Contacts of the strand formed by residues 403 - 410 (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 CYS 403 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    336B  ALA*     3.4    22.9    -      -       -      +
    338B  LEU*     4.1    12.1    -      -       +      -
    394B  ILE*     4.2    20.9    -      -       -      -
    401B  ILE*     3.3    21.6    +      -       -      -
    402B  PRO*     1.3    75.3    -      -       -      +
    404B  ASP*     1.3    65.5    +      -       -      +
    405B  PHE*     3.5    24.9    -      -       +      -
    435B  LEU*     5.5     0.4    -      -       -      -
    472B  PRO      3.6     6.1    +      -       -      -
    473B  THR*     3.2    11.8    -      -       +      +
    474B  ASN*     2.9    25.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 404 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    319B  LEU*     5.1     3.0    -      -       -      +
    335B  HIS*     2.9    33.1    +      -       -      +
    336B  ALA      2.8    13.7    +      -       -      +
    337B  MET*     4.4     4.2    -      -       -      +
    338B  LEU*     2.8    30.5    +      -       -      +
    403B  CYS*     1.3    73.5    -      -       -      +
    405B  PHE*     1.3    59.9    +      -       -      +
    406B  LEU*     3.4     8.8    -      -       +      +
    474B  ASN*     2.9    36.6    +      -       -      +
    476B  ILE*     4.6     5.7    -      -       +      +
    493B  TYR*     2.7    34.4    +      -       -      +
    496B  LYS*     4.4     1.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 405 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    338B  LEU*     3.4    13.7    -      -       +      -
    340B  TYR*     3.6    21.1    -      +       -      -
    391B  TYR*     3.6    29.2    -      +       -      -
    394B  ILE*     6.2     0.2    -      -       +      -
    403B  CYS*     3.5    27.4    -      -       +      -
    404B  ASP*     1.3    75.4    -      -       -      +
    406B  LEU*     1.3    54.5    +      -       -      +
    428B  PHE*     3.3    26.0    -      +       +      -
    431B  GLN*     3.7    20.9    -      -       +      -
    432B  THR*     3.6    21.3    -      -       +      -
    435B  LEU*     4.0    20.2    -      -       +      -
    473B  THR*     3.9    13.9    -      -       +      -
    474B  ASN      2.8    14.3    +      -       -      +
    475B  SER*     3.3     2.0    -      -       -      +
    476B  ILE*     2.7    32.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 406 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    337B  MET*     4.9     3.1    -      -       +      -
    338B  LEU      3.2    17.2    +      -       -      +
    339B  PRO*     4.1    15.3    -      -       +      -
    340B  TYR*     2.7    33.1    +      -       -      +
    344B  LEU*     5.7     2.0    -      -       +      -
    347B  PHE*     4.2    17.7    -      -       +      -
    404B  ASP*     3.4    27.1    -      -       +      +
    405B  PHE*     1.3    77.2    -      -       -      +
    407B  ILE*     1.3    61.5    +      -       -      +
    428B  PHE*     3.6     2.0    -      -       -      -
    476B  ILE*     3.1    30.7    -      -       +      +
    478B  PHE*     4.0    13.9    -      -       +      -
    489B  LEU*     4.9     7.0    -      -       +      -
    493B  TYR*     3.9    25.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 407 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    548A  ILE*     5.7     0.2    -      -       +      -
    340B  TYR*     3.4    25.8    -      -       +      +
    341B  ASP*     5.6     0.4    -      -       -      -
    406B  LEU*     1.3    77.4    -      -       -      +
    408B  PRO*     1.3    83.0    -      -       +      +
    421B  HIS*     4.4     2.5    -      -       +      -
    424B  LEU*     4.1    12.1    -      -       +      -
    425B  LEU*     3.5    35.7    -      -       +      -
    428B  PHE*     3.7    42.8    -      -       +      -
    476B  ILE      3.1     7.1    +      -       -      -
    477B  VAL*     3.4    14.8    -      -       +      +
    478B  PHE*     3.1    29.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 408 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    340B  TYR      4.1     4.7    -      -       -      +
    341B  ASP*     3.6    28.3    -      -       +      +
    407B  ILE*     1.3    99.6    -      -       +      +
    409B  VAL*     1.3    61.2    +      -       -      +
    410B  GLN      3.7    17.0    -      -       -      +
    411B  THR*     5.3     2.2    -      -       -      -
    421B  HIS*     2.9    30.2    +      -       +      -
    425B  LEU*     4.5     0.5    -      -       -      +
    478B  PHE*     3.1    33.9    -      -       +      +
    480B  LYS*     4.1     0.7    -      -       -      -
    481B  LEU*     3.8    14.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 409 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    547A  PHE*     4.4     2.9    -      -       +      -
    548A  ILE*     3.4    42.0    -      -       +      +
    551A  GLN*     3.9    19.3    -      -       +      +
    552A  ARG*     3.8    20.4    -      -       +      +
    407B  ILE      3.9     0.2    +      -       -      -
    408B  PRO*     1.3    72.1    -      -       -      +
    410B  GLN*     1.3    58.4    -      -       +      +
    421B  HIS*     2.9    22.0    +      -       -      -
    425B  LEU*     4.5     8.7    -      -       +      +
    477B  VAL*     3.5    27.4    -      -       +      -
    478B  PHE      2.7    16.0    +      -       -      +
    479B  THR*     3.3     8.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 410 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    551A  GLN      2.9    23.3    -      -       -      +
    552A  ARG*     3.4    14.6    -      -       -      +
    554A  ALA      2.6    28.8    +      -       -      +
    555A  ARG*     4.6    14.2    -      -       -      +
    556A  VAL*     5.1     4.0    -      -       -      +
    408B  PRO*     3.7    14.8    -      -       -      +
    409B  VAL*     1.3    82.2    -      -       +      +
    411B  THR*     1.3    63.6    +      -       -      +
    412B  GLN*     4.2     0.5    +      -       -      +
    421B  HIS*     4.2     2.2    -      -       -      -
    479B  THR*     2.8    24.0    +      -       -      +
    480B  LYS*     3.7    42.8    -      -       +      +
    481B  LEU      4.6     0.3    +      -       -      -
----------------------------------------------------------
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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