Contacts of the strand formed by residues 775 - 782 (chain B) in PDB entry 3H44


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 GLY 775 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    771B  LEU*     6.1     0.2    -      -       -      -
    772B  PRO*     2.9    32.9    +      -       -      -
    773B  ASP      3.4     1.4    +      -       -      -
    774B  ARG*     1.3    78.6    -      -       -      +
    776B  TRP*     1.3    62.6    +      -       -      +
    777B  PHE*     4.2     6.7    -      -       -      -
    951B  ARG*     3.4     3.2    +      -       -      +
    953B  LYS*     3.2    27.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 776 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    774B  ARG      3.9     1.9    +      -       -      +
    775B  GLY*     1.3    74.6    -      -       -      +
    777B  PHE*     1.3    73.5    +      -       -      +
    778B  VAL*     3.5    18.5    -      -       +      +
    860B  GLU*     3.6    21.8    -      -       +      -
    953B  LYS*     3.1    46.6    -      -       +      +
    955B  SER*     2.8    19.6    +      -       -      -
    957B  HIS*     5.2     1.3    -      -       -      -
    986B  LEU*     4.0    28.9    -      -       +      -
    987B  PRO*     3.0    47.3    -      -       +      -
    988B  GLN      5.3     1.1    -      -       -      +
    989B  PRO*     3.4    27.2    -      -       +      +
    990B  GLU*     2.9    26.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 777 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    771B  LEU*     4.5    11.0    -      -       +      -
    772B  PRO*     3.5    41.7    -      -       +      -
    775B  GLY*     4.3    10.8    -      -       -      -
    776B  TRP*     1.3    80.0    -      -       -      +
    778B  VAL*     1.3    62.9    +      -       -      +
    953B  LYS      3.0    12.2    +      -       -      -
    954B  VAL*     3.3    11.4    -      -       +      -
    955B  SER      2.9    25.0    +      -       -      -
    990B  GLU*     3.2    46.9    -      -       +      -
    992B  ILE*     3.6    21.5    -      -       +      -
    998B  PHE*     3.8    24.9    -      +       +      -
   1002B  LEU*     4.5    14.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 778 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    776B  TRP*     3.5    28.7    -      -       +      +
    777B  PHE*     1.3    78.5    -      -       -      +
    779B  TYR*     1.3    72.7    +      -       -      +
    780B  GLN*     4.5     6.5    -      -       +      -
    955B  SER*     3.2    11.7    -      -       -      +
    957B  HIS*     4.0    29.4    -      -       +      +
    989B  PRO*     3.6    24.5    -      -       +      -
    990B  GLU      3.0     6.8    +      -       -      +
    991B  VAL*     3.4    15.0    -      -       +      +
    992B  ILE*     3.1    23.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 779 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    685B  TYR*     3.8    32.3    -      +       +      -
    689B  LEU*     3.7    27.4    -      -       +      -
    778B  VAL*     1.3    74.5    -      -       -      +
    780B  GLN*     1.3    67.2    +      -       -      +
    781B  GLN*     2.6    45.2    +      -       +      -
    955B  SER      3.0     7.0    +      -       -      +
    956B  VAL*     3.5     8.5    -      -       +      -
    957B  HIS      3.1    22.0    +      -       -      -
    991B  VAL*     5.9     0.2    -      -       -      -
    992B  ILE*     3.8    37.5    -      -       +      +
    993B  GLN      5.2     2.7    -      -       -      -
    994B  ASN*     5.2     3.4    -      -       -      -
    995B  MET*     3.2    34.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 780 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    778B  VAL*     4.5     7.9    -      -       +      -
    779B  TYR*     1.3    86.1    -      -       -      +
    781B  GLN*     1.3    70.6    +      -       -      +
    956B  VAL*     5.7     0.4    -      -       -      -
    957B  HIS*     3.3    25.0    -      -       +      +
    959B  LEU*     4.0    29.9    -      -       -      +
    964B  ASP      5.5     2.0    +      -       -      -
    991B  VAL*     5.5    10.5    -      -       +      +
    992B  ILE      5.0     2.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 781 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    685B  TYR*     3.6    43.4    +      -       +      +
    779B  TYR*     2.6    37.2    +      -       +      -
    780B  GLN*     1.3    83.0    -      -       -      +
    782B  ARG*     1.3    60.8    +      -       -      +
    956B  VAL*     6.0     0.2    -      -       -      +
    957B  HIS      3.0     6.5    +      -       -      +
    958B  VAL*     3.2     5.5    -      -       +      -
    959B  LEU*     2.7    37.3    +      -       -      +
    995B  MET*     5.3     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 782 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    681B  HIS*     5.1     1.7    +      -       -      -
    685B  TYR*     4.9     4.0    +      -       -      -
    781B  GLN*     1.3    84.6    +      -       -      +
    783B  ASN*     1.3    72.2    +      -       -      +
    784B  GLU*     3.9    20.2    +      -       +      +
    958B  VAL*     4.1     3.1    -      -       -      +
    959B  LEU*     3.4    13.9    -      -       +      +
    960B  ALA      3.7     6.1    +      -       -      -
    961B  ARG*     3.5    20.9    +      -       -      -
    962B  GLU      4.1     0.8    -      -       -      -
    963B  MET*     2.5    45.1    +      -       -      +
    964B  ASP      3.6    14.8    +      -       -      -
----------------------------------------------------------
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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