Contacts of the strand formed by residues 15 - 22 (chain 1) in PDB entry 3J7Y


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 ASN 15 (chain 1).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     141  LYS*     1.3    92.0    -      -       -      +
     161  ILE*     1.3    58.6    +      -       -      +
     331  LYS*     3.8    44.1    +      -       +      +
     341  ARG      3.4    11.8    +      -       -      +
     351  ASN*     3.0    26.7    +      -       -      +
     641  SER*     4.1     0.2    -      -       -      -
     651  LEU*     2.8    45.7    +      -       +      +
   2848A    A      4.6     5.3    -      -       -      +
   2849A    G      3.3    21.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 16 (chain 1). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     141  LYS      4.1     0.6    +      -       -      -
     151  ASN*     1.3    75.1    -      -       -      +
     171  LEU*     1.3    77.3    +      -       -      +
     181  VAL*     3.6    18.6    +      -       +      +
     321  THR      3.7     0.3    -      -       -      +
     331  LYS*     3.4     7.5    -      -       -      +
     341  ARG*     2.8    43.5    +      -       -      +
     361  ARG*     3.6    41.5    -      -       +      +
     611  LYS*     3.7    30.5    -      -       +      +
     631  ARG      4.2     2.5    -      -       -      +
     641  SER*     3.9    20.4    -      -       -      -
     651  LEU*     4.5     1.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 17 (chain 1). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     161  ILE*     1.3    83.1    -      -       -      +
     181  VAL*     1.3    60.8    +      -       -      +
     311  ASN*     3.9    25.8    -      -       +      -
     321  THR      3.5    20.4    -      -       -      +
     331  LYS*     5.3     2.9    -      -       +      -
     611  LYS*     3.4     0.2    -      -       -      -
     621  ILE*     2.8    48.6    +      -       +      +
     631  ARG*     3.1    24.4    +      -       +      +
     651  LEU*     4.1     7.7    -      -       +      +
    1343  TRP*     3.6    52.9    -      -       +      +
   2908A    U      4.3    10.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 18 (chain 1). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     161  ILE*     3.6    17.3    -      -       +      +
     171  LEU*     1.3    79.4    -      -       -      +
     191  ARG*     1.3    60.7    +      -       -      +
     201  MET*     4.3     6.0    -      -       -      +
     301  PHE      3.8     0.2    -      -       -      +
     311  ASN*     3.4     2.9    -      -       -      -
     321  THR*     2.8    57.1    +      -       -      +
     341  ARG*     3.9    24.7    -      -       +      +
     411  LEU*     5.1     1.6    -      -       +      -
     581  GLU*     3.7    36.8    -      -       +      +
     601  LYS      3.9     3.4    -      -       -      +
     611  LYS*     3.7    14.1    -      -       +      -
     621  ILE*     4.0     6.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 19 (chain 1). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     181  VAL*     1.3    72.6    -      -       -      +
     201  MET*     1.3    65.2    +      -       -      +
     211  VAL*     4.4     6.1    -      -       +      -
     291  CYS*     3.7    24.9    -      -       +      -
     301  PHE      3.5     6.7    -      -       -      +
     311  ASN*     4.3     8.0    +      -       -      +
     581  GLU*     3.5     4.7    -      -       -      +
     591  LYS*     2.9    41.5    +      -       -      +
     601  LYS*     3.3    32.7    +      -       -      +
     621  ILE*     3.4    36.0    -      -       +      +
   2903A    U      5.2     1.8    +      -       -      -
   2905A    A      4.1    18.2    -      -       -      +
   2906A    C      2.8    53.0    +      -       -      +
   2907A    U      3.9     3.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with MET 20 (chain 1). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     181  VAL*     4.3     4.0    -      -       -      +
     191  ARG*     1.3    76.9    -      -       -      +
     211  VAL*     1.3    62.2    +      -       -      +
     291  CYS*     3.4     6.8    -      -       -      -
     301  PHE*     2.9    52.4    +      -       +      +
     321  THR*     4.0    15.7    -      -       -      +
     411  LEU*     3.7    24.9    -      -       +      +
     431  LEU*     3.5    41.3    -      -       +      -
     561  PHE*     3.4    26.2    -      -       +      +
     571  VAL      3.4     4.5    -      -       -      -
     581  GLU*     3.6    31.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 21 (chain 1). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     191  ARG*     4.4     8.1    -      -       +      -
     201  MET*     1.3    75.9    -      -       -      +
     221  SER*     1.3    73.8    +      -       -      +
     231  GLU*     3.7     4.0    +      -       -      +
     261  THR*     6.0     1.1    -      -       +      -
     271  GLY      5.6     5.4    -      -       -      +
     281  PHE      4.3     3.4    -      -       -      +
     291  CYS*     3.9    23.1    -      -       -      -
     551  LEU      4.3     0.2    -      -       -      +
     561  PHE*     3.3     3.4    -      -       -      -
     571  VAL*     2.8    35.9    +      -       +      +
     591  LYS*     4.0    38.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 22 (chain 1). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     211  VAL*     1.3    85.1    -      -       -      +
     231  GLU*     1.3    64.8    +      -       -      +
     241  ALA      3.4    11.0    -      -       -      -
     251  GLY      3.2     8.4    +      -       -      -
     261  THR*     4.1    12.3    -      -       -      +
     281  PHE      2.8    19.6    +      -       -      -
     471  ASP*     3.1    27.8    +      -       -      -
     541  VAL*     4.5     0.2    -      -       -      -
     551  LEU      3.8     6.1    -      -       -      -
     561  PHE*     3.1    25.7    -      -       -      -
----------------------------------------------------------
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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