Contacts of the strand formed by residues 67 - 71 (chain 4) in PDB entry 1NJI


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 LEU 67 (chain 4).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      34  MET*     4.2    10.5    -      -       -      -
     224  VAL*     3.9    16.4    -      -       +      -
     234  GLU      3.4    11.7    -      -       -      +
     244  LYS*     3.8    16.8    -      -       +      -
     254  VAL*     3.7     6.5    -      -       -      +
     654  THR*     3.1    31.2    +      -       +      +
     664  ASP*     1.3    80.2    +      -       -      +
     684  LYS*     1.3    60.8    +      -       -      +
     694  TYR*     3.6    34.4    -      -       +      +
     794  LEU*     3.4    22.2    -      -       -      +
     804  ARG      4.8     4.0    +      -       -      +
     834  TRP*     4.3     0.7    -      -       +      -
     884  LEU*     3.7    27.6    -      -       +      -
     904  PHE*     3.9     8.3    -      -       +      -
   85044   CL      3.9     2.0    -      -       +      -
   2457A    U      5.5     3.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 68 (chain 4). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     214  GLU      3.4     4.5    -      -       -      +
     224  VAL*     3.5     3.6    -      -       -      +
     234  GLU*     2.8    54.2    +      -       +      +
     254  VAL*     3.6    29.6    -      -       +      +
     264  ARG      5.2     4.4    +      -       -      +
     674  LEU*     1.3    73.2    -      -       -      +
     694  TYR*     1.3    64.2    +      -       -      +
     704  ARG*     3.8    18.2    +      -       +      +
     774  ALA*     4.8     7.2    -      -       +      -
     784  HIS      4.2     3.8    -      -       -      -
     794  LEU*     4.4     3.1    -      -       +      -
   2435A    U      3.0    32.8    +      -       -      +
   2436A    U      2.7    35.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 69 (chain 4). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      34  MET*     4.4     6.5    -      -       +      +
      74  PHE*     4.0    25.1    -      +       -      -
      94  THR*     5.5     0.4    -      -       +      -
     204  HIS*     4.1     8.7    -      -       +      -
     214  GLU      3.7     3.1    -      -       -      -
     224  VAL*     3.8    22.7    -      -       +      -
     654  THR*     4.8     1.2    -      -       -      +
     674  LEU*     3.6    34.2    -      -       +      +
     684  LYS*     1.3    76.3    -      -       -      +
     704  ARG*     1.3    60.5    +      -       -      +
     714  CYS      4.0     0.3    +      -       -      -
     774  ALA*     3.0     2.9    -      -       -      -
     784  HIS*     2.8    65.3    +      +       +      +
     804  ARG*     3.5    54.8    +      -       +      +
     814  GLU      5.0     0.3    +      -       -      -
     834  TRP*     3.9    17.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 70 (chain 4). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     204  HIS*     3.0     5.9    -      -       -      -
     214  GLU*     2.8    57.5    +      -       +      +
     234  GLU*     4.4    17.6    +      -       +      -
     684  LYS*     4.3    16.4    -      -       +      +
     694  TYR*     1.3    71.7    -      -       -      +
     714  CYS*     1.3    70.0    +      -       -      +
     724  GLY      3.4     0.7    +      -       -      -
     754  GLY*     3.2    25.5    +      -       -      +
     774  ALA*     3.3    28.8    -      -       +      +
   2436A    U      3.8    20.2    +      -       -      -
   2437A    A      3.8    11.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 71 (chain 4). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     114  CYS*     3.5    14.6    -      -       -      -
     144  CYS*     4.2     0.2    -      -       -      -
     184  GLN*     4.2    15.3    -      -       -      -
     204  HIS*     3.4    14.5    -      -       -      +
     704  ARG*     1.3    73.0    -      -       -      +
     724  GLY*     1.3    63.3    +      -       -      +
     734  GLU      3.7     3.6    -      -       -      -
     744  CYS*     3.3    21.1    -      -       -      -
     754  GLY*     3.1    23.5    +      -       -      +
     764  LYS      3.1    22.8    +      -       -      +
   84044   CD      2.2    32.8    -      -       -      -
----------------------------------------------------------
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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