Contacts of the strand formed by residues 732 - 742 (chain A) in PDB entry 3I7N


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 CYS 732 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    726A  TYR*     3.3     8.6    -      -       -      -
    727A  GLN      3.1    27.2    +      -       -      -
    730A  SER*     3.6    28.7    -      -       -      +
    731A  GLN*     1.3    79.1    -      -       -      +
    733A  PHE*     1.3    63.5    +      -       -      +
    793A  ILE*     4.1    23.6    -      -       +      -
    794A  ILE      3.1    20.2    -      -       -      +
    795A  ASP*     4.4     2.9    -      -       -      -
    796A  GLN*     3.7     4.4    -      -       -      +
    802A  LEU*     4.6     4.9    -      -       +      -
    829A  PHE*     4.2    16.4    -      -       -      -
    853A  TYR*     4.5     3.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 733 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    363A  CYS*     4.1     8.3    -      -       -      -
    365A  VAL*     3.6    15.0    -      -       +      -
    367A  LEU*     3.9    23.8    -      -       +      -
    376A  VAL*     4.0    17.5    -      -       +      -
    387A  LEU*     5.3     0.7    -      -       +      -
    724A  ILE*     4.4    18.6    -      -       +      -
    725A  CYS      3.0    17.7    -      -       -      +
    726A  TYR*     3.5    29.6    -      +       +      -
    732A  CYS*     1.3    77.1    -      -       -      +
    734A  GLY*     1.3    62.7    +      -       -      +
    735A  VAL*     4.8     0.7    -      -       +      -
    792A  LEU      3.5     2.4    -      -       -      +
    793A  ILE*     3.6     3.8    -      -       -      +
    794A  ILE*     2.8    48.6    +      -       +      +
    796A  GLN*     4.3     8.5    -      -       +      -
    799A  PHE*     3.5    39.0    -      +       -      -
    829A  PHE*     4.3     3.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 734 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    724A  ILE*     3.4     0.2    -      -       -      -
    725A  CYS      2.7    36.6    +      -       -      +
    733A  PHE*     1.3    73.5    -      -       -      +
    735A  VAL*     1.3    65.9    +      -       -      +
    791A  LEU*     4.0    10.8    -      -       -      -
    792A  LEU      3.4     7.0    -      -       -      -
    793A  ILE*     4.5     0.7    -      -       -      -
    816A  LEU*     3.3    10.0    -      -       -      +
    829A  PHE*     3.9    19.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 735 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    378A  CYS*     4.8     0.2    -      -       -      -
    387A  LEU*     4.1     7.9    -      -       +      -
    717A  LEU*     5.1     2.9    -      -       +      -
    721A  PRO*     4.4    16.8    -      -       +      -
    723A  LYS      3.2     7.6    -      -       -      +
    724A  ILE*     3.0    39.0    -      -       +      -
    733A  PHE*     4.8     2.0    -      -       +      -
    734A  GLY*     1.3    74.1    -      -       -      +
    736A  LEU*     1.3    76.8    +      -       -      +
    737A  SER*     4.5     1.6    -      -       -      -
    790A  ASN      3.5     1.4    -      -       -      +
    791A  LEU*     3.6     2.5    -      -       -      +
    792A  LEU*     2.9    46.9    +      -       +      +
    794A  ILE*     4.0    24.9    -      -       +      -
    816A  LEU*     4.5     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 736 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    722A  ARG*     2.6    34.7    +      -       +      -
    723A  LYS*     3.0    25.6    +      -       +      +
    735A  VAL*     1.3    77.5    -      -       -      +
    737A  SER*     1.3    54.0    +      -       -      +
    789A  HIS*     6.0     0.9    -      -       -      +
    790A  ASN      3.3    10.8    -      -       -      +
    791A  LEU*     4.0    25.6    -      -       +      -
    813A  ALA*     3.4    44.9    -      -       +      +
    814A  LEU      4.0     2.2    -      -       -      -
    815A  SER      3.5    32.3    -      -       -      +
    816A  LEU*     4.2     7.6    -      -       +      -
    831A  VAL*     4.1    14.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 737 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    717A  LEU*     6.5     0.7    -      -       -      -
    719A  GLU*     2.5    30.2    +      -       -      -
    720A  SER      3.8     7.2    -      -       -      -
    721A  PRO*     4.7     4.0    -      -       -      -
    722A  ARG*     4.9     1.8    -      -       -      -
    735A  VAL*     4.5     2.7    -      -       -      -
    736A  LEU*     1.3    76.9    -      -       -      +
    738A  SER*     1.3    61.3    +      -       -      +
    788A  VAL      3.8     0.3    -      -       -      +
    789A  HIS*     3.3     9.2    +      -       -      +
    790A  ASN*     2.9    47.3    +      -       -      +
    792A  LEU*     3.5    22.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 738 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    382A  PHE*     5.6     0.5    -      -       -      -
    719A  GLU*     3.4     4.4    -      -       -      +
    720A  SER*     2.9    39.8    +      -       -      -
    722A  ARG*     3.5    27.9    +      -       -      -
    737A  SER*     1.3    78.5    -      -       -      +
    739A  ARG*     1.3    63.0    +      -       -      +
    740A  ILE*     5.7     1.4    -      -       -      +
    787A  GLU*     2.9    34.5    +      -       -      +
    788A  VAL      3.4     4.3    -      -       -      -
    789A  HIS*     3.9    10.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 739 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    719A  GLU*     3.8    18.8    +      -       +      +
    738A  SER*     1.3    76.3    -      -       -      +
    740A  ILE*     1.3    66.2    +      -       -      +
    741A  GLU*     2.9    27.3    +      -       -      +
    751A  ALA*     4.8     5.1    -      -       -      +
    753A  ARG      5.6     0.2    -      -       -      -
    755A  SER*     3.6    17.0    -      -       -      +
    757A  SER*     2.8    36.6    +      -       -      +
    758A  THR*     3.6    18.1    -      -       -      +
    787A  GLU*     3.1     5.2    -      -       -      -
    788A  VAL*     2.7    51.9    +      -       +      +
    790A  ASN*     3.1    19.3    +      -       -      +
    806A  GLN*     3.5    18.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 740 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    276A  MET*     5.7     2.9    -      -       +      -
    382A  PHE*     3.2    43.1    -      -       +      -
    720A  SER*     5.9     0.7    -      -       -      +
    738A  SER*     5.8     1.3    -      -       -      +
    739A  ARG*     1.3    80.2    -      -       -      +
    741A  GLU*     1.3    76.5    +      -       -      +
    751A  ALA*     4.2     6.8    -      -       -      +
    752A  LEU*     3.8    30.5    +      -       +      +
    785A  GLU*     4.2    26.7    -      -       +      +
    786A  VAL      3.1    10.1    -      -       -      +
    787A  GLU*     4.5    14.4    -      -       +      +
      8B  ARG*     6.0     2.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 741 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    739A  ARG*     2.9    38.7    +      -       +      +
    740A  ILE*     1.3    86.9    -      -       -      +
    742A  VAL*     1.3    65.5    +      -       -      +
    749A  THR*     3.1    34.4    +      -       -      +
    750A  THR      3.0    23.1    -      -       -      +
    751A  ALA*     3.5    16.3    -      -       +      +
    752A  LEU*     5.0     1.1    -      -       -      -
    784A  GLU      3.7     0.5    -      -       -      +
    785A  GLU*     3.4     6.4    -      -       -      +
    786A  VAL*     2.8    37.3    +      -       +      +
    788A  VAL*     3.7    16.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 742 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    741A  GLU*     1.3    80.5    -      -       -      +
    743A  GLN*     1.3    68.5    +      -       -      +
    749A  THR*     3.2     6.8    -      -       -      -
    750A  THR*     3.0    41.4    +      -       -      +
    751A  ALA*     4.2     1.2    -      -       -      +
    752A  LEU*     3.7    37.2    -      -       +      +
    783A  GLY*     3.6    20.0    -      -       -      +
    784A  GLU      3.3     2.9    -      -       -      -
    785A  GLU*     4.2    17.0    -      -       +      +
----------------------------------------------------------
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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