Contacts of the strand formed by residues 100 - 115 (chain A) in PDB entry 3B4V


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 A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30A  ILE*     4.0    18.6    -      -       +      -
     92A  LEU*     3.8    33.2    -      -       +      -
     93A  TYR      3.7     3.6    -      -       -      -
     94A  TYR*     4.2     2.7    -      -       +      -
     99A  ASN*     1.3    69.5    -      -       -      +
    101A  ILE*     1.3    66.8    +      -       -      +
    157D  VAL*     3.9    24.0    -      -       +      -
    158D  VAL      3.7    26.7    -      -       -      +
    159D  ASP*     3.7     3.2    -      -       -      -
    160D  GLN*     3.3    22.5    +      -       -      +
    202D  THR*     4.0    19.1    -      -       +      +
    203D  CYS*     5.4     0.7    -      -       -      -
    207D  ARG*     3.9    11.2    -      -       -      +
    208D  SER*     2.8    30.6    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 101 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92A  LEU*     3.4     4.8    -      -       -      -
     93A  TYR*     2.8    72.9    +      -       +      +
     95A  ASP*     3.6    34.8    -      -       +      +
     99A  ASN*     3.7    13.5    -      -       +      +
    100A  ILE*     1.3    83.4    -      -       -      +
    102A  LYS*     1.3    66.5    +      -       -      +
    103A  LYS*     4.7     4.7    -      -       +      -
     63C  LEU*     6.3     0.2    -      -       +      -
    160D  GLN*     3.3    27.1    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 102 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90A  SER*     3.8    25.1    -      -       -      +
     91A  MET      3.4     7.2    -      -       -      +
     92A  LEU*     3.5    16.1    -      -       +      +
    101A  ILE*     1.3    71.0    -      -       -      +
    103A  LYS*     1.3    64.8    +      -       -      +
    112D  ASP      5.1     7.8    +      -       -      -
    113D  GLY*     5.0    11.9    +      -       -      -
    159D  ASP*     3.3    25.4    -      -       +      +
    160D  GLN*     2.7    34.5    +      -       -      +
    161D  THR*     5.4     6.4    -      -       +      +
    163D  SER*     3.9    16.8    +      -       -      -
    165D  HIS*     4.3    14.1    -      -       +      +
    189G  ASN*     4.3    20.3    +      -       -      +
    190G  VAL*     5.9     1.0    -      -       -      +
    218G  ALA*     4.3     5.7    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 103 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90A  SER*     4.2     1.6    -      -       -      -
     91A  MET*     2.8    31.2    +      -       -      +
     93A  TYR*     3.3    31.1    +      -       +      +
    101A  ILE*     4.1     5.1    -      -       +      -
    102A  LYS*     1.3    78.0    -      -       -      +
    104A  ASP*     1.3    73.4    +      -       +      +
    105A  ILE*     3.5    21.9    +      -       -      +
     60C  PHE      5.0     1.6    +      -       -      -
     61C  LEU      3.6    15.8    +      -       -      -
     62C  GLY*     4.2     8.5    +      -       -      +
    160D  GLN*     5.5     0.2    -      -       -      +
    217G  CYS      5.4     3.1    -      -       -      +
    218G  ALA*     5.3    18.4    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 104 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88A  PRO*     4.4    14.3    -      -       +      +
     89A  MET*     3.3     6.2    -      -       -      +
     90A  SER*     3.4    27.1    -      -       -      -
    103A  LYS*     1.3    85.6    -      -       +      +
    105A  ILE*     1.3    64.8    +      -       -      +
    106A  GLN*     4.1    19.5    +      -       -      +
    191G  THR*     3.7    35.3    +      -       -      +
    193G  ILE*     5.7     0.9    -      -       -      +
    216G  SER*     4.3     8.8    +      -       -      +
    217G  CYS      5.8     1.2    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 105 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88A  PRO*     3.2     2.8    -      -       -      +
     89A  MET      2.7    32.2    +      -       -      -
     91A  MET*     4.0    14.6    -      -       +      -
     93A  TYR*     4.1     6.3    -      -       +      -
    103A  LYS*     3.8    29.6    -      -       -      +
    104A  ASP*     1.3    80.5    -      -       -      +
    106A  GLN*     1.3    69.5    +      -       -      +
    108A  MET*     3.3    15.9    -      -       -      +
     58B  PHE*     3.9    26.5    -      -       +      -
     60C  PHE*     3.9    24.7    -      -       +      +
     61C  LEU*     3.8    28.7    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 106 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87A  ARG      5.1     0.2    -      -       -      -
     88A  PRO*     3.3    38.4    -      -       -      +
    104A  ASP*     4.2    17.6    +      -       -      +
    105A  ILE*     1.3    82.7    -      -       -      +
    107A  ASN*     1.3    86.0    +      -       -      +
    108A  MET*     3.2     9.2    +      -       -      +
     58B  PHE*     3.9     5.0    -      -       -      +
    183G  GLU*     5.3     8.6    +      -       -      +
    216G  SER*     5.0     6.3    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASN 107 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86A  LEU*     3.8    35.5    -      -       +      +
     87A  ARG      3.5     7.3    +      -       -      +
    106A  GLN*     1.3    84.5    +      -       -      +
    108A  MET*     1.3    58.9    +      -       -      +
    109A  ILE      3.8     0.9    -      -       -      -
     57B  SER*     4.0    19.5    -      -       -      +
     58B  PHE*     3.3     5.0    -      -       +      +
     59B  HIS*     2.9    30.4    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with MET 108 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35A  TYR*     2.7    61.9    +      -       +      -
     87A  ARG      2.8     9.3    +      -       -      +
     89A  MET*     3.8    22.0    -      -       +      +
     91A  MET*     3.7    31.0    -      -       -      +
    105A  ILE*     3.3    38.4    -      -       -      +
    106A  GLN      3.5     7.2    -      -       -      +
    107A  ASN*     1.3    77.5    -      -       -      +
    109A  ILE*     1.3    66.6    +      -       +      +
     58B  PHE*     3.8    21.8    -      -       +      -
     59B  HIS*     3.2    17.0    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 109 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35A  TYR*     3.7    16.8    -      -       +      -
     36A  HIS      3.4    18.4    -      -       -      +
     37A  ALA      3.8     2.5    -      -       -      -
     38A  ASN*     3.6     8.1    -      -       -      +
     86A  LEU*     3.2     9.9    -      -       -      -
     87A  ARG*     2.9    63.5    +      -       +      +
     88A  PRO      3.9    21.3    -      -       -      +
     89A  MET*     4.2    20.6    -      -       +      -
    108A  MET*     1.3    86.6    -      -       +      +
    110A  VAL*     1.3    78.5    +      -       -      +
    111A  GLU      3.4     0.3    +      -       -      -
    132D  ASP*     5.5     3.4    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 110 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13A  LYS*     3.7    14.8    +      -       +      +
     37A  ALA      3.0    13.6    +      -       -      +
     38A  ASN*     3.2    31.0    +      -       +      +
     39A  TYR*     4.3     3.4    -      -       -      -
     40A  CYS*     3.8     2.9    -      -       -      -
     83A  PRO*     3.7    17.5    -      -       +      -
     85A  LYS      3.9     3.1    -      -       -      -
     86A  LEU*     4.0     3.4    -      -       +      -
     87A  ARG*     5.2     0.3    +      -       -      -
    109A  ILE*     1.3    75.1    -      -       -      +
    111A  GLU*     1.3    61.7    +      -       -      +
    112A  GLU      3.9    10.5    -      -       -      +
    113A  CYS*     3.6    29.8    -      -       -      -
     59B  HIS*     3.0    37.7    -      -       +      +
----------------------------------------------------------
 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
----------------------------------------------------------
     13A  LYS*     3.1    34.8    +      -       -      +
     85A  LYS*     2.8    31.6    +      -       +      +
     87A  ARG*     2.6    44.6    +      -       +      +
    109A  ILE      3.4     3.5    +      -       -      +
    110A  VAL*     1.3    74.5    -      -       -      +
    112A  GLU*     1.3    68.6    +      -       +      +
    176G  VAL*     3.8    35.9    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 112 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1A  GLY*     4.2    25.1    +      -       -      +
     13A  LYS*     4.8     1.8    -      -       -      -
     83A  PRO*     3.5     6.1    -      -       -      +
     84A  THR*     2.9    36.5    +      -       -      +
     85A  LYS*     3.3    37.8    +      -       +      +
    110A  VAL*     3.9     2.4    -      -       -      +
    111A  GLU*     1.3    94.7    -      -       +      +
    113A  CYS*     1.3    67.6    +      -       -      +
     16D  GLN*     4.7     8.5    +      -       -      -
    176G  VAL*     4.9     2.9    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with CYS 113 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1A  GLY*     4.4    19.6    +      -       -      -
      2A  LEU*     5.1     7.8    +      -       -      +
     11A  CYS*     4.2     8.4    -      -       -      +
     12A  CYS*     4.0    15.7    -      -       -      -
     13A  LYS*     3.5    26.0    -      -       -      +
     40A  CYS*     2.0    56.5    -      -       +      -
     82A  VAL      3.6     4.0    -      -       -      -
     84A  THR*     3.9     6.4    +      -       -      -
    110A  VAL*     3.6     8.7    -      -       -      -
    112A  GLU*     1.3    74.5    -      -       -      +
    114A  GLY*     1.3    58.2    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 114 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  CYS*     3.6    12.2    -      -       -      -
     55A  SER      5.8     2.9    -      -       -      -
     80A  CYS      3.6     0.7    -      -       -      +
     82A  VAL*     3.0    34.4    +      -       -      +
     84A  THR*     3.6    15.2    -      -       -      +
    113A  CYS*     1.3    75.2    -      -       -      +
    115A  CYS*     1.3    64.5    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with CYS 115 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  CYS*     3.6    15.5    -      -       -      -
     43A  GLU      3.8     1.8    -      -       -      -
     44A  CYS*     2.0    50.5    -      -       -      -
     45A  PRO*     3.8     3.8    -      -       +      -
     55A  SER      5.4     4.1    +      -       -      -
     56A  LEU*     3.6    23.0    -      -       +      +
     57A  SER*     5.0     2.1    +      -       -      -
     60A  SER*     2.5    26.7    +      -       -      -
     79A  SER*     3.6     9.9    -      -       -      +
     80A  CYS      3.5     4.7    -      -       -      -
     82A  VAL*     5.1     0.2    -      -       -      -
     84A  THR*     5.5     2.8    -      -       -      +
    114A  GLY*     1.3    73.6    -      -       -      -
    116A  SER*     1.3    55.0    +      -       -      +
----------------------------------------------------------
 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