Contacts of the strand formed by residues 203 - 208 (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 SER 203 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    148B  ILE*     4.2     1.1    -      -       -      -
    150B  ASP*     3.3     8.1    +      -       -      +
    152B  ILE*     3.7    16.8    -      -       -      -
    198B  LEU*     3.4    26.9    -      -       -      +
    199B  ASN      2.9    21.5    +      -       -      -
    200B  PRO      3.9     3.4    +      -       -      +
    201B  GLU      3.8     1.2    -      -       -      -
    202B  SER*     1.3    78.4    +      -       -      +
    204B  LEU*     1.3    60.7    +      -       -      +
    205B  PHE*     4.2    16.6    +      -       -      -
    227B  TRP*     4.7     2.2    -      -       -      -
    241B  HIS*     2.9    28.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 204 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    131B  PHE*     3.7    30.1    -      -       +      -
    135B  VAL*     4.2    21.1    -      -       +      -
    140B  TRP*     4.5     5.4    -      -       +      +
    148B  ILE*     3.7    20.2    -      -       +      -
    150B  ASP      2.8     9.2    +      -       -      +
    151B  VAL*     3.2     9.0    -      -       +      +
    152B  ILE*     2.7    30.7    +      -       -      -
    203B  SER*     1.3    74.6    -      -       -      +
    205B  PHE*     1.3    61.0    +      -       -      +
    206B  ILE*     5.0     2.0    -      -       +      -
    240B  LYS      4.1     8.1    -      -       -      +
    241B  HIS*     3.6    27.8    -      -       -      +
    242B  PHE      4.1     1.8    -      -       -      +
    243B  VAL*     4.2    20.0    -      -       +      -
    285B  LEU*     4.5    11.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 205 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    152B  ILE*     3.4    43.7    -      -       +      +
    154B  ILE*     3.9    13.5    -      -       +      -
    195B  LEU*     3.9    17.9    -      -       +      -
    198B  LEU*     4.4     0.9    -      -       +      -
    203B  SER*     4.2    15.0    -      -       -      -
    204B  LEU*     1.3    75.9    -      -       -      +
    206B  ILE*     1.3    63.0    +      -       -      +
    207B  ILE*     4.0     6.7    -      -       +      -
    224B  ALA*     3.8    14.8    -      -       +      -
    227B  TRP*     3.6    34.5    -      +       -      -
    228B  PHE*     5.1     3.8    -      +       +      -
    241B  HIS      2.7    18.7    +      -       -      -
    242B  PHE*     3.4    41.2    -      +       +      -
    243B  VAL*     2.9    30.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 206 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    151B  VAL*     3.5    31.0    -      -       +      -
    152B  ILE      2.8    10.4    +      -       -      +
    153B  ASN*     3.6    12.9    +      -       -      +
    154B  ILE*     2.8    29.8    +      -       -      +
    204B  LEU*     4.8     2.9    -      -       +      +
    205B  PHE*     1.3    76.2    -      -       -      +
    207B  ILE*     1.3    62.6    +      -       -      +
    208B  ALA      3.5     0.7    +      -       -      -
    243B  VAL*     3.6    17.0    -      -       +      -
    245B  LEU*     3.5    42.8    -      -       +      -
    281B  LEU*     4.2     5.2    -      -       +      -
    282B  SER*     4.0    21.1    -      -       -      +
    285B  LEU*     3.6    21.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 207 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    154B  ILE*     3.8    20.9    -      -       +      -
    205B  PHE*     4.3     2.9    -      -       +      +
    206B  ILE*     1.3    78.1    -      -       -      +
    208B  ALA*     1.3    60.6    +      -       -      +
    209B  SER*     3.5     2.1    +      -       -      -
    212B  PHE*     3.4    38.2    -      -       +      -
    217B  THR*     4.0    17.3    -      -       +      -
    218B  ILE*     4.5     3.4    -      -       +      -
    221B  ALA*     3.7    33.9    -      -       +      -
    242B  PHE*     4.2    21.3    -      -       +      -
    243B  VAL      2.9    16.7    +      -       -      +
    244B  ALA*     3.4     1.2    -      -       -      -
    245B  LEU*     2.8    25.0    +      -       -      -
    255B  PHE*     4.7     1.8    -      -       +      -
    257B  ILE*     4.4     7.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 208 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    153B  ASN*     4.5     6.5    -      -       -      +
    154B  ILE      3.0    16.0    +      -       -      +
    155B  GLY*     3.8     2.1    -      -       -      -
    156B  ILE      4.9     0.2    +      -       -      -
    159B  SER*     3.6    40.7    +      -       -      +
    206B  ILE      3.5     1.2    +      -       -      -
    207B  ILE*     1.3    69.3    -      -       -      +
    209B  SER*     1.3    64.4    +      -       -      +
    217B  THR*     3.6    12.5    +      -       -      +
    245B  LEU*     3.8    27.4    -      -       +      -
    279B  ILE*     4.0     6.3    -      -       +      -
----------------------------------------------------------
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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