Contacts of the strand formed by residues 707 - 715 (chain A) in PDB entry 3SQ4


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 ARG 707 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    702A  TRP*     3.5     0.7    -      -       -      -
    703A  THR*     2.9    46.2    +      -       -      +
    704A  GLY*     3.2    10.2    +      -       -      +
    705A  LYS      3.0     9.4    +      -       -      +
    706A  LYS*     1.3    83.4    -      -       +      +
    708A  TYR*     1.3    64.9    +      -       -      +
    728A  MET      3.3     3.8    -      -       -      -
    729A  GLY*     3.4    25.0    +      -       -      -
    730A  LEU*     3.7    23.8    -      -       +      +
    731A  GLU*     2.8    33.3    +      -       -      -
    734A  LYS*     5.4     2.4    -      -       -      +
    879A  PRO*     5.3     2.8    +      -       -      +
    882A  GLY*     6.1     1.6    -      -       -      -
    883A  PHE*     3.8     9.9    -      -       -      -
      9T    C      3.3    34.0    -      -       -      +
     10T    G      3.4    28.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 708 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    619A  TYR*     4.0    13.5    -      +       -      -
    626A  TYR*     2.9    33.6    +      +       -      -
    701A  PHE*     3.3    16.2    -      -       -      +
    702A  TRP*     3.4    41.5    -      +       +      +
    703A  THR      4.8     0.2    -      -       -      +
    706A  LYS*     4.7     4.0    -      -       -      -
    707A  ARG*     1.3    81.6    -      -       -      +
    709A  ALA*     1.3    65.5    +      -       -      +
    710A  LEU*     4.4     8.3    -      -       +      -
    726A  LYS*     3.1    23.2    +      -       +      -
    727A  ILE*     3.6     3.3    -      -       -      +
    728A  MET*     2.9    58.7    +      -       +      +
    730A  LEU*     3.9     8.2    -      -       -      +
    114P    G      4.6     0.7    -      -       -      -
    115P  2DA      2.6    29.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 709 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    700A  GLY*     3.1     3.6    -      -       -      -
    701A  PHE*     2.9    51.3    +      -       +      +
    708A  TYR*     1.3    75.4    -      -       -      +
    710A  LEU*     1.3    66.1    +      -       -      +
    726A  LYS      3.3     6.3    -      -       -      -
    727A  ILE*     4.1     8.1    -      -       +      +
    730A  LEU*     4.1     6.7    -      -       +      +
    749A  ILE*     3.8    29.6    -      -       +      -
    753A  LEU*     3.9     3.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 710 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    407A  VAL*     3.8    26.2    -      -       +      -
    409A  SER*     5.8     0.2    -      -       -      -
    626A  TYR*     4.0    29.2    -      -       +      -
    687A  ALA*     5.3     5.4    -      -       +      -
    689A  ALA*     3.9    18.2    -      -       +      -
    699A  GLY      3.8     2.5    -      -       -      +
    700A  GLY*     4.0     9.2    -      -       -      +
    702A  TRP*     3.7    31.2    -      -       +      -
    708A  TYR*     4.4     9.6    -      -       +      -
    709A  ALA*     1.3    79.6    -      -       -      +
    711A  ASN*     1.3    59.1    +      -       -      +
    712A  VAL*     3.5    11.4    +      -       +      -
    725A  LEU*     3.5     5.4    -      -       -      +
    726A  LYS*     2.8    42.9    +      -       +      +
    753A  LEU*     3.7     6.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 711 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    689A  ALA*     3.2     2.6    -      -       -      +
    690A  GLY      3.0    47.2    +      -       -      +
    691A  PRO*     4.4     0.2    -      -       -      +
    692A  PRO*     4.0     4.4    -      -       -      +
    699A  GLY      2.9    20.4    +      -       -      +
    710A  LEU*     1.3    72.0    -      -       -      +
    712A  VAL*     1.3    59.2    +      -       -      +
    713A  TRP*     3.6    25.3    -      -       -      +
    723A  PRO*     3.5    10.9    -      -       -      +
    724A  LYS      4.1     2.0    -      -       -      +
    725A  LEU*     3.7     6.4    -      -       -      +
    753A  LEU*     3.7    14.6    -      -       +      +
    754A  GLN*     3.0    42.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 712 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    687A  ALA*     4.2    21.5    -      -       +      -
    688A  ILE      3.5     5.8    -      -       -      +
    689A  ALA*     4.5     2.9    -      -       +      -
    710A  LEU*     4.1    12.6    -      -       +      +
    711A  ASN*     1.3    73.3    -      -       -      +
    713A  TRP*     1.3    63.5    +      -       -      +
    714A  ASP      3.5    28.9    -      -       -      +
    715A  MET*     4.2     9.4    -      -       +      +
    720A  TYR*     3.7    15.5    -      -       +      -
    723A  PRO*     3.5     4.3    -      -       -      +
    724A  LYS*     2.9    40.6    +      -       +      +
    726A  LYS*     3.8    29.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 713 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    644A  THR*     3.5    32.1    -      -       +      -
    645A  ASN*     6.0     0.7    -      -       -      -
    647A  TRP*     3.6    23.4    -      +       -      -
    648A  VAL*     3.7    23.3    -      -       +      -
    688A  ILE      2.9    10.6    +      -       -      +
    690A  GLY      2.8    23.8    +      -       -      -
    692A  PRO*     3.7    28.0    -      -       +      -
    711A  ASN*     3.6    29.2    -      -       -      +
    712A  VAL*     1.3    72.4    -      -       -      +
    714A  ASP*     1.3    61.5    +      -       -      +
    719A  ARG*     3.6     7.9    -      -       -      -
    720A  TYR*     3.1    37.5    +      -       +      +
    721A  ALA      6.0     0.4    -      -       -      -
    722A  GLU      5.4     0.4    -      -       -      -
    723A  PRO*     3.7    37.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 714 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    648A  VAL*     4.2    10.3    -      -       +      -
    652A  ASP*     5.3     0.3    -      -       -      +
    685A  ARG*     2.9    40.4    +      -       -      +
    687A  ALA*     3.4     3.3    -      -       -      -
    688A  ILE*     3.0    32.7    +      -       +      -
    712A  VAL*     3.5     5.0    -      -       -      +
    713A  TRP*     1.3    80.9    -      -       -      +
    715A  MET*     1.3    58.7    +      -       -      +
    717A  GLY*     3.2    19.3    +      -       -      +
    718A  THR      3.2    10.2    -      -       -      -
    719A  ARG*     2.7    44.0    +      -       -      +
    720A  TYR*     4.5     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with MET 715 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    493A  GLN*     4.5     3.6    -      -       -      +
    686A  GLU*     3.6    38.4    -      -       -      +
    687A  ALA*     3.8    18.6    -      -       +      -
    712A  VAL*     4.3     9.9    -      -       +      -
    714A  ASP*     1.3    73.1    +      -       -      +
    716A  GLU*     1.3    88.0    +      -       +      +
    717A  GLY      3.2     1.1    -      -       -      -
    718A  THR*     2.9    27.4    +      -       -      -
    720A  TYR*     3.1    31.3    -      -       +      +
    726A  LYS*     4.2    27.4    -      -       +      +
----------------------------------------------------------
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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