Contacts of the strand formed by residues 1004 - 1009 (chain B) in PDB entry 3I8E


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 VAL1004 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    955B  SER*     3.4    31.6    +      -       -      +
    956B  ALA*     3.9     2.9    -      -       +      +
    968B  ALA*     3.8    14.6    -      -       +      +
    969B  GLU      5.8     1.6    +      -       -      +
    974B  LEU*     3.9    15.7    -      -       +      -
   1000B  LEU*     3.7    22.4    -      -       +      -
   1002B  GLU      3.5    14.8    +      -       -      +
   1003B  PHE*     1.3    76.3    -      -       -      +
   1005B  ASN*     1.3    62.8    +      -       -      +
   1006B  VAL      4.1     6.5    -      -       -      +
   1007B  PHE*     4.2    11.0    -      -       +      -
   1030B  PHE*     3.6    36.6    -      -       +      -
   1031B  GLY      4.1     7.0    -      -       -      +
   1032B  THR*     4.4     2.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASN1005 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    359B  ILE      2.6    32.6    +      -       -      +
    360B  VAL*     3.8    10.7    -      -       -      +
    913B  TYR*     5.8     0.2    -      -       -      -
    955B  SER*     3.4    17.0    -      -       -      +
    956B  ALA*     4.0     3.1    -      -       -      +
   1003B  PHE*     3.5    11.2    +      -       -      -
   1004B  VAL*     1.3    73.0    -      -       -      +
   1006B  VAL*     1.3    63.3    +      -       +      +
   1031B  GLY      3.1     9.3    +      -       -      +
   1033B  VAL*     3.4    19.9    -      -       -      +
    162D  GLU*     3.1    59.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL1006 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    359B  ILE*     4.4     3.4    -      -       +      -
    360B  VAL      4.5     1.3    -      -       -      +
    361B  ASP*     3.7    37.0    -      -       -      +
    362B  MET*     3.9    34.9    -      -       +      +
    915B  LYS*     5.6     1.1    -      -       -      +
    956B  ALA*     4.4     2.9    -      -       -      -
   1004B  VAL*     3.7     3.1    -      -       -      +
   1005B  ASN*     1.3    85.1    -      -       +      +
   1007B  PHE*     1.3    77.8    +      -       -      +
   1008B  CYS*     5.1     0.7    -      -       +      -
   1029B  LEU      3.8     0.3    -      -       -      +
   1030B  PHE*     3.2     5.9    -      -       -      +
   1031B  GLY      2.9    36.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE1007 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    915B  LYS*     3.5    12.3    +      -       -      +
    956B  ALA*     3.5    39.3    -      -       +      +
    957B  VAL      3.9     5.8    -      -       -      -
    958B  GLU*     3.2    39.3    -      -       +      +
    966B  LEU*     3.8    33.4    -      -       +      -
    967B  GLY      4.2     5.6    -      -       -      -
    968B  ALA*     3.9    17.9    -      -       +      -
    974B  LEU*     4.3     8.1    -      -       +      -
   1004B  VAL*     4.2     3.6    -      -       +      -
   1006B  VAL*     1.3    86.1    -      -       -      +
   1008B  CYS*     1.3    65.0    +      -       -      +
   1028B  VAL*     3.8    15.9    -      -       +      -
   1029B  LEU      3.3     3.1    -      -       -      -
   1030B  PHE*     3.3    37.7    -      +       +      -
   1040B  VAL*     5.1     0.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS1008 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    362B  MET*     4.1    28.3    -      -       -      +
    363B  CYS*     4.5    13.5    -      -       -      -
    364B  VAL*     3.8    28.7    -      -       -      -
    915B  LYS*     6.0     0.2    -      -       -      +
    958B  GLU*     3.8     7.6    -      -       -      -
   1006B  VAL*     5.1     1.6    -      -       +      -
   1007B  PHE*     1.3    76.8    -      -       -      +
   1009B  HIS*     1.3    64.2    +      -       -      +
   1028B  VAL*     3.5     6.2    -      -       -      -
   1029B  LEU*     2.9    33.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with HIS1009 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    364B  VAL*     3.9     6.2    -      -       -      +
    958B  GLU*     2.9    26.6    +      -       -      -
    959B  ILE      3.1    22.8    +      -       -      -
    960B  LEU      4.6     8.3    -      -       -      -
   1008B  CYS*     1.3    83.3    -      -       -      +
   1010B  GLY*     1.3    57.9    +      -       -      +
   1027B  SER      3.5    11.5    +      -       -      +
   1028B  VAL*     3.5    27.3    -      -       +      +
----------------------------------------------------------
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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