Contacts of the strand formed by residues 620 - 627 (chain C) in PDB entry 3HR4


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 620 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    584C  ARG      3.4    14.4    +      -       -      +
    585C  LEU*     3.2    13.7    -      -       +      -
    586C  LEU      2.6    30.1    +      -       -      -
    618C  LYS      5.5     2.2    +      -       -      -
    619C  PHE*     1.3    90.3    -      -       -      +
    621C  TYR*     1.3    55.3    +      -       -      +
    651C  SER*     3.7    27.3    +      -       -      +
    653C  LEU*     4.2    22.2    -      -       +      +
    683C  THR*     4.3    28.9    +      -       -      +
    684C  PHE*     4.7    16.5    -      -       +      -
    616G  ASN      3.9    17.0    +      -       -      -
    617G  ASN*     5.0     2.0    +      -       -      +
    618G  LYS*     3.8    28.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 621 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    585C  LEU*     4.5     1.3    -      -       -      -
    586C  LEU*     3.1    23.1    -      -       +      +
    587C  LEU*     4.7     1.3    -      -       -      -
    619C  PHE*     4.2     3.4    -      -       +      -
    620C  ARG*     1.3    77.0    -      -       -      +
    622C  ALA*     1.3    67.1    +      -       -      +
    623C  VAL*     4.1     7.0    -      -       +      -
    642C  ASP*     3.4    24.6    +      -       -      -
    645C  LEU*     3.4    39.0    -      -       +      -
    646C  SER*     3.7    25.4    +      -       -      -
    650C  ALA*     3.2    30.9    +      -       +      -
    651C  SER      3.1     7.1    +      -       -      -
    652C  GLN*     2.9    44.5    +      -       +      +
    653C  LEU*     2.9    29.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 622 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    586C  LEU      3.2     3.9    +      -       -      +
    587C  LEU*     3.6    16.4    -      -       +      -
    588C  VAL*     3.0    25.1    +      -       -      +
    621C  TYR*     1.3    84.3    -      -       -      +
    623C  VAL*     1.3    64.4    +      -       -      +
    653C  LEU*     4.5     1.8    -      -       +      -
    654C  THR*     3.4    37.5    -      -       +      +
    672C  TRP*     3.5    11.5    -      -       +      -
    676C  THR*     3.9     2.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 623 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    588C  VAL*     3.4    23.6    -      -       +      +
    621C  TYR*     4.1    10.5    -      -       +      -
    622C  ALA*     1.3    79.2    -      -       -      +
    624C  PHE*     1.3    71.0    +      -       -      +
    638C  ALA*     3.7    27.6    -      -       +      +
    641C  ILE*     4.5     5.2    -      -       +      -
    642C  ASP*     3.7    32.9    +      -       +      +
    645C  LEU*     4.5     7.2    -      -       +      -
    654C  THR      4.7     3.4    +      -       -      -
    656C  MET*     3.4    17.9    -      -       +      +
    657C  GLY      3.0    21.6    +      -       -      -
    672C  TRP*     3.3    10.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 624 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    553C  LEU*     5.1     1.6    -      -       +      -
    588C  VAL      2.8    11.4    +      -       -      +
    589C  VAL*     3.3     9.8    -      -       +      +
    590C  THR      3.0    24.3    +      -       -      -
    623C  VAL*     1.3    79.4    -      -       -      +
    625C  GLY*     1.3    58.8    +      -       -      +
    626C  LEU*     3.5    29.4    -      -       +      -
    657C  GLY*     3.5    16.2    -      -       -      -
    658C  GLU      3.7    15.3    -      -       -      -
    659C  GLY*     3.5    27.1    -      -       -      -
    665C  GLN*     4.9     0.7    -      -       +      -
    668C  ALA      3.8     6.3    -      -       -      -
    669C  PHE*     3.2    57.2    -      +       +      -
    672C  TRP*     3.6    34.3    -      +       +      -
----------------------------------------------------------
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Residues in contact with GLY 625 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    590C  THR      3.1     8.3    -      -       -      -
    623C  VAL      4.3     0.2    -      -       -      -
    624C  PHE*     1.3    75.2    -      -       -      +
    626C  LEU*     1.3    59.5    +      -       -      -
    635C  CYS*     3.3    12.8    -      -       -      -
    638C  ALA*     3.3    23.6    -      -       -      +
    656C  MET*     4.3     0.4    -      -       -      +
    657C  GLY      2.9    10.2    +      -       -      -
    658C  GLU*     3.3     1.2    -      -       -      -
    659C  GLY      2.7    31.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 626 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    549C  LYS*     4.3     3.4    -      -       +      -
    550C  SER*     3.1    36.3    -      -       -      +
    553C  LEU*     3.7    19.7    -      -       +      -
    589C  VAL*     4.2    11.9    -      -       +      -
    590C  THR      2.9     8.8    +      -       -      +
    591C  SER*     3.8     1.0    -      -       -      -
    592C  THR*     3.3    25.5    +      -       -      -
    624C  PHE*     3.5    30.7    -      -       +      -
    625C  GLY*     1.3    76.3    -      -       -      -
    627C  GLY*     1.3    58.3    +      -       -      +
    635C  CYS*     3.8     7.1    -      -       -      -
    659C  GLY      3.6     4.0    -      -       -      -
    665C  GLN*     3.4    37.0    -      -       +      +
    999C  FMN      3.8    14.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 627 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    626C  LEU*     1.3    78.5    -      -       -      +
    628C  SER*     1.3    60.8    +      -       -      -
    634C  PHE*     3.3     6.3    -      -       -      -
    635C  CYS*     4.1     1.4    -      -       -      -
    659C  GLY      3.2     3.8    +      -       -      -
    660C  ASP*     3.1    10.0    -      -       -      -
    661C  GLU      2.9    21.9    +      -       -      -
    665C  GLN*     3.9     0.2    -      -       -      +
    999C  FMN      3.4    35.9    -      -       -      -
----------------------------------------------------------
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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