Contacts of the strand formed by residues 713 - 721 (chain D) in PDB entry 4OIN


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 ILE 713 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1032C  PHE*     3.6    36.3    -      -       +      -
   1036C  GLU*     3.9     9.2    -      -       +      +
   1039C  ALA*     3.8    23.6    -      -       +      -
   1040C  LEU*     4.3     3.6    -      -       +      -
   1043C  TYR*     2.8    24.9    +      -       -      -
    701D  LEU*     4.0    20.0    -      -       +      -
    702D  LEU      3.2    10.8    -      -       -      +
    703D  ASN*     3.4    24.2    -      -       +      +
    707D  THR*     4.3     1.3    -      -       +      +
    710D  ARG      2.9    10.2    +      -       -      +
    712D  GLY*     1.3    76.4    -      -       -      +
    714D  GLN*     1.3    65.3    +      -       -      +
    748D  HIS*     6.2     0.2    -      -       +      -
    763D  MET*     3.5    24.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 714 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1043C  TYR*     3.7    10.1    -      -       -      +
    701D  LEU*     3.5     6.7    -      -       -      -
    702D  LEU      2.9    33.1    +      -       -      +
    711D  LEU*     3.0    43.7    +      -       +      +
    713D  ILE*     1.3    81.4    -      -       -      +
    715D  ALA*     1.3    60.4    +      -       -      +
    716D  PHE*     3.5    12.7    -      -       +      -
    732D  VAL*     3.5    13.3    -      -       -      +
    735D  ALA*     3.7    14.1    -      -       -      +
    736D  PHE*     3.5    23.9    -      -       +      -
    763D  MET*     3.7     9.4    -      -       -      +
    765D  SER*     3.5    28.1    -      -       -      +
    768D  ASN*     5.5     0.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 715 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    699D  VAL*     4.1     6.7    -      -       +      -
    700D  VAL      3.4     6.1    -      -       -      +
    701D  LEU*     3.8    19.1    -      -       +      -
    714D  GLN*     1.3    72.7    -      -       -      +
    716D  PHE*     1.3    67.1    +      -       -      +
    759D  ALA*     3.3    32.3    -      -       +      +
    763D  MET*     2.8    15.8    +      -       +      +
    764D  LEU*     3.5     9.5    -      -       +      +
    765D  SER*     3.2    21.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 716 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    639D  LEU      3.7     7.0    -      -       -      -
    640D  HIS      3.3     6.1    -      -       -      +
    641D  GLN      3.3    21.1    -      -       -      -
    642D  CYS*     3.6    25.4    -      -       +      +
    699D  VAL*     3.2     7.3    -      -       -      -
    700D  VAL*     2.9    33.6    +      -       -      +
    702D  LEU*     3.9    28.0    -      -       +      -
    714D  GLN*     3.5    32.1    -      -       +      -
    715D  ALA*     1.3    74.4    -      -       -      +
    717D  GLN*     1.3    61.6    +      -       -      +
    718D  PRO*     3.3     1.0    -      -       -      +
    728D  LEU*     4.1     5.6    -      -       +      -
    729D  HIS*     4.6     4.5    -      -       +      -
    732D  VAL*     3.9    28.5    -      -       +      -
    736D  PHE*     4.1     3.6    -      +       -      -
    764D  LEU*     4.7     0.4    -      -       -      -
    765D  SER*     3.6    33.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 717 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    640D  HIS*     2.7    39.6    +      -       +      +
    641D  GLN*     3.3    14.5    +      -       +      +
    642D  CYS      3.0    22.3    +      -       -      +
    697D  GLY*     3.7    28.3    +      -       -      -
    698D  LYS      3.6    12.8    -      -       -      +
    699D  VAL*     3.7    11.4    -      -       +      +
    716D  PHE*     1.3    70.5    -      -       -      +
    718D  PRO*     1.3    69.3    -      -       +      +
    719D  VAL*     3.6     1.2    +      -       +      -
    760D  ARG*     4.4     9.9    -      -       -      +
    764D  LEU*     5.6     1.8    -      -       +      -
      3E  GLU*     4.7     5.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 718 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    642D  CYS*     3.5    10.5    -      -       -      +
    644D  LEU*     3.7    30.5    -      -       +      -
    653D  PHE*     4.8     3.6    -      -       +      -
    695D  ILE*     3.6    38.3    -      -       +      +
    698D  LYS      3.1    19.7    -      -       -      +
    699D  VAL*     3.9     4.5    -      -       -      -
    700D  VAL*     4.0    15.7    -      -       +      +
    716D  PHE      3.3     8.7    -      -       -      +
    717D  GLN*     1.3    86.4    -      -       +      +
    719D  VAL*     1.3    62.0    +      -       -      +
    720D  LEU*     4.0     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 719 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    637D  LEU*     4.8     7.6    -      -       +      -
    641D  GLN*     3.9    35.2    -      -       +      +
    642D  CYS      2.9    15.7    +      -       -      +
    643D  GLY*     3.4     1.7    -      -       -      -
    644D  LEU*     2.9    21.0    +      -       -      +
    695D  ILE*     5.2     0.2    -      -       -      -
    717D  GLN*     4.2     5.8    -      -       +      +
    718D  PRO*     1.3    76.1    -      -       -      +
    720D  LEU*     1.3    72.5    +      -       -      +
    721D  VAL*     3.2    10.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 720 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    185B  ARG*     6.1     0.5    -      -       -      -
    644D  LEU*     3.2    13.9    -      -       +      +
    646D  LYS*     4.4    18.4    -      -       +      -
    649D  ALA*     3.5    31.2    -      -       +      -
    688D  TRP*     4.4     4.7    -      -       +      +
    691D  LEU*     4.0    23.8    -      -       +      -
    692D  GLU*     3.7    42.1    +      -       +      +
    695D  ILE*     3.7    22.8    -      -       +      +
    718D  PRO      4.0     0.4    +      -       -      -
    719D  VAL*     1.3    79.1    -      -       -      +
    721D  VAL*     1.3    61.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 721 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    636D  GLN*     5.7     0.9    -      -       -      +
    637D  LEU*     6.1     0.4    -      -       +      -
    643D  GLY*     3.9     5.6    -      -       -      -
    644D  LEU      2.9    27.0    +      -       -      +
    645D  PRO*     3.5     7.3    -      -       +      +
    646D  LYS*     3.1    29.4    +      -       -      +
    719D  VAL*     3.4    19.1    -      -       +      +
    720D  LEU*     1.3    75.3    -      -       -      +
    722D  GLU*     1.3    69.3    +      -       -      +
    723D  GLY      3.9     0.7    +      -       -      -
    725D  SER      4.0    14.8    -      -       -      +
    727D  GLN*     3.7    32.8    -      -       -      +
----------------------------------------------------------
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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