Contacts of the strand formed by residues 60 - 68 (chain N) 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 ILE 60 (chain N).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136A    C      5.2     0.9    +      -       -      -
     39N  ARG*     5.0     4.0    +      -       -      -
     53N  GLY      4.9     0.2    -      -       -      +
     54N  TYR*     3.8    26.9    -      -       +      -
     55N  LYS*     2.8    53.8    -      -       +      +
     57N  LYS*     3.3    24.9    +      -       +      +
     58N  GLN      3.3     1.0    -      -       -      -
     59N  GLY*     1.3    80.4    +      -       -      +
     61N  ILE*     1.3    67.8    +      -       -      +
     62N  VAL*     4.5     0.3    +      -       -      +
    132N  ILE*     4.4     7.2    -      -       +      -
    133N  LEU      3.7     3.4    -      -       -      +
    134N  ILE*     3.7    20.2    -      -       +      -
    141N  ILE*     4.4     7.6    -      -       +      -
    147N  LEU*     4.0    16.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 61 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135A    G      3.6    29.2    -      -       -      +
    136A    C      4.5     1.8    -      -       -      +
     39N  ARG*     3.9    33.2    -      -       -      +
     59N  GLY*     3.5    20.2    -      -       -      +
     60N  ILE*     1.3    83.0    -      -       -      +
     62N  VAL*     1.3    70.0    +      -       -      +
     63N  VAL*     3.6    23.3    -      -       +      -
    109N  PHE*     4.6     3.6    -      -       +      -
    112N  LEU*     4.0    27.4    -      -       +      -
    131N  VAL      3.7     0.2    -      -       -      +
    132N  ILE*     3.4     4.7    -      -       -      +
    133N  LEU*     2.6    43.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 62 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39N  ARG*     3.6     4.2    -      -       -      +
     40N  ILE*     3.0    55.9    +      -       +      +
     41N  GLU      5.7     1.6    -      -       -      +
     43N  PRO*     3.9    20.2    -      -       +      -
     54N  TYR*     3.7    36.1    -      -       +      -
     60N  ILE      5.5     0.4    -      -       -      +
     61N  ILE*     1.3    79.3    -      -       -      +
     63N  VAL*     1.3    73.5    +      -       -      +
    118N  TYR*     4.7     1.1    -      -       -      +
    130N  GLU*     4.3    13.2    -      -       +      -
    131N  VAL      3.3     9.0    -      -       -      +
    132N  ILE*     4.7    10.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 63 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37N  VAL*     3.2    28.5    -      -       +      -
     38N  VAL      2.9    33.4    -      -       -      +
     39N  ARG*     3.5     3.6    -      -       -      +
     40N  ILE*     4.3     1.1    -      -       -      +
     61N  ILE*     3.6    11.4    -      -       +      -
     62N  VAL*     1.3    85.5    -      -       -      +
     64N  ARG*     1.3    61.5    +      -       -      +
     65N  VAL*     3.8     1.0    +      -       +      +
    105N  ALA*     5.1     3.4    -      -       +      -
    109N  PHE*     3.4    31.0    -      -       +      -
    129N  HIS      3.5     0.5    -      -       -      +
    130N  GLU*     3.2     5.4    -      -       -      -
    131N  VAL*     2.7    40.1    +      -       -      +
    133N  LEU*     3.9     9.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 64 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55H  GLN*     5.5     5.7    -      -       -      +
     31N  TRP*     3.0    57.8    -      -       -      +
     34N  GLU*     3.0    26.6    +      -       -      -
     35N  PRO      5.4     0.2    -      -       -      +
     36N  ALA      3.8     1.0    -      -       -      +
     37N  VAL*     3.6     4.0    -      -       -      -
     38N  VAL*     2.9    37.0    +      -       +      +
     40N  ILE*     3.8    26.1    -      -       +      +
     44N  THR*     3.8     6.3    +      -       -      -
     63N  VAL*     1.3    73.2    -      -       -      +
     65N  VAL*     1.3    62.8    +      -       -      +
     66N  ALA      4.3     0.2    -      -       -      -
    120N  VAL*     4.4     1.8    -      -       +      -
    128N  TRP*     4.0    26.0    -      -       +      -
    129N  HIS      3.4     7.2    -      -       -      +
    130N  GLU*     3.3    31.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 65 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36N  ALA*     3.3    10.5    -      -       +      +
     37N  VAL*     4.0    13.9    -      -       +      -
     63N  VAL*     4.4     2.5    -      -       +      +
     64N  ARG*     1.3    81.0    -      -       -      +
     66N  ALA*     1.3    72.6    +      -       -      +
     67N  ILE*     3.8    18.6    -      -       +      +
    101N  ALA*     3.8    20.6    -      -       +      +
    104N  ARG*     4.3     9.9    -      -       +      -
    105N  ALA*     3.6    31.2    -      -       +      -
    127N  LYS      3.5     1.7    -      -       -      +
    128N  TRP*     3.3     8.7    -      -       -      -
    129N  HIS*     2.8    35.9    +      -       -      +
    131N  VAL*     4.4     7.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 66 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1468A    G      4.4     8.9    +      -       -      +
     35N  PRO      4.4    11.4    +      -       -      +
     36N  ALA*     3.0    18.9    +      -       -      +
     64N  ARG      4.3     0.2    -      -       -      -
     65N  VAL*     1.3    72.4    -      -       -      +
     67N  ILE*     1.3    74.9    +      -       -      +
    104N  ARG*     3.9     5.5    +      -       -      -
    126N  HIS*     4.0    16.6    -      -       +      -
    127N  LYS      3.6     4.3    -      -       -      -
    128N  TRP*     3.4    25.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 67 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1468A    G      5.7     0.7    -      -       -      -
     65N  VAL*     3.8     7.6    -      -       +      +
     66N  ALA*     1.3    87.0    -      -       -      +
     68N  ARG*     1.3    83.2    +      -       -      +
     97N  ILE*     3.5    27.1    -      -       +      -
    100N  ILE*     4.1    13.9    -      -       +      -
    101N  ALA*     3.8    29.4    -      -       +      +
    104N  ARG*     2.9    50.3    -      -       -      +
    126N  HIS*     3.4     5.7    -      -       -      -
    127N  LYS*     2.9    35.4    +      -       -      +
    129N  HIS*     5.4     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 68 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1468A    G      5.8     1.0    +      -       -      -
   1469A    C      3.4    29.3    +      -       -      +
   1470A    A      2.8    44.8    +      -       -      -
     67N  ILE*     1.3    86.3    -      -       -      +
     69N  LYS*     1.3    55.0    +      -       -      +
     70N  GLY      3.3    18.4    +      -       -      -
     71N  SER      3.6    17.4    +      -       -      -
     72N  SER*     4.4     1.2    -      -       -      +
     73N  ARG*     3.1    36.3    -      -       -      +
     93N  ARG*     4.4     5.7    -      -       -      +
     97N  ILE*     3.5    21.4    -      -       -      +
    100N  ILE*     4.7     7.1    -      -       -      +
    104N  ARG*     4.8     2.8    -      -       -      +
    125N  ARG      3.4     8.5    -      -       -      +
    126N  HIS*     4.7     0.9    -      -       -      +
----------------------------------------------------------
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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