Contacts of the strand formed by residues 100 - 115 (chain B) in PDB entry 2ARV


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 ILE 100 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30B  ILE*     3.6    27.8    -      -       +      -
     92B  LEU*     4.1    22.4    -      -       +      -
     93B  TYR      3.4     5.4    -      -       -      +
     94B  TYR*     3.5    30.1    -      -       +      +
     99B  ASN*     1.3    72.1    -      -       -      +
    101B  ILE*     1.3    66.3    +      -       -      +
    102B  LYS      4.2     0.5    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 101 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91B  MET      3.5     1.7    -      -       -      +
     92B  LEU*     3.1     7.2    -      -       -      +
     93B  TYR*     2.7    69.8    +      -       +      +
     95B  ASP*     3.8    28.0    -      -       +      +
     99B  ASN*     3.6    18.4    -      -       +      +
    100B  ILE*     1.3    81.9    -      -       -      +
    102B  LYS*     1.3    72.3    +      -       -      +
    103B  LYS*     4.1     4.3    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 102 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90B  SER*     3.3    23.7    +      -       -      +
     91B  MET      3.4     5.2    -      -       -      +
     92B  LEU*     3.3    27.1    -      -       +      +
    100B  ILE      4.2     1.2    +      -       -      -
    101B  ILE*     1.3    74.9    -      -       -      +
    103B  LYS*     1.3    67.5    +      -       -      +
    104B  ASP*     5.0     4.4    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 103 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90B  SER*     4.6     2.0    -      -       -      -
     91B  MET*     3.0    30.5    +      -       -      +
     93B  TYR*     3.3    31.4    +      -       +      +
    101B  ILE*     4.1     4.7    -      -       +      -
    102B  LYS*     1.3    80.7    -      -       -      +
    104B  ASP*     1.3    80.9    +      -       -      +
    105B  ILE*     3.4    19.9    +      -       +      +
    106B  GLN*     6.5     0.2    -      -       -      -
    117B  1PG      4.9     9.3    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 104 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88B  PRO*     4.2    17.2    -      -       +      +
     89B  MET*     3.7     4.6    +      -       -      +
     90B  SER*     4.0    23.7    +      -       -      +
    102B  LYS*     5.0     4.2    +      -       -      -
    103B  LYS*     1.3    93.3    -      -       -      +
    105B  ILE*     1.3    60.2    +      -       -      +
    106B  GLN*     3.9    20.1    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 105 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     58A  PHE*     4.0    17.3    -      -       +      -
     88B  PRO*     3.0     4.6    -      -       -      +
     89B  MET      2.9    29.3    +      -       -      -
     91B  MET*     3.8    31.9    -      -       +      -
     93B  TYR*     4.0    12.1    -      -       +      +
    103B  LYS*     3.9    33.9    -      -       +      +
    104B  ASP*     1.3    74.4    -      -       -      +
    106B  GLN*     1.3    70.8    +      -       -      +
    108B  MET*     3.7    24.3    -      -       +      +
    117B  1PG      3.8    23.3    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 106 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57A  SER*     5.2     0.3    -      -       -      -
     58A  PHE*     4.5     4.0    +      -       -      +
     88B  PRO*     3.5    29.5    -      -       -      +
    103B  LYS*     6.5     0.2    -      -       -      -
    104B  ASP*     3.9    18.8    +      -       -      +
    105B  ILE*     1.3    82.4    -      -       -      +
    107B  ASN*     1.3    86.8    +      -       -      +
    108B  MET      3.2     3.7    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASN 107 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57A  SER*     3.8    21.0    -      -       -      -
     58A  PHE      3.9     0.2    +      -       -      -
     59A  HIS*     2.9    29.3    +      -       -      +
    123A  GOL      4.6     3.4    -      -       -      +
     86B  LEU*     3.6    36.4    -      -       +      +
     87B  ARG      3.7    11.2    +      -       -      -
    106B  GLN*     1.3    88.3    +      -       -      +
    108B  MET*     1.3    58.9    -      -       -      +
    109B  ILE      3.8     0.7    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with MET 108 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     58A  PHE*     3.6    25.1    -      -       +      -
     59A  HIS*     3.3    16.6    -      -       -      +
     20B  PHE*     4.7     0.9    -      -       +      -
     35B  TYR*     2.6    66.1    +      -       +      -
     87B  ARG      3.2     7.2    +      -       -      +
     89B  MET*     3.8    30.3    -      -       +      +
     91B  MET*     3.6    32.8    -      -       +      -
    105B  ILE*     3.7    30.5    -      -       +      +
    106B  GLN      3.2     0.2    -      -       -      -
    107B  ASN*     1.3    77.3    -      -       -      +
    109B  ILE*     1.3    65.1    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 109 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35B  TYR*     3.6    17.3    -      -       +      -
     36B  HIS*     3.6    15.5    -      -       +      +
     37B  ALA      3.9     2.5    -      -       -      -
     38B  ASN*     4.0     4.9    -      -       -      +
     86B  LEU*     3.1     9.3    -      -       -      -
     87B  ARG*     2.8    73.2    +      -       +      +
     88B  PRO      4.0     7.6    -      -       -      +
     89B  MET*     4.1    19.5    -      -       +      -
    108B  MET*     1.3    84.8    -      -       +      +
    110B  VAL*     1.3    74.7    +      -       -      +
    111B  GLU*     3.4    13.1    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 110 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59A  HIS*     3.2    37.1    -      -       +      +
     13B  LYS*     3.3    11.0    -      -       +      +
     37B  ALA      2.9    16.4    +      -       -      +
     38B  ASN*     3.0    31.7    +      -       -      +
     39B  TYR*     4.5     6.7    -      -       -      -
     40B  CYS*     3.8     6.3    -      -       -      -
     83B  PRO*     3.8    28.9    -      -       +      -
     85B  LYS      4.1     2.9    -      -       -      -
     86B  LEU*     4.0     5.2    -      -       +      -
    109B  ILE*     1.3    70.5    -      -       -      +
    111B  GLU*     1.3    60.1    +      -       -      +
    112B  GLU      4.1     4.5    -      -       -      +
    113B  CYS*     3.8    28.5    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 111 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3B  GLU*     5.5     0.7    -      -       -      +
     13B  LYS*     3.5    27.7    +      -       -      +
     38B  ASN*     5.5     0.2    +      -       -      -
     85B  LYS*     3.0    42.5    +      -       +      +
     87B  ARG*     4.7    17.5    -      -       +      +
    109B  ILE*     3.4    17.3    +      -       +      +
    110B  VAL*     1.3    73.1    -      -       -      +
    112B  GLU*     1.3    81.2    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 112 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1B  GLY*     2.6    41.7    +      -       -      +
      2B  LEU      5.7     1.1    -      -       -      +
      3B  GLU*     5.3     4.2    -      -       -      +
     13B  LYS*     4.6     4.5    -      -       +      -
     83B  PRO*     3.4     5.4    -      -       -      +
     84B  THR*     2.7    39.9    +      -       -      +
     85B  LYS*     3.4    18.3    +      -       +      +
    110B  VAL*     3.7     0.9    -      -       -      +
    111B  GLU*     1.3    96.1    -      -       +      +
    113B  CYS*     1.3    62.3    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with CYS 113 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1B  GLY*     4.0    20.5    -      -       -      -
      2B  LEU      4.9     2.6    +      -       -      +
     11B  CYS*     4.0    11.9    -      -       -      +
     12B  CYS*     4.0    16.2    -      -       -      -
     13B  LYS*     3.6    21.4    -      -       -      +
     39B  TYR      3.8     0.7    -      -       -      -
     40B  CYS*     2.0    55.4    -      -       +      -
     82B  VAL      3.4     3.6    -      -       -      -
     84B  THR*     3.6     4.9    +      -       -      -
    110B  VAL*     3.8     8.7    -      -       -      -
    112B  GLU*     1.3    81.0    -      -       -      +
    114B  GLY*     1.3    56.9    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 114 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11B  CYS*     3.6     9.6    -      -       -      -
     81B  CYS*     3.4     2.4    -      -       -      -
     82B  VAL*     2.9    34.2    +      -       -      +
     84B  THR*     3.3    16.6    -      -       -      +
    113B  CYS*     1.3    76.4    -      -       -      +
    115B  CYS*     1.3    62.5    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with CYS 115 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11B  CYS*     3.7    15.7    -      -       -      -
     43B  GLU      4.1     0.9    -      -       -      -
     44B  CYS*     2.0    50.0    -      -       +      -
     45B  PRO*     5.5     0.4    -      -       -      -
     57B  SER*     5.6     0.7    -      -       -      -
     60B  SER*     4.0    13.5    +      -       -      -
     79B  SER*     3.5     8.1    -      -       -      +
     80B  CYS      3.4     2.9    -      -       -      -
     82B  VAL*     5.0     0.9    -      -       -      -
     84B  THR*     5.4     2.5    -      -       -      +
    114B  GLY*     1.3    74.8    -      -       -      -
    116B  SER*     1.3    62.8    +      -       -      +
----------------------------------------------------------
 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