Contacts of the strand formed by residues 105 - 113 (chain A) in PDB entry 1RUV


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 HIS 105 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74A  GLN*     4.0    16.1    +      -       +      -
     75A  SER*     3.0    30.3    +      -       -      +
     76A  TYR      3.4    19.1    -      -       -      -
     77A  SER      3.4    15.7    +      -       -      -
     78A  THR*     3.6    16.1    -      -       +      +
    104A  LYS*     1.3    77.6    -      -       -      +
    106A  ILE*     1.3    62.3    -      -       -      +
    123A  SER*     3.2     4.9    -      -       -      -
    124A  VAL*     2.8    58.8    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 106 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47A  VAL*     4.6     6.1    -      -       +      -
     54A  VAL*     4.2    17.7    -      -       +      -
     57A  VAL*     4.4     8.1    -      -       +      -
     73A  TYR      3.7     1.0    -      -       -      +
     74A  GLN*     3.3     3.3    -      -       -      +
     75A  SER*     2.9    43.3    +      -       -      +
     79A  MET*     3.6    26.0    -      -       +      -
     81A  ILE*     3.9    24.9    -      -       +      -
    104A  LYS      4.1     5.2    -      -       -      +
    105A  HIS*     1.3    80.1    -      -       -      +
    107A  ILE*     1.4    63.3    +      -       -      +
    108A  VAL*     4.0    20.9    -      -       +      -
    120A  PHE*     3.9    27.8    -      -       +      -
    122A  ALA      3.6     3.1    -      -       -      -
    123A  SER*     4.9     1.6    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 107 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63A  VAL*     3.8    14.6    -      -       +      -
     64A  ALA      5.2     1.6    -      -       -      +
     72A  CYS*     3.8    24.0    -      -       +      -
     73A  TYR      3.3     7.6    -      -       -      +
     74A  GLN*     4.0    21.8    -      -       +      +
    106A  ILE*     1.4    75.6    -      -       -      +
    108A  VAL*     1.3    63.0    -      -       -      +
    120A  PHE*     3.8     2.1    -      -       -      -
    121A  ASP*     2.8    42.9    +      -       +      +
    122A  ALA*     2.7    28.7    +      -       +      +
    124A  VAL*     3.8    33.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 108 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8A  PHE*     3.9    24.2    -      -       +      -
     54A  VAL*     5.0     1.3    -      -       +      +
     57A  VAL*     4.0    24.0    -      -       +      -
     71A  ASN      3.9     0.3    -      -       -      +
     72A  CYS*     3.1     7.1    -      -       -      -
     73A  TYR*     2.8    32.0    +      -       +      +
    106A  ILE*     4.0    21.1    -      -       +      -
    107A  ILE*     1.3    80.0    -      -       -      +
    109A  ALA*     1.3    62.0    -      -       -      +
    110A  CYS*     3.9    20.9    -      -       -      -
    117A  PRO*     4.0    15.0    -      -       +      -
    119A  HIS      3.2    12.8    -      -       -      +
    120A  PHE*     4.2     6.7    -      -       +      -
    121A  ASP      4.2     0.7    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 109 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65A  CYS*     4.2     3.6    -      -       -      -
     69A  GLN*     4.9     4.7    -      -       -      +
     71A  ASN*     3.3    21.1    -      -       -      +
     72A  CYS*     3.7    16.8    -      -       -      -
    108A  VAL*     1.3    75.1    -      -       -      +
    110A  CYS*     1.3    55.9    +      -       -      +
    117A  PRO*     3.3     3.5    -      -       -      +
    118A  VAL*     2.8    36.9    +      -       +      +
    119A  HIS*     2.9    31.5    +      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with CYS 110 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     58A  CYS*     2.0    54.1    -      -       -      -
     71A  ASN*     2.9    24.7    +      -       -      +
     73A  TYR*     3.7    12.1    -      -       +      -
    108A  VAL*     3.9    11.9    -      -       -      -
    109A  ALA*     1.3    78.8    -      -       -      +
    111A  GLU*     1.3    66.7    -      -       -      +
    115A  TYR*     3.4    34.9    +      -       +      +
    116A  VAL      3.1     4.7    -      -       -      +
    117A  PRO*     4.1     0.2    -      -       -      -
    118A  VAL*     4.4     0.2    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 111 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4A  ALA*     5.1     4.9    -      -       -      +
     69A  GLN*     5.5     2.6    +      -       -      -
     71A  ASN*     3.9    12.6    +      -       -      +
    110A  CYS*     1.3    81.9    -      -       -      +
    112A  GLY*     1.3    63.3    +      -       -      +
    114A  PRO      3.6     1.9    -      -       -      +
    115A  TYR*     3.6     9.9    -      -       -      -
    116A  VAL*     3.0    30.8    +      -       -      +
    118A  VAL*     3.8    31.2    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 112 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    111A  GLU*     1.3    75.6    -      -       -      +
    113A  ASN*     1.3    62.7    +      -       -      +
    114A  PRO      3.2     8.3    -      -       -      -
    115A  TYR*     3.2    25.2    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ASN 113 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112A  GLY*     1.3    76.8    -      -       -      +
    114A  PRO*     1.4    69.0    +      -       -      +
    115A  TYR      3.7     0.8    -      -       -      +
----------------------------------------------------------
 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