A  GLY*     3.3    21.1    +      -       -      +
    104A  ASP      3.7     9.9    -      -       -      +
    105A  VAL*     4.4     5.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 101 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80A  ASP*     3.7    26.2    -      -       +      -
     99A  VAL*     3.7     2.4    +      -       +      +
    100A  LYS*     1.3    73.9    -      -       -      +
    102A  GLY*     1.3    63.9    +      -       -      +
    103A  ASN      3.5     0.5    +      -       -      -
    104A  ASP*     2.9    28.4    +      -       -      +
    106A  GLN*     4.0    17.8    +      -       -      +
    144A  GLN*     3.5    38.8    -      -       +      -
    145A  GLN      3.8    24.0    -      -       -      -
    146A  ILE*     3.8    36.1    -      -       +      -
----------------------------------------------------------
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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