Contacts of the strand formed by residues 110 - 119 (chain J) in PDB entry 4CDC


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 TRP 110 (chain J).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    108G  ARG*     6.1     0.4    -      -       -      -
     21J  SER      3.7     0.2    -      -       -      +
     23J  GLY      3.7     3.6    +      -       -      -
     24J  SER*     2.8    32.4    +      -       -      +
     25J  GLN      3.7    14.8    -      -       -      +
     26J  ARG*     3.3    35.7    -      -       +      +
     28J  VAL*     3.9    19.5    -      -       +      -
    101J  TRP*     3.8    24.9    -      +       +      -
    102J  VAL      3.3     7.0    -      -       -      -
    103J  HIS*     3.4    35.4    -      +       +      +
    107J  GLY*     3.0    31.1    +      -       -      -
    108J  ARG      3.7     3.1    -      -       -      -
    109J  ASN*     1.3    79.8    -      -       -      +
    111J  ALA*     1.3    64.9    +      -       -      +
    270K  TYR*     3.5    23.6    -      -       -      -
    289K  ASP*     3.8    17.9    -      -       +      -
    290K  PHE*     3.7    22.0    -      +       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 111 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    439I  LEU*     5.0     3.4    -      -       +      -
     19J  VAL*     3.7    13.0    -      -       +      -
     20J  GLY      3.4    14.4    -      -       -      +
     21J  SER*     3.7    10.8    -      -       -      +
     22J  SER*     4.0     6.7    -      -       -      -
     23J  GLY      4.9     0.2    -      -       -      +
     24J  SER*     5.1     1.1    -      -       -      -
     28J  VAL*     5.1     2.7    -      -       -      -
     30J  CYS*     4.2     2.9    -      -       -      -
    101J  TRP*     3.6     4.3    -      -       -      +
    102J  VAL*     2.7    47.8    +      -       +      +
    110J  TRP*     1.3    79.7    -      -       -      +
    112J  CYS*     1.3    60.2    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with CYS 112 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19J  VAL*     3.5     3.8    -      -       -      +
     20J  GLY      2.9    30.8    +      -       -      +
     21J  SER*     4.4    10.1    -      -       -      +
     28J  VAL*     3.8    14.6    -      -       -      -
     29J  ASN      3.9     4.0    -      -       -      -
     30J  CYS*     2.1    51.6    -      -       -      -
     33J  MET*     4.0    16.6    -      -       +      -
     99J  THR*     3.8    12.3    -      -       +      -
    100J  GLY      3.2     7.0    -      -       -      +
    111J  ALA*     1.3    75.9    -      -       -      +
    113J  PHE*     1.3    64.1    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 113 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17J  PHE*     3.9    28.9    -      +       -      -
     18J  GLN      3.1    17.3    -      -       -      +
     19J  VAL*     4.1     2.5    -      -       +      -
     33J  MET*     3.7     4.9    -      -       -      -
     68J  PHE*     4.5     4.9    -      +       -      -
     77J  TRP*     3.8    36.6    -      +       +      -
     78J  PHE      3.3    34.1    -      -       -      -
     79J  ALA*     3.6    17.9    -      -       +      -
     97J  THR*     4.6     0.2    -      -       -      -
     98J  MET      4.0     0.2    -      -       -      +
     99J  THR*     3.4     2.8    -      -       -      -
    100J  GLY      2.6    47.4    +      -       -      -
    101J  TRP      3.4    23.3    -      -       -      -
    102J  VAL*     3.9     4.0    -      -       +      -
    112J  CYS*     1.3    78.1    -      -       -      +
    114J  THR*     1.3    74.9    +      -       -      +
    115J  GLY      4.6     1.6    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 114 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16J  VAL      4.0     0.3    -      -       -      +
     17J  PHE*     3.6     2.1    -      -       -      -
     18J  GLN*     2.9    39.6    +      -       -      +
     33J  MET*     3.2    27.3    -      -       +      +
     36J  GLN*     4.9     2.9    +      -       -      -
     97J  THR*     3.6    11.4    -      -       -      +
     98J  MET      4.3     2.0    -      -       -      +
     99J  THR*     3.7    25.8    -      -       -      +
    113J  PHE*     1.3    81.7    -      -       -      +
    115J  GLY*     1.3    59.5    +      -       -      +
    116J  LYS*     5.8     2.1    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 115 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15J  TRP*     4.0     5.6    -      -       -      -
     16J  VAL      3.3     9.2    -      -       -      -
     17J  PHE*     3.6    17.5    -      -       -      -
     96J  GLU*     3.3     4.7    -      -       -      +
     97J  THR*     2.8    38.0    +      -       -      +
    113J  PHE*     4.3     0.2    -      -       -      -
    114J  THR*     1.3    77.7    -      -       -      +
    116J  LYS*     1.3    66.2    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 116 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15J  TRP*     3.6     4.5    -      -       -      -
     16J  VAL*     2.9    40.1    +      -       +      +
     18J  GLN*     6.2     4.3    -      -       +      -
     95J  ASN      3.5     6.1    -      -       -      +
     96J  GLU*     4.2    22.0    -      -       +      +
    114J  THR*     5.8     2.7    -      -       -      +
    115J  GLY*     1.3    78.6    -      -       -      +
    117J  LYS*     1.3    64.7    +      -       -      +
    118J  VAL      3.7     0.5    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 117 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9J  LEU      3.7     4.6    +      -       -      -
     10J  ASP*     2.6    35.5    +      -       -      +
     12J  LEU      2.7    27.7    +      -       -      -
     13J  GLY*     4.5     0.2    -      -       -      -
     14J  THR      3.3    16.4    -      -       -      +
     15J  TRP*     3.6    23.0    -      -       +      +
     95J  ASN*     2.8    38.7    +      -       +      +
    116J  LYS*     1.3    76.7    -      -       -      +
    118J  VAL*     1.3    63.6    +      -       -      +
    119J  GLY*     3.7    25.8    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 118 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14J  THR*     2.9    33.9    +      -       +      +
     16J  VAL*     3.5    30.7    -      -       +      -
    116J  LYS      3.7     0.2    +      -       -      -
    117J  LYS*     1.3    73.7    -      -       -      +
    119J  GLY*     1.3    59.7    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 119 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12J  LEU      5.0     0.4    -      -       -      -
     13J  GLY*     3.6     8.4    -      -       -      -
     14J  THR*     3.1    28.6    +      -       -      -
    117J  LYS*     3.6    22.0    -      -       -      +
    118J  VAL*     1.3    82.9    -      -       -      +
----------------------------------------------------------
 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