Contacts of the strand formed by residues 612 - 619 (chain B) in PDB entry 1J1B


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 612 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    545B  GLY*     3.5    26.6    -      -       -      -
    546B  GLN*     4.3     3.6    +      -       -      +
    598B  LEU*     3.8    25.1    -      -       +      -
    601B  MET*     3.6    32.4    +      -       +      +
    602B  ARG*     3.9    18.8    -      -       +      +
    610B  VAL      3.8     2.8    +      -       -      -
    611B  ARG*     1.3    80.5    -      -       -      +
    613B  ARG*     1.3    63.3    +      -       -      +
    614B  TYR      3.5    22.0    -      -       -      +
    615B  PHE*     4.4     2.9    -      -       +      -
    630B  LEU*     3.7    31.4    -      -       +      -
    631B  VAL      3.7     5.2    -      -       -      +
    632B  LEU*     3.8     7.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 613 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    544B  PRO*     3.7     1.7    -      -       -      +
    545B  GLY      2.7    22.6    +      -       -      -
    546B  GLN      4.6     0.3    +      -       -      -
    552B  GLN*     5.0     0.2    +      -       -      -
    575B  LEU*     3.0    33.5    -      -       -      +
    580B  GLU*     2.6    39.8    +      -       -      +
    581B  LEU      4.5     3.6    +      -       -      -
    582B  VAL*     3.4    23.6    -      -       -      +
    611B  ARG*     3.5    23.2    +      -       -      +
    612B  LEU*     1.3    72.8    -      -       -      +
    614B  TYR*     1.3    87.6    +      -       +      +
    631B  VAL*     2.7    18.7    +      -       -      +
    632B  LEU      4.8     0.2    -      -       -      -
    633B  ASP*     2.8    36.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 614 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    542B  ALA*     3.7    15.9    -      -       +      -
    543B  THR      2.9    24.2    -      -       -      +
    545B  GLY*     3.5     5.2    -      -       -      +
    552B  GLN*     3.4    37.5    -      -       +      -
    554B  VAL*     3.7    33.3    -      -       +      +
    575B  LEU*     3.9    20.1    -      -       +      +
    612B  LEU*     3.5     7.2    -      -       -      +
    613B  ARG*     1.3   101.1    +      -       +      +
    615B  PHE*     1.3    64.1    +      -       -      +
    616B  PHE*     5.6     0.2    -      +       -      -
    631B  VAL*     2.8    64.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 615 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    542B  ALA*     3.5     0.7    -      -       -      +
    543B  THR*     3.0    65.8    +      -       +      -
    544B  PRO      3.9     5.2    -      -       -      -
    545B  GLY*     4.8     0.2    -      -       -      -
    598B  LEU*     3.8    32.3    -      -       +      -
    602B  ARG*     3.7    38.6    -      -       +      -
    612B  LEU*     4.4     6.3    -      -       +      -
    614B  TYR*     1.3    79.6    -      -       -      +
    616B  PHE*     1.3    67.5    +      -       -      +
    617B  TYR*     4.3    16.8    -      +       -      -
    628B  LEU*     4.0     8.7    -      -       +      -
    629B  ASN      3.0    13.9    -      -       -      +
    630B  LEU*     4.0    16.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 616 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    525B  SER      6.0     0.2    -      -       -      -
    526B  MET*     4.7     4.5    -      -       +      -
    540B  VAL*     3.9    37.5    -      -       +      -
    541B  VAL      3.8    21.1    -      -       -      +
    542B  ALA*     4.0     6.7    -      -       +      +
    556B  TYR*     3.8    26.2    -      +       -      -
    584B  ILE*     4.6     6.5    -      -       +      -
    615B  PHE*     1.3    79.5    -      -       -      +
    617B  TYR*     1.3    78.2    +      -       -      +
    618B  SER*     4.4     8.3    -      -       -      -
    628B  LEU*     3.7     0.6    -      -       -      -
    629B  ASN*     2.7    73.7    +      -       +      +
    631B  VAL*     3.7    24.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 617 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    523B  PHE      3.8    26.0    -      -       -      +
    524B  GLY*     3.7    25.1    -      -       -      +
    525B  SER*     4.0     4.3    +      -       -      +
    589B  GLN*     3.9    25.8    +      -       +      +
    595B  ASN*     5.7     0.9    -      -       -      +
    598B  LEU*     4.0    13.2    -      -       -      +
    615B  PHE*     4.3    19.8    -      +       -      -
    616B  PHE*     1.3    87.3    -      -       -      +
    618B  SER*     1.3    61.2    +      -       -      +
    626B  VAL*     4.1    14.8    -      -       +      -
    627B  TYR      3.1    15.0    -      -       -      +
    628B  LEU*     3.8    26.3    -      -       +      +
    629B  ASN*     4.0     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 618 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    524B  GLY      4.4     4.0    -      -       -      -
    525B  SER*     5.3     0.4    -      -       -      +
    526B  MET*     4.3    27.4    -      -       -      -
    586B  LYS*     3.4    25.0    +      -       -      -
    616B  PHE*     4.4     4.5    -      -       -      -
    617B  TYR*     1.3    75.1    -      -       -      +
    619B  SER*     1.3    63.6    +      -       -      +
    620B  GLY      3.3     0.7    +      -       -      -
    626B  VAL*     3.9     3.8    -      -       -      -
    627B  TYR*     2.9    31.1    +      -       -      +
    629B  ASN*     3.0    19.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 619 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    524B  GLY      3.4    17.9    +      -       -      +
    525B  SER*     4.7     5.9    -      -       -      +
    586B  LYS*     5.8     0.8    +      -       -      -
    618B  SER*     1.3    71.9    -      -       -      +
    620B  GLY*     1.3    61.7    +      -       -      +
    621B  GLU*     3.0    28.2    +      -       -      +
    623B  LYS      5.7     2.0    -      -       -      -
    625B  GLU      4.0     5.4    -      -       -      -
    626B  VAL*     4.9     4.9    -      -       -      +
----------------------------------------------------------
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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