Contacts of the strand formed by residues 698 - 704 (chain A) in PDB entry 3I7H


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 THR 698 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    401A  SER*     3.1    27.8    -      -       -      +
    402A  ILE      3.6    10.5    -      -       -      +
    403A  ASP*     4.4    12.0    +      -       -      +
    404A  LEU      5.3     0.2    -      -       -      -
    407A  ILE*     5.0     2.9    -      -       -      -
    693A  LEU      3.6     0.7    -      -       -      +
    694A  ALA*     3.2     8.3    -      -       -      +
    695A  ASN*     2.4    65.8    +      -       -      -
    697A  SER*     1.3    74.4    +      -       -      +
    699A  LEU*     1.3    64.5    +      -       -      +
    700A  THR*     4.5     7.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 699 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    400A  ALA      3.9     0.7    -      -       -      +
    401A  SER*     3.5     6.4    -      -       -      -
    402A  ILE*     2.8    42.9    +      -       +      +
    404A  LEU*     5.3     2.2    -      -       +      +
    407A  ILE*     4.8     7.8    -      -       +      +
    410A  LEU*     4.2     7.9    -      -       +      -
    425A  LEU*     3.8    28.0    -      -       +      -
    427A  LEU*     3.9    27.4    -      -       +      -
    436A  LEU*     5.4     4.9    -      -       +      -
    692A  ALA*     4.8     4.0    -      -       +      -
    693A  LEU      3.2    10.1    -      -       -      +
    694A  ALA*     5.0     1.3    -      -       +      -
    698A  THR*     1.3    75.0    -      -       -      +
    700A  THR*     1.3    96.7    +      -       -      +
    701A  ILE*     3.8    19.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 700 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    396A  ILE*     5.8     4.3    -      -       +      -
    398A  GLU*     3.2    43.7    +      -       +      +
    400A  ALA      3.5    14.6    -      -       -      +
    401A  SER*     4.8     2.4    +      -       -      -
    692A  ALA*     3.2     5.7    -      -       -      -
    693A  LEU*     2.8    48.0    +      -       -      +
    698A  THR*     4.5     9.9    -      -       -      +
    699A  LEU*     1.3    82.5    +      -       -      +
    701A  ILE*     1.3    73.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 701 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    397A  HIS      4.8     0.2    -      -       -      -
    398A  GLU*     5.1     0.4    -      -       -      -
    399A  HIS*     2.9    26.4    +      -       -      +
    400A  ALA*     3.6    35.9    +      -       +      +
    402A  ILE*     4.6     7.4    -      -       +      -
    682A  LEU*     4.1    17.9    -      -       +      -
    687A  TYR*     4.1    28.2    -      -       +      -
    690A  SER*     3.8     5.2    -      -       -      +
    691A  LEU      3.0    15.5    -      -       -      +
    692A  ALA*     3.9    13.9    -      -       +      -
    693A  LEU*     5.5     0.2    -      -       -      -
    699A  LEU*     3.8    17.0    -      -       +      -
    700A  THR*     1.3    89.3    -      -       -      +
    702A  GLY*     1.3    57.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 702 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    396A  ILE*     4.9     8.3    -      -       -      +
    397A  HIS      3.3    18.2    -      -       -      -
    398A  GLU*     5.0     0.2    -      -       -      -
    399A  HIS*     3.3     7.4    -      -       -      -
    690A  SER*     2.5    34.0    +      -       -      -
    691A  LEU*     3.1    12.3    +      -       -      +
    693A  LEU*     5.5     2.4    -      -       -      +
    701A  ILE*     1.3    73.7    -      -       -      +
    703A  THR*     1.3    63.4    +      -       -      -
    704A  ILE      4.3     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 703 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    396A  ILE*     3.6    17.5    -      -       -      +
    397A  HIS*     3.8    16.7    +      -       -      +
    399A  HIS*     4.0    14.9    -      -       +      +
    688A  PRO      4.9     1.1    -      -       -      +
    689A  ASP      3.3    25.4    -      -       -      +
    690A  SER*     4.3     5.2    -      -       -      +
    702A  GLY*     1.3    76.7    -      -       -      +
    704A  ILE*     1.3    70.4    +      -       -      +
    705A  ASP*     3.5     1.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 704 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    394A  ILE*     3.1    35.0    -      -       +      -
    395A  GLY      3.6     1.8    -      -       -      +
    396A  ILE*     3.5    19.5    -      -       +      +
    641A  PHE*     6.0     8.1    -      -       +      -
    643A  SER*     5.3    13.0    -      -       -      -
    644A  LEU*     6.2     2.0    -      -       +      -
    650A  PHE*     5.5     6.1    -      -       +      -
    658A  VAL*     5.3    10.3    -      -       +      -
    660A  TYR*     4.0    14.4    -      -       -      +
    671A  VAL*     5.0    10.1    -      -       +      -
    690A  SER      5.9     0.2    -      -       -      -
    691A  LEU*     3.7    29.3    -      -       +      +
    703A  THR*     1.3    79.4    +      -       -      +
    705A  ASP*     1.3    74.9    +      -       -      +
    706A  GLU      4.2     0.2    -      -       -      +
----------------------------------------------------------
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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