Contacts of the strand formed by residues 62 - 69 (chain J) in PDB entry 1N33


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 HIS 62 (chain J).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1188A    A      6.1     3.4    -      -       -      -
   1367A    C      3.6    14.7    +      -       -      -
   1368A    G      3.4    27.6    +      -       -      -
    111I  ARG*     3.7     5.8    +      -       -      -
    114I  TYR*     4.5    12.5    -      +       -      -
     46J  ARG*     5.3     4.5    -      -       +      -
     47J  PHE      3.6     3.6    -      -       -      -
     48J  THR*     2.6    37.7    +      -       +      -
     60J  ARG*     4.6     0.2    -      -       +      -
     61J  GLU*     1.3    80.3    +      -       -      +
     63J  PHE*     1.3    64.9    +      -       -      +
     58N  LYS*     3.4     8.2    +      -       -      +
     59N  ALA*     2.6    46.4    +      -       +      +
     61N  TRP*     3.1    30.1    -      +       +      -
----------------------------------------------------------
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Residues in contact with PHE 63 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46J  ARG*     3.5     1.6    -      -       -      +
     47J  PHE*     2.5    58.1    +      -       +      +
     48J  THR      5.6     0.4    -      -       -      -
     49J  VAL*     5.7     4.5    -      -       +      -
     61J  GLU*     3.5    28.0    -      -       +      -
     62J  HIS*     1.3    80.2    -      -       -      +
     64J  GLU*     1.3    61.4    +      -       -      +
     44N  LEU*     4.2    16.6    -      -       +      -
     45N  ARG*     3.3    30.1    -      -       +      -
     48N  ALA*     3.8    23.6    -      -       +      -
     49N  HIS*     4.0     7.6    -      +       -      -
     56N  VAL*     4.5    10.5    -      -       +      -
     57N  ARG      3.0    23.3    -      -       -      +
     58N  LYS*     3.3    28.3    -      -       +      -
     59N  ALA*     3.4     5.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 64 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1114A    C      4.9     7.1    +      -       -      -
     44J  VAL*     4.1     6.5    -      -       +      -
     45J  ARG      3.2     9.9    -      -       -      +
     46J  ARG*     3.0    27.8    +      -       -      +
     47J  PHE*     4.0     6.2    -      -       -      -
     63J  PHE*     1.3    75.0    -      -       -      +
     65J  LEU*     1.3    66.3    +      -       -      +
     66J  ARG*     2.6    56.2    +      -       -      +
     55N  GLY      4.7     0.3    -      -       -      +
     56N  VAL*     3.7    17.3    -      -       -      +
     57N  ARG*     3.4    31.6    +      -       +      +
     58N  LYS      5.0     1.1    -      -       -      +
     59N  ALA*     3.4    21.2    -      -       -      +
     60N  SER      4.7     4.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 65 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29C  TYR*     4.1     6.5    -      -       +      -
     11J  PHE*     3.6    38.6    -      -       +      -
     43J  ARG      3.9     3.3    -      -       -      +
     44J  VAL*     4.2     1.2    -      -       -      +
     45J  ARG*     3.2    33.9    +      -       +      +
     47J  PHE*     4.1     9.9    -      -       +      -
     64J  GLU*     1.3    82.8    -      -       -      +
     66J  ARG*     1.3    62.2    +      -       -      +
     67J  THR*     3.3     6.1    +      -       -      +
     36N  PHE*     3.7    33.2    -      -       +      -
     37N  PHE*     4.5     0.2    -      -       +      -
     55N  GLY      3.8    12.1    -      -       -      -
     56N  VAL*     3.6    31.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 66 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1115A    C      5.4    10.1    +      -       -      -
     11J  PHE*     3.0    32.9    -      -       -      +
     42J  THR*     3.9    17.1    -      -       +      +
     44J  VAL*     4.1    24.1    -      -       +      +
     46J  ARG*     4.9     6.9    -      -       -      +
     64J  GLU*     2.6    59.1    +      -       -      +
     65J  LEU*     1.3    72.5    -      -       -      +
     67J  THR*     1.3    61.3    +      -       -      +
     68J  HIS*     3.7    29.0    +      -       +      +
     55N  GLY      4.5     4.8    +      -       -      +
     57N  ARG*     5.1    13.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 67 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23C  TYR*     3.9    23.1    -      -       +      +
     26C  LYS*     5.2    10.6    +      -       -      +
      9J  ARG*     3.7    26.5    -      -       +      +
     10J  GLY      3.6     4.7    -      -       -      +
     11J  PHE*     3.4    21.8    -      -       -      -
     42J  THR*     2.9    20.4    -      -       -      +
     43J  ARG*     3.5    21.4    +      -       +      +
     45J  ARG*     5.8     1.7    -      -       -      +
     65J  LEU*     3.3     9.1    +      -       -      +
     66J  ARG*     1.3    69.9    -      -       -      +
     68J  HIS*     1.3    64.7    +      -       -      +
     69J  ASN*     3.8     4.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 68 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1152A    A      2.4    34.4    +      -       -      +
      8J  LEU      4.6     0.2    -      -       -      -
      9J  ARG*     3.4    20.1    -      -       -      -
     10J  GLY      3.0    12.6    +      -       -      +
     11J  PHE      3.5    17.3    +      -       -      -
     12J  ASP*     3.4     7.8    -      -       -      -
     13J  HIS*     3.2    38.0    +      -       +      +
     16J  LEU*     5.1     8.3    -      -       +      -
     42J  THR*     3.4    17.6    +      -       -      +
     66J  ARG*     3.7    37.7    +      -       +      -
     67J  THR*     1.3    78.9    -      -       -      +
     69J  ASN*     1.3    65.3    +      -       -      +
     70J  ARG*     5.4     3.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 69 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1151A    A      5.8     0.5    -      -       -      +
   1280A    A      5.0     2.0    +      -       -      -
      7J  LYS*     6.1     0.3    -      -       -      +
      8J  LEU      3.2     4.4    -      -       -      +
      9J  ARG*     2.7    41.6    +      -       -      +
     39J  PRO*     2.4    25.4    +      -       -      +
     40J  LEU*     3.0    33.1    +      -       +      +
     41J  PRO      2.7    25.3    +      -       -      -
     42J  THR*     4.2     1.4    +      -       -      +
     43J  ARG*     4.5     5.1    -      -       -      +
     67J  THR*     3.8    10.5    +      -       -      +
     68J  HIS*     1.3    73.5    -      -       -      +
     70J  ARG*     1.3    81.4    +      -       -      +
----------------------------------------------------------
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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