Contacts of the strand formed by residues 93 - 100 (chain A) in PDB entry 4IQJ


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 TYR 93 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74A  TYR*     3.4    37.2    -      +       +      -
     75A  VAL      3.3    12.6    -      -       -      +
     76A  ALA*     4.5     1.1    -      -       -      +
     77A  ALA      4.6     0.4    -      -       -      +
     92A  GLY*     1.3    81.8    -      -       -      +
     94A  PHE*     1.3    77.3    +      -       -      +
     95A  HIS*     4.5     9.4    -      +       -      -
    122A  TYR*     6.5     0.7    -      +       -      -
    123A  GLU*     3.7    25.5    +      -       +      +
    124A  LYS*     3.7    36.6    +      -       +      +
    126A  ARG*     3.8    28.0    -      -       +      -
    147A  GLY      4.8     1.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 94 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74A  TYR*     3.2     4.5    -      -       -      -
     75A  VAL*     2.3    53.0    +      -       +      +
     76A  ALA      4.9     1.1    -      -       -      -
     77A  ALA*     4.4    25.4    -      -       +      -
     92A  GLY      6.0     1.3    -      -       -      -
     93A  TYR*     1.3    84.7    -      -       -      +
     95A  HIS*     1.3    64.1    +      -       -      +
    147A  GLY      3.5    15.9    -      -       -      -
    148A  ALA      3.6     0.7    -      -       -      -
    149A  GLU*     3.5    44.2    -      -       +      +
    152A  GLN*     3.6    35.7    -      -       +      -
    153A  PHE*     4.9    17.9    -      +       -      -
    165A  ARG*     5.4     2.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 95 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47A  HIS*     3.7    22.9    -      +       -      -
     72A  GLU*     2.8    30.1    +      -       +      +
     73A  ALA      3.5     4.5    -      -       -      -
     74A  TYR*     3.5    28.2    -      +       -      -
     75A  VAL*     4.5     0.3    -      -       -      +
     93A  TYR*     4.5     9.2    -      +       -      -
     94A  PHE*     1.3    80.5    -      -       -      +
     96A  LEU*     1.3    65.2    +      -       -      +
    144A  GLY*     5.4     0.2    -      -       -      -
    145A  CYS*     3.9    14.5    -      -       -      +
    147A  GLY*     3.1    30.2    +      -       -      +
    148A  ALA*     3.1    25.3    -      -       +      +
    149A  GLU*     4.0     4.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 96 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71A  TYR      3.5     0.9    -      -       -      +
     72A  GLU*     4.3     4.7    -      -       -      +
     73A  ALA*     2.8    37.2    +      -       +      +
     75A  VAL*     3.4    26.0    -      -       +      -
     95A  HIS*     1.3    80.2    -      -       -      +
     97A  THR*     1.3    60.9    +      -       -      +
     98A  LEU*     3.7    17.3    +      -       +      +
    127A  ILE*     5.5     0.7    -      -       +      -
    132A  LEU*     3.5    32.1    -      -       +      -
    141A  ALA*     5.2     1.6    -      -       +      -
    142A  LEU      3.3    24.2    -      -       -      +
    143A  SER*     4.5     8.7    -      -       -      +
    144A  GLY*     5.0     3.8    -      -       -      -
    148A  ALA*     5.5     0.4    -      -       +      -
    149A  GLU*     4.2    13.9    -      -       +      +
    169A  ASP*     4.9     8.5    -      -       -      +
    173A  PHE*     5.2     2.0    -      -       +      -
    177A  PHE*     5.0    10.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 97 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10A  LEU      4.5     4.0    -      -       -      +
     11A  HIS*     3.0    37.2    +      -       +      +
     45A  THR*     4.1    24.7    -      -       +      -
     71A  TYR      4.1     2.0    -      -       -      -
     72A  GLU*     4.3     4.0    -      -       -      +
     96A  LEU*     1.3    72.9    -      -       -      +
     98A  LEU*     1.3    72.0    +      -       -      +
     99A  LEU*     4.6     3.1    -      -       +      -
    140A  ILE      4.1     0.2    -      -       -      +
    141A  ALA*     3.5     0.2    -      -       -      -
    142A  LEU*     3.0    48.0    +      -       +      +
    144A  GLY*     4.1     5.5    -      -       -      -
    180A  GLU*     3.1    16.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 98 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70A  GLY*     3.2     3.8    -      -       -      -
     71A  TYR*     2.8    44.8    +      -       +      +
     73A  ALA*     4.1    20.2    -      -       +      -
     96A  LEU*     4.0    20.0    -      -       +      +
     97A  THR*     1.3    86.0    -      -       -      +
     99A  LEU*     1.3    63.5    +      -       -      +
    109A  LEU*     4.0    14.2    -      -       +      +
    112A  LEU*     4.0    15.3    -      -       +      -
    127A  ILE*     5.3     0.2    -      -       +      -
    132A  LEU*     3.6    23.6    -      -       +      -
    139A  LEU*     4.2     7.6    -      -       +      -
    140A  ILE      3.6     2.5    -      -       -      +
    141A  ALA*     3.9    21.3    -      -       +      -
    173A  PHE*     4.1    15.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 99 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10A  LEU*     3.7    55.6    -      -       +      +
     43A  ALA*     4.0    11.9    -      -       +      -
     45A  THR*     4.0    11.9    -      -       +      -
     68A  ILE*     4.0    10.8    -      -       +      -
     69A  ILE      4.2     1.3    -      -       -      -
     70A  GLY*     4.0     7.0    -      -       -      -
     97A  THR*     4.6     6.5    -      -       +      -
     98A  LEU*     1.3    80.8    -      -       -      +
    100A  ALA*     1.3    61.6    +      -       -      +
    101A  LYS      3.4     0.5    +      -       -      -
    109A  LEU*     4.4     2.7    -      -       -      -
    139A  LEU*     3.6     5.0    -      -       -      -
    140A  ILE*     2.7    47.9    +      -       +      +
    142A  LEU*     4.7    15.9    -      -       +      -
    277A  ILE*     4.5    12.1    -      -       +      -
    281A  CYS*     4.8     3.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 100 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68A  ILE*     4.6     2.4    -      -       -      +
     69A  ILE*     3.1    30.3    +      -       +      +
     99A  LEU*     1.3    70.4    -      -       -      +
    101A  LYS*     1.3    63.3    +      -       -      +
    106A  TYR*     4.1    17.3    -      -       -      +
    109A  LEU*     3.6    16.2    -      -       +      +
    138A  GLY      3.9     4.7    -      -       -      -
    139A  LEU*     4.4     1.1    -      -       -      -
    281A  CYS*     3.4    18.6    -      -       -      +
    283A  VAL*     3.5    24.8    -      -       +      +
----------------------------------------------------------
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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