Contacts of the strand formed by residues 41 - 48 (chain A) in PDB entry 7RSA


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 LYS 41 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  GLN*     4.2    26.0    +      -       -      +
     12A  HIS*     4.2     5.3    -      -       -      -
     30A  MET*     3.9    18.2    -      -       +      +
     35A  LEU*     3.7    26.3    +      -       +      +
     39A  ARG*     3.2    22.3    +      -       +      +
     40A  CYS*     1.3    71.4    -      -       -      +
     42A  PRO*     1.3    65.9    -      -       +      +
     43A  VAL      3.4    21.7    +      -       -      +
     44A  ASN*     2.7    29.4    +      -       +      +
     97A  TYR*     2.6    34.8    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PRO 42 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39A  ARG*     3.8    16.2    -      -       -      +
     40A  CYS      3.5     7.4    -      -       -      +
     41A  LYS*     1.3    89.0    -      -       +      +
     43A  VAL*     1.3    71.5    +      -       +      +
     85A  ARG*     3.7     2.9    -      -       -      +
     86A  GLU*     2.9    48.3    +      -       +      +
     97A  TYR*     4.4     1.1    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 43 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30A  MET*     4.9     0.9    -      -       -      -
     41A  LYS*     3.4    23.6    +      -       -      +
     42A  PRO*     1.3    93.7    -      -       +      +
     44A  ASN*     1.3    74.5    -      -       -      +
     45A  THR*     5.4     1.8    -      -       -      +
     83A  ASP*     4.8     3.4    -      -       -      +
     84A  CYS      3.3    12.6    -      -       -      +
     85A  ARG*     3.6    36.1    -      -       -      +
     97A  TYR*     5.3     0.2    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASN 44 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  GLN*     2.8    25.4    +      -       -      +
     12A  HIS*     3.1    18.1    -      -       -      -
     30A  MET*     3.6    24.9    -      -       +      -
     35A  LEU*     3.6    10.2    -      -       -      +
     41A  LYS*     2.7    25.2    +      -       -      +
     43A  VAL*     1.3    80.9    -      -       -      +
     45A  THR*     1.3    65.4    +      -       -      +
     46A  PHE*     3.4    26.2    -      -       -      -
     83A  ASP*     3.7     0.9    -      -       -      -
     84A  CYS*     2.8    37.5    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 45 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12A  HIS*     2.8    35.9    +      -       -      +
     43A  VAL*     5.4     2.8    -      -       -      +
     44A  ASN*     1.3    80.1    +      -       -      +
     46A  PHE*     1.3    73.7    +      -       -      +
     47A  VAL*     4.9     0.7    -      -       -      +
     81A  ILE*     4.0    16.4    -      -       +      -
     82A  THR      3.3    11.2    -      -       -      +
     83A  ASP*     3.2    22.5    +      -       -      +
    120A  PHE*     3.6    45.7    -      -       +      -
    123A  SER*     5.6     0.2    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 46 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10A  ARG      4.5     0.2    -      -       -      -
     11A  GLN      3.3    22.7    -      -       -      -
     12A  HIS      3.3    10.5    -      -       -      -
     13A  MET      4.5     5.4    -      -       -      -
     14A  ASP*     4.6     2.9    -      -       +      -
     25A  TYR*     3.7    30.5    -      +       +      +
     29A  MET*     3.8    42.8    -      -       +      -
     30A  MET*     4.0     5.8    -      -       -      -
     33A  ARG*     4.3    11.2    -      -       +      -
     35A  LEU*     4.2    11.2    -      -       +      -
     44A  ASN*     3.4    19.7    -      -       -      -
     45A  THR*     1.3    73.9    -      -       -      +
     47A  VAL*     1.3    62.6    +      -       -      +
     48A  HIS*     4.1     3.2    +      -       -      +
     81A  ILE*     3.2     7.8    -      -       -      +
     82A  THR*     2.9    35.6    +      -       -      +
     84A  CYS*     3.8    27.8    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 47 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8A  PHE*     5.6     1.1    -      -       +      -
     12A  HIS*     2.7    21.7    +      -       +      +
     13A  MET*     3.8    12.1    -      -       -      +
     14A  ASP      2.9    26.5    +      -       -      +
     45A  THR*     4.7     0.4    -      -       +      -
     46A  PHE*     1.3    78.5    -      -       -      +
     48A  HIS*     1.3    64.1    +      -       -      +
     49A  GLU*     3.4    20.7    +      -       +      -
     54A  VAL*     3.7    27.6    -      -       +      -
     79A  MET*     4.2     9.4    -      -       +      -
     80A  SER      3.7     5.8    -      -       -      +
     81A  ILE*     4.2    10.1    -      -       +      -
    106A  ILE*     4.7     6.5    -      -       +      -
    120A  PHE*     3.8    31.9    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with HIS 48 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14A  ASP*     3.3    15.4    +      -       +      +
     15A  SER*     4.9     1.3    -      -       -      -
     17A  THR*     3.0    41.3    +      -       -      +
     18A  SER*     3.5    17.5    -      -       -      +
     19A  ALA*     3.9    12.3    -      -       +      -
     20A  ALA      3.9     1.4    +      -       -      -
     25A  TYR*     3.2    30.7    -      +       -      -
     46A  PHE*     4.1     4.1    +      -       +      +
     47A  VAL*     1.3    69.1    -      -       -      +
     49A  GLU*     1.3    71.9    +      -       -      +
     80A  SER*     2.8    33.0    +      -       -      +
     81A  ILE      3.9     8.5    -      -       -      -
     82A  THR*     2.6    31.6    +      -       -      -
----------------------------------------------------------
 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