Contacts of the strand formed by residues 616 - 623 (chain A) 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 LEU 616 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    530A  PHE*     4.1    18.2    -      -       +      +
    611A  ALA*     3.0    34.3    +      -       +      +
    612A  GLU*     3.2     7.2    +      -       -      +
    614A  ALA*     4.5     4.7    -      -       +      +
    615A  GLY*     1.3    76.5    -      -       -      +
    617A  SER*     1.3    61.5    +      -       -      +
    631A  VAL*     4.2     7.6    -      -       +      -
    632A  LYS      3.6    13.2    -      -       -      +
    634A  TYR*     3.8    16.8    -      -       +      +
    637A  LYS*     3.8    27.8    -      -       +      +
    638A  GLN*     3.6    29.8    -      -       +      +
    641A  LEU*     3.9    23.7    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 617 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    612A  GLU*     3.9    27.6    -      -       -      -
    615A  GLY      4.1     1.1    -      -       -      -
    616A  LEU*     1.3    77.9    -      -       -      +
    618A  TYR*     1.3    64.6    +      -       -      +
    630A  SER      4.0     0.2    -      -       -      +
    631A  VAL*     3.5     4.2    -      -       -      +
    632A  LYS*     2.9    45.5    +      -       -      +
    641A  LEU*     4.5     4.7    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 618 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    601A  LYS*     3.4    37.2    +      -       +      +
    604A  LEU*     3.7    20.5    -      -       +      +
    605A  ASN*     5.2     0.7    +      -       -      -
    608A  ALA*     4.0    24.0    -      -       +      -
    617A  SER*     1.3    80.1    -      -       -      +
    619A  ASP*     1.3    65.2    +      -       -      +
    620A  LEU*     3.9    32.3    -      -       +      -
    629A  LEU*     4.0     3.6    -      -       +      -
    630A  SER      3.2    10.8    -      -       -      +
    631A  VAL*     4.1     7.6    -      -       +      -
    641A  LEU*     4.3    12.3    -      -       +      -
    645A  ILE*     3.6    36.8    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 619 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    601A  LYS*     6.1     0.2    -      -       -      -
    618A  TYR*     1.3    77.7    -      -       -      +
    620A  LEU*     1.3    60.4    +      -       -      +
    621A  GLN*     3.0    26.9    +      -       -      +
    628A  TYR*     3.6    22.9    +      -       -      +
    629A  LEU*     3.4     3.0    -      -       -      +
    630A  SER*     2.8    40.8    +      -       -      +
    632A  LYS*     5.5     5.4    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 620 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    578A  PHE*     5.4     1.6    -      -       +      -
    597A  LEU*     4.0    29.1    -      -       +      +
    600A  LEU*     3.6    33.0    -      -       +      -
    601A  LYS*     3.1    37.0    +      -       +      +
    618A  TYR*     3.9    21.6    -      -       +      -
    619A  ASP*     1.3    77.3    +      -       -      +
    621A  GLN*     1.3    63.0    +      -       -      +
    627A  MET*     4.9     6.1    -      -       +      -
    628A  TYR      3.0    26.5    -      -       -      +
    629A  LEU*     3.8    18.6    -      -       +      -
    645A  ILE*     4.5    11.0    -      -       +      -
    649A  MET*     4.9    11.0    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 621 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    597A  LEU*     3.4    12.5    -      -       -      +
    601A  LYS*     4.7     7.6    +      -       -      +
    619A  ASP*     3.0    26.2    +      -       -      +
    620A  LEU*     1.3    73.6    -      -       -      +
    622A  ASN*     1.3    72.4    +      -       -      +
    623A  THR*     5.1     2.7    -      -       +      +
    627A  MET*     3.5     1.2    -      -       -      -
    628A  TYR*     2.7    58.4    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ASN 622 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    590A  SER*     4.2     4.3    -      -       -      +
    593A  ALA*     3.8    25.7    -      -       +      +
    594A  TYR*     3.5    48.6    +      -       -      +
    597A  LEU*     3.3    10.5    -      -       +      +
    598A  GLU*     5.8     0.4    +      -       -      -
    621A  GLN*     1.3    87.3    -      -       -      +
    623A  THR*     1.3    64.2    +      -       -      +
    626A  GLY      3.3    11.9    -      -       -      +
    627A  MET*     5.2     0.2    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 623 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    577A  GLU*     3.6    23.3    +      -       -      +
    583A  ALA*     4.1    11.3    -      -       -      +
    584A  TYR*     4.6     2.1    -      -       -      -
    621A  GLN*     4.1     4.7    -      -       +      +
    622A  ASN*     1.3    81.7    -      -       -      +
    624A  ILE*     1.3    63.2    +      -       -      +
    625A  TYR*     2.9    25.2    +      -       -      +
    626A  GLY*     2.8    28.1    +      -       -      +
    627A  MET      3.7     1.0    +      -       -      -
    628A  TYR*     3.9    22.7    -      -       +      +
----------------------------------------------------------
 Back to top of page


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