Contacts of the strand formed by residues 473 - 480 (chain B) in PDB entry 1JLH


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 473 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53B  ASP      4.3     1.6    -      -       -      +
     56B  LYS*     3.1    32.5    +      -       -      +
     57B  ASN*     3.6    12.5    +      -       -      -
    403B  CYS*     3.2    15.5    -      -       +      +
    405B  PHE*     3.9    21.5    -      -       +      -
    432B  THR*     3.4    30.2    -      -       +      +
    435B  LEU*     4.1    18.6    -      -       +      -
    471B  ARG      3.9     9.1    +      -       -      +
    472B  PRO*     1.3    81.7    -      -       -      +
    474B  ASN*     1.3    65.7    +      -       -      +
    475B  SER*     4.7     0.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 474 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52B  VAL*     5.9     1.1    -      -       +      -
     53B  ASP      3.6     4.9    -      -       -      +
     54B  TYR*     3.4    12.6    -      -       -      +
     57B  ASN*     2.8    32.0    +      -       -      +
    319B  LEU*     3.8    26.2    +      -       +      +
    322B  LEU*     3.8    11.3    -      -       -      +
    326B  TYR*     6.2     0.6    -      -       -      -
    335B  HIS*     5.1     3.2    -      -       -      -
    403B  CYS      2.9     6.5    +      -       -      +
    404B  ASP*     2.9    29.1    +      -       +      +
    405B  PHE*     2.8    27.1    +      -       -      +
    473B  THR*     1.3    76.6    -      -       -      +
    475B  SER*     1.3    62.7    +      -       -      +
    476B  ILE*     4.1     7.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 475 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    544A  LEU*     3.8    35.2    -      -       -      +
     51B  LEU      3.3     2.8    -      -       -      +
     53B  ASP*     2.9    39.0    +      -       -      +
     56B  LYS*     4.5     2.0    +      -       -      +
    405B  PHE*     3.3     4.2    -      -       -      +
    428B  PHE*     3.9    13.8    -      -       -      -
    432B  THR*     3.6    27.5    +      -       -      +
    473B  THR*     4.7     0.7    +      -       -      -
    474B  ASN*     1.3    71.7    -      -       -      +
    476B  ILE*     1.3    62.8    +      -       -      +
    477B  VAL*     3.9     1.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 476 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50B  ILE*     4.2    22.7    -      -       +      -
     51B  LEU      3.3     3.6    -      -       -      +
     52B  VAL*     4.5    16.4    -      -       +      -
    319B  LEU*     4.6    11.7    -      -       +      -
    404B  ASP*     4.6    10.3    -      -       +      +
    405B  PHE      2.7    12.1    +      -       -      +
    406B  LEU*     3.1    25.5    -      -       +      +
    407B  ILE      3.1    24.4    +      -       -      +
    428B  PHE*     4.3     0.2    -      -       -      -
    474B  ASN*     4.8     3.6    -      -       +      -
    475B  SER*     1.3    78.5    -      -       -      +
    477B  VAL*     1.3    61.8    +      -       -      +
    478B  PHE*     3.9     4.5    -      -       +      -
    489B  LEU*     4.3    13.0    -      -       +      -
    492B  MET*     4.1    16.4    -      -       +      -
    493B  TYR*     3.3    26.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 477 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    544A  LEU*     3.9    23.8    -      -       +      -
    547A  PHE*     3.5    19.3    -      -       +      -
    548A  ILE*     4.3    12.1    -      -       +      -
     50B  ILE*     3.5     1.6    -      -       -      -
     51B  LEU*     2.7    39.1    +      -       +      +
    407B  ILE*     3.4    16.2    -      -       +      +
    409B  VAL*     3.5    28.0    -      -       +      -
    425B  LEU*     5.8     0.2    -      -       +      -
    428B  PHE*     3.8    28.0    -      -       +      -
    476B  ILE*     1.3    77.6    -      -       -      +
    478B  PHE*     1.3    64.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 478 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    547A  PHE*     4.8     0.9    -      -       -      -
     49B  HIS      3.2    11.0    -      -       -      +
     50B  ILE*     4.3     5.4    -      -       +      -
    344B  LEU*     4.4    12.8    -      -       +      -
    406B  LEU*     4.0    10.5    -      -       +      -
    407B  ILE*     3.1    30.5    +      -       -      -
    408B  PRO*     3.1    31.0    -      -       +      +
    409B  VAL*     2.7    35.7    +      -       -      -
    476B  ILE*     3.9     8.7    -      -       +      -
    477B  VAL*     1.3    78.8    -      -       -      +
    479B  THR*     1.3    57.0    +      -       -      +
    480B  LYS      4.1     4.3    -      -       -      -
    481B  LEU*     3.7    22.4    -      -       +      -
    485B  MET*     3.8    30.1    -      -       +      -
    489B  LEU*     3.6    31.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 479 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    547A  PHE*     5.1     1.2    -      -       -      -
    551A  GLN*     2.6    34.1    +      -       -      +
    554A  ALA*     3.9     4.3    -      -       +      -
    556A  VAL*     3.7    22.9    -      -       +      -
     48B  GLY*     3.6     8.6    -      -       -      -
     49B  HIS      2.8    29.7    +      -       -      -
    409B  VAL*     3.6     8.4    -      -       -      +
    410B  GLN*     2.8    52.1    +      -       -      +
    478B  PHE*     1.3    71.7    -      -       -      +
    480B  LYS*     1.3    60.7    +      -       +      +
    485B  MET*     4.8     1.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 480 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    555A  ARG*     5.3     7.3    -      -       -      +
    556A  VAL*     5.1    10.6    -      -       +      +
     47B  HIS      5.6     0.5    -      -       -      +
    173B  TYR*     4.5     4.4    +      -       -      -
    408B  PRO*     4.1     2.9    -      -       -      -
    410B  GLN*     3.7    39.5    -      -       +      +
    411B  THR      4.3    14.3    +      -       -      -
    412B  GLN*     3.6    30.7    +      -       -      +
    478B  PHE*     3.3     6.5    +      -       -      +
    479B  THR*     1.3    85.8    -      -       +      +
    481B  LEU*     1.3    63.3    +      -       -      +
    482B  THR*     3.0    28.0    +      -       +      +
    485B  MET*     3.2    21.0    -      -       -      +
----------------------------------------------------------
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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