Contacts of the strand formed by residues 615 - 624 (chain I) in PDB entry 5A31


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 615 (chain I).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    588I  PHE*     3.9    26.5    -      -       +      -
    599I  CYS*     4.2     7.9    -      -       +      -
    600I  ILE      3.6    13.7    -      -       -      +
    601I  LEU*     4.2     8.7    -      -       +      -
    613I  ASN*     4.5     5.6    -      -       -      -
    614I  GLY*     1.3    80.5    -      -       -      +
    616I  ILE*     1.3    71.5    +      -       -      +
    683I  TYR      5.5     0.3    -      -       -      +
    684I  GLN*     5.5     0.2    -      -       -      -
    685I  PHE*     4.2    29.3    +      -       +      +
    689I  TYR*     4.8     5.5    +      -       +      -
    693I  LEU*     3.4    38.4    -      -       +      -
    700I  ILE*     4.0    30.3    -      -       +      -
    701I  PRO*     3.5    18.7    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 616 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    599I  CYS*     3.5     1.8    -      -       -      -
    600I  ILE*     2.8    43.9    +      -       +      +
    613I  ASN*     5.1     8.3    -      -       +      -
    615I  LEU*     1.3    79.4    -      -       -      +
    617I  ALA*     1.3    71.1    +      -       -      +
    674I  VAL*     3.7    46.4    -      -       +      +
    675I  TYR*     3.9    21.8    -      -       +      +
    683I  TYR*     4.1    16.8    -      -       +      +
    700I  ILE*     4.6     3.1    -      -       -      -
    701I  PRO*     3.8    16.6    -      -       +      +
    703I  ARG*     3.8    19.3    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 617 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    597I  LYS*     4.0    13.2    -      -       +      -
    598I  MET      3.2    11.9    -      -       -      +
    599I  CYS*     4.0    10.3    -      -       -      +
    616I  ILE*     1.3    76.8    -      -       -      +
    618I  ILE*     1.3    76.4    +      -       -      +
    700I  ILE*     3.7    21.5    -      -       +      +
    701I  PRO      3.0    12.0    +      -       -      +
    702I  THR*     3.7    13.5    -      -       -      +
    703I  ARG      3.3    18.2    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 618 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    597I  LYS*     3.7    16.0    -      -       -      +
    598I  MET*     2.9    26.1    +      -       +      +
    600I  ILE*     4.3    17.3    -      -       +      -
    616I  ILE      5.1     0.4    -      -       -      +
    617I  ALA*     1.3    94.9    -      -       -      +
    619I  LYS*     1.3    66.7    +      -       -      +
    620I  PHE*     3.5    42.1    -      -       +      -
    669I  LEU*     4.4     7.2    -      -       +      -
    674I  VAL*     4.1    24.5    -      -       +      -
    702I  THR*     4.0     3.4    -      -       -      -
    703I  ARG*     3.8     6.5    -      -       +      +
    705I  MET*     3.5    37.2    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 619 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    597I  LYS*     4.5     8.3    -      -       -      +
    618I  ILE*     1.3    77.8    -      -       -      +
    620I  PHE*     1.3    70.2    +      -       -      +
    621I  GLY*     5.3     1.8    -      -       -      -
    702I  THR*     3.5    19.0    -      -       +      +
    703I  ARG      3.2     8.4    +      -       -      +
    704I  THR*     3.1    36.7    +      -       -      +
    705I  MET*     3.0    24.8    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 620 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    598I  MET*     4.6    15.5    -      -       +      -
    618I  ILE*     3.5    36.6    -      -       +      -
    619I  LYS*     1.3    78.8    -      -       -      +
    621I  GLY*     1.3    62.8    +      -       -      +
    622I  SER      3.8     0.7    -      -       -      -
    623I  PHE*     3.6    21.3    -      +       +      -
    634I  SER      4.3     3.8    -      -       -      +
    636I  TYR*     3.5    29.1    -      -       +      +
    638I  CYS*     5.0     2.5    -      -       +      -
    651I  VAL*     3.9    33.9    -      -       +      -
    653I  LEU*     3.6    33.4    -      -       +      -
    667I  VAL*     4.6     2.7    -      -       +      -
    669I  LEU*     4.7     3.4    -      -       +      -
    705I  MET      3.8     4.3    -      -       -      -
    707I  PHE*     3.5    28.7    -      +       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 621 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    619I  LYS*     3.6     6.3    +      -       -      -
    620I  PHE*     1.3    74.5    -      -       -      +
    622I  SER*     1.3    60.1    +      -       -      +
    623I  PHE*     5.1     1.3    -      -       -      -
    632I  ARG      4.0     0.2    -      -       -      +
    633I  ARG*     3.7    26.5    -      -       -      +
    634I  SER      4.3     4.3    +      -       -      +
    636I  TYR*     4.8     0.4    -      -       -      -
    704I  THR*     4.1    18.2    -      -       -      -
    705I  MET      2.9    17.4    +      -       -      +
    706I  HIS*     4.6     5.4    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 622 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    620I  PHE      3.8     1.0    -      -       -      -
    621I  GLY*     1.3    79.7    -      -       -      +
    623I  PHE*     1.3    64.7    +      -       -      +
    624I  THR*     5.5     2.4    -      -       -      +
    631I  VAL*     3.8    22.0    -      -       -      -
    632I  ARG      3.3     5.8    -      -       -      -
    633I  ARG*     4.2    15.3    -      -       -      -
    705I  MET      3.9     2.2    +      -       -      -
    706I  HIS*     3.2    29.8    +      -       -      +
    707I  PHE*     2.7    36.7    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 623 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    620I  PHE*     3.6    31.9    -      +       +      -
    622I  SER*     1.3    78.5    -      -       -      +
    624I  THR*     1.3    60.6    +      -       -      +
    631I  VAL*     4.5     0.4    -      -       -      -
    632I  ARG*     2.5    52.1    +      -       +      +
    636I  TYR*     3.7    33.4    -      +       -      -
    653I  LEU*     3.5    22.4    -      -       +      -
    665I  LEU*     3.9    11.4    -      -       +      -
    667I  VAL*     3.5    31.2    -      -       +      -
    707I  PHE*     3.3    24.2    -      +       +      -
    711I  TRP*     3.6    35.4    -      +       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 624 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    622I  SER*     5.5     3.1    -      -       -      +
    623I  PHE*     1.3    76.2    -      -       -      +
    625I  TYR*     1.3    73.1    +      -       -      +
    628I  THR*     3.9     0.2    +      -       -      -
    629I  GLU*     4.8     1.7    +      -       -      -
    630I  LYS      3.2    23.3    +      -       -      -
    631I  VAL*     4.1    16.2    -      -       +      +
    632I  ARG*     5.7     0.2    -      -       -      -
    707I  PHE      3.0     9.3    +      -       -      +
    708I  GLU*     2.7    41.9    -      -       +      +
    711I  TRP*     2.7    27.1    +      -       -      -
----------------------------------------------------------
 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