Contacts of the strand formed by residues 57 - 65 (chain N) in PDB entry 1JJ2


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 THR 57 (chain N).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26N  TRP*     6.2     0.7    -      -       +      -
     55N  ASP      4.1     1.5    +      -       -      -
     56N  GLU*     1.3    70.5    -      -       -      +
     58N  VAL*     1.3    72.6    +      -       -      +
     59N  VAL*     3.6    11.2    +      -       +      -
     75N  THR*     3.5    33.4    -      -       +      +
     77N  ALA*     4.3    11.9    -      -       +      -
    101N  ALA*     5.6     4.3    -      -       +      -
    105N  ASN*     5.7     5.1    +      -       -      -
    109N  SER      5.7     1.3    -      -       -      -
    110N  HIS      3.0    13.2    +      -       -      -
    111N  VAL*     3.2     7.7    -      -       -      +
    112N  ARG      2.8    25.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 58 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48N  ILE*     4.2    15.0    -      -       +      -
     52N  ALA*     3.5    33.4    -      -       +      -
     56N  GLU      4.3     6.5    -      -       -      +
     57N  THR*     1.3    74.5    -      -       -      +
     59N  VAL*     1.3    61.5    +      -       -      +
     60N  VAL*     4.3    13.2    -      -       +      -
     74N  VAL*     4.5     4.5    -      -       +      -
     75N  THR      2.9    13.5    +      -       -      +
     76N  VAL*     3.5    15.2    -      -       +      -
     77N  ALA      2.8    27.7    +      -       -      -
    112N  ARG*     3.4     9.0    -      -       +      +
    114N  ILE*     3.6    30.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 59 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25N  VAL*     5.7     0.7    -      -       +      -
     26N  TRP*     4.2    24.9    -      -       +      -
     29N  VAL*     3.8    28.7    -      -       +      -
     57N  THR*     4.0    11.0    -      -       +      +
     58N  VAL*     1.3    77.6    -      -       -      +
     60N  VAL*     1.3    67.1    +      -       -      +
     61N  PRO*     3.4     5.1    -      -       +      +
     77N  ALA*     3.4    10.5    -      -       +      +
     98N  LEU*     4.3     7.4    -      -       +      -
    111N  VAL*     3.2    31.0    -      -       +      -
    112N  ARG      2.8    11.2    +      -       -      +
    113N  VAL*     3.3    10.4    -      -       +      +
    114N  ILE      3.0    21.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 60 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41N  ALA*     4.0     3.8    -      -       +      -
     43N  VAL*     3.9    26.7    -      -       +      -
     48N  ILE*     4.7     4.7    -      -       +      -
     58N  VAL*     4.3    16.4    -      -       +      -
     59N  VAL*     1.3    75.9    -      -       -      +
     61N  PRO*     1.3    56.8    -      -       -      +
     62N  GLY      2.7    33.4    +      -       -      +
     63N  LYS      3.9     7.9    -      -       -      +
     64N  VAL*     3.7    20.4    -      -       +      -
     76N  VAL*     4.3     4.9    -      -       +      -
     77N  ALA      2.8     9.1    +      -       -      +
     78N  ALA*     3.5    25.7    -      -       +      -
     79N  VAL*     3.9     2.8    +      -       -      +
     98N  LEU*     4.5     4.2    -      -       -      +
    114N  ILE*     3.6    12.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with PRO 61 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    7210    A      5.9     0.2    -      -       +      -
     29N  VAL*     4.2    33.4    -      -       +      +
     32N  ARG*     4.0    28.5    -      -       +      +
     33N  LEU*     3.7    16.1    -      -       +      +
     40N  HIS*     4.1     1.6    -      -       -      -
     41N  ALA*     3.4    23.2    +      -       +      -
     59N  VAL*     3.4     8.5    -      -       +      +
     60N  VAL*     1.3    79.5    -      -       +      +
     62N  GLY*     1.3    55.6    +      -       -      +
     79N  VAL*     4.9     0.4    -      -       +      -
    113N  VAL*     4.1    15.3    -      -       +      -
    114N  ILE      3.3    15.5    -      -       -      +
    115N  ARG*     4.5     8.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 62 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33N  LEU*     4.7     0.7    -      -       -      -
     40N  HIS*     4.5     7.9    -      -       -      -
     41N  ALA      3.3    13.5    -      -       -      -
     60N  VAL*     2.7    15.6    +      -       -      +
     61N  PRO*     1.3    75.8    -      -       -      +
     63N  LYS*     1.3    60.8    +      -       -      -
     78N  ALA*     3.8     0.9    -      -       -      +
     79N  VAL*     2.9    43.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 63 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    6580    C      4.3    15.3    +      -       +      -
    6590    A      2.8    72.2    +      -       -      +
     41N  ALA      2.8    12.7    +      -       -      +
     42N  GLU*     3.3     7.4    -      -       +      -
     43N  VAL      3.0    23.7    +      -       -      -
     60N  VAL*     3.9     3.1    -      -       -      +
     62N  GLY*     1.3    74.0    -      -       -      +
     64N  VAL*     1.3    66.7    +      -       -      +
     65N  LEU*     4.0     9.4    +      -       +      +
     79N  VAL*     5.6     0.7    -      -       +      -
     80N  ASP*     3.2    40.4    +      -       +      +
     82N  SER      3.8    15.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 64 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43N  VAL*     3.2    10.5    -      -       +      +
     45N  LEU*     3.9    18.6    -      -       +      -
     48N  ILE*     3.8    20.0    -      -       +      -
     60N  VAL*     3.7    23.1    -      -       +      -
     63N  LYS*     1.3    72.1    -      -       -      +
     65N  LEU*     1.3    67.1    +      -       -      +
     76N  VAL*     4.0    11.4    -      -       +      -
     78N  ALA*     3.7    24.5    -      -       +      -
     80N  ASP      3.0     6.3    +      -       -      -
     81N  PHE*     3.8    12.3    -      -       +      -
     82N  SER      3.1    25.6    +      -       -      -
     85N  ALA*     3.3     6.8    -      -       +      +
     89N  ILE*     3.9    10.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 65 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    6590    A      3.4    60.3    -      -       +      +
    6600    A      3.6    10.3    -      -       -      +
    7460    A      3.4    26.0    -      -       +      +
     42N  GLU*     4.5    11.2    -      -       +      -
     43N  VAL      2.5    14.3    +      -       -      +
     44N  ASN*     3.1    34.0    -      -       -      +
     45N  LEU*     3.3    13.9    +      -       -      +
     63N  LYS*     4.0    15.5    -      -       +      +
     64N  VAL*     1.3    80.9    -      -       -      +
     66N  GLY*     1.3    59.0    -      -       -      +
     67N  SER      3.5     1.1    -      -       -      -
     82N  SER*     3.9     9.6    -      -       -      -
     85N  ALA*     3.6     4.3    -      -       -      -
----------------------------------------------------------
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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