Contacts of the strand formed by residues 141 - 152 (chain A) in PDB entry 3NJ0


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 VAL 141 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44A  HIS*     4.6     4.3    +      -       -      +
     45A  ALA*     4.5     7.1    +      -       -      -
     46A  PRO*     3.9    38.4    -      -       +      -
    132A  GLU*     4.2    18.2    -      -       -      +
    133A  PHE      3.3    13.5    -      -       -      +
    134A  LEU*     4.2    13.2    -      -       +      -
    139A  GLY      4.7     3.4    -      -       -      +
    140A  LYS*     1.3    81.2    -      -       -      +
    142A  TYR*     1.3    64.3    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 142 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14A  GLU*     2.6    38.0    +      -       -      +
     42A  ARG*     3.4    29.6    -      -       +      -
     43A  ILE      3.5    12.3    -      -       -      +
     44A  HIS*     3.7    21.8    -      +       -      +
     45A  ALA      3.7     5.8    -      -       -      +
    132A  GLU*     3.4     6.4    -      -       -      +
    133A  PHE*     2.8    60.4    +      +       +      +
    134A  LEU      4.3     2.6    +      -       -      -
    135A  ASN*     4.3    37.2    -      -       +      -
    141A  VAL*     1.3    77.6    -      -       -      +
    143A  THR*     1.3    65.4    +      -       -      +
    144A  VAL*     3.9     8.7    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 143 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42A  ARG*     3.4     5.0    -      -       -      +
     43A  ILE*     2.7    40.3    +      -       +      -
     45A  ALA      2.8    20.7    +      -       -      -
     46A  PRO      3.5     0.5    +      -       -      -
     47A  ALA*     3.2    22.2    +      -       -      +
     50A  VAL*     4.1     9.4    -      -       +      -
    130A  VAL*     3.5    30.5    -      -       +      -
    131A  ASN      3.3     8.9    +      -       -      +
    142A  TYR*     1.3    75.4    +      -       -      +
    144A  VAL*     1.3    74.1    +      -       -      +
    145A  VAL*     3.9    10.8    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 144 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10A  LEU*     3.6    26.9    -      -       +      -
     14A  GLU*     4.2    13.7    -      -       -      +
     18A  LEU*     3.9    13.0    -      -       +      -
     41A  GLN      3.3    10.3    -      -       -      +
     42A  ARG*     4.3     7.9    -      -       +      -
    131A  ASN*     2.7    40.3    +      -       -      -
    133A  PHE*     3.7    29.2    -      -       +      -
    142A  TYR*     3.9    13.7    -      -       +      -
    143A  THR*     1.3    80.2    -      -       -      +
    145A  VAL*     1.3    68.0    +      -       -      +
    146A  LEU*     4.1     6.1    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 145 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39A  ILE      3.9     0.3    -      -       -      +
     40A  THR*     3.4     4.7    -      -       -      -
     41A  GLN*     2.8    41.0    +      -       +      +
     43A  ILE*     3.7    26.9    -      -       +      -
     50A  VAL*     3.8    20.2    -      -       +      -
     54A  ILE*     4.5     1.3    -      -       +      -
    128A  THR*     3.7    22.9    -      -       +      -
    129A  SER      3.3     9.6    -      -       -      +
    130A  VAL*     4.3     4.3    -      -       +      -
    143A  THR*     3.9     7.2    -      -       +      -
    144A  VAL*     1.3    75.9    -      -       -      +
    146A  LEU*     1.3    65.4    +      -       -      +
    174A  LEU*     3.9    21.5    -      -       +      +
    177A  LEU*     4.0     7.2    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 146 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10A  LEU*     4.7     2.5    -      -       +      -
     18A  LEU*     4.3    20.0    -      -       +      -
     21A  VAL*     4.4     4.5    -      -       +      -
     22A  ILE*     3.6    31.0    -      -       +      -
     26A  HIS*     3.4    14.4    -      -       +      +
     38A  LEU*     4.1    11.7    -      -       +      -
     39A  ILE      3.5     2.0    -      -       -      +
     40A  THR*     3.4    31.6    -      -       +      -
    128A  THR*     3.2     5.5    -      -       -      +
    129A  SER*     2.8    48.4    +      -       -      +
    131A  ASN*     4.0    13.0    -      -       -      +
    144A  VAL*     4.1    11.4    -      -       +      -
    145A  VAL*     1.3    77.2    -      -       -      +
    147A  GLU*     1.3    60.6    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 147 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37A  SER      4.1     0.2    -      -       -      +
     38A  LEU*     3.7     2.3    -      -       -      -
     39A  ILE*     2.8    41.4    +      -       -      +
     63A  TYR*     5.1     9.1    +      -       -      -
     64A  LYS*     5.5     3.4    +      -       -      -
    112A  PHE*     4.7     5.2    -      -       -      -
    124A  TYR*     3.7    11.3    +      -       -      +
    126A  SER*     2.7    31.4    +      -       -      +
    127A  VAL      3.3     2.7    -      -       -      +
    128A  THR*     3.6    14.5    +      -       -      +
    145A  VAL      4.2     0.2    -      -       -      -
    146A  LEU*     1.3    75.4    -      -       -      +
    148A  SER*     1.3    65.6    +      -       -      +
    149A  TYR*     5.0     1.5    -      -       +      -
    170A  VAL*     3.7    31.6    -      -       +      +
    173A  ASN*     5.7     1.9    -      -       -      +
    174A  LEU*     3.7    24.7    -      -       +      +
    300A  PYV      4.7     4.2    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 148 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26A  HIS*     2.9    50.7    +      -       -      +
     28A  PHE*     3.6     9.3    -      -       -      -
     37A  SER      3.1    13.5    -      -       -      -
     38A  LEU*     3.9     8.7    -      -       -      -
    126A  SER*     3.3     5.9    +      -       -      -
    127A  VAL*     2.9    33.4    +      -       -      +
    147A  GLU*     1.3    76.8    -      -       -      +
    149A  TYR*     1.3    62.9    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 149 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28A  PHE*     3.6     8.4    -      -       -      -
     35A  CYS*     3.9    11.4    -      -       -      -
     36A  THR*     3.1    25.8    -      -       -      -
     37A  SER*     3.0    32.4    +      -       -      +
     39A  ILE*     4.6     6.3    -      -       +      -
    124A  TYR*     3.6    24.9    -      +       +      +
    125A  LYS      3.2    14.1    -      -       -      +
    126A  SER*     4.6     0.2    -      -       -      -
    147A  GLU*     5.0     1.6    -      -       +      -
    148A  SER*     1.3    77.8    -      -       -      +
    150A  THR*     1.3    72.3    +      -       -      +
    151A  VAL*     3.9    14.6    -      -       +      -
    163A  LYS*     3.4    14.2    +      -       -      +
    166A  VAL*     3.3    40.7    -      -       +      +
    167A  ASP*     2.6    32.5    +      -       -      -
    170A  VAL*     4.3    13.0    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 150 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28A  PHE*     3.6    19.5    -      -       +      +
     29A  GLU      5.4     0.5    +      -       -      -
     34A  THR*     3.7    17.8    +      -       -      +
     35A  CYS      3.4     5.2    -      -       -      -
     36A  THR*     3.5    22.0    -      -       -      +
    123A  ASN      3.4     2.9    -      -       -      +
    124A  TYR*     3.3     4.7    -      -       -      -
    125A  LYS*     3.0    66.1    +      -       +      +
    149A  TYR*     1.3    76.0    -      -       -      +
    151A  VAL*     1.3    65.6    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 151 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34A  THR*     3.2     3.8    -      -       -      -
     35A  CYS*     2.9    50.3    +      -       -      +
    121A  LEU*     3.7    32.3    -      -       +      +
    122A  LYS      3.7    13.0    -      -       -      +
    123A  ASN      4.1     2.5    -      -       -      -
    124A  TYR*     4.0    20.6    -      -       +      -
    149A  TYR*     3.9    11.9    -      -       +      -
    150A  THR*     1.3    78.6    +      -       -      +
    152A  ASP*     1.3    69.1    +      -       -      +
    162A  THR*     4.2    13.2    -      -       +      -
    166A  VAL*     4.4     6.1    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 152 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33A  THR*     3.5    11.3    +      -       -      +
     34A  THR*     3.6    17.4    -      -       -      +
    121A  LEU*     4.1     4.9    -      -       -      +
    122A  LYS*     2.9    37.3    +      -       +      +
    123A  ASN*     2.6    35.5    +      -       -      +
    151A  VAL*     1.3    84.2    -      -       -      +
    153A  ILE*     1.3    66.9    +      -       -      +
    154A  PRO*     3.4     8.9    -      -       +      +
    162A  THR*     4.8     0.2    -      -       -      +
----------------------------------------------------------
 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