Contacts of the strand formed by residues 269 - 274 (chain C) in PDB entry 1JWL


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 269 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    174C  LEU*     4.4     4.0    -      -       -      -
    179C  HIS*     3.5    18.9    +      -       -      -
    240C  THR      2.9    16.5    +      -       -      -
    241C  ALA*     3.1     7.7    -      -       -      -
    242C  MET      3.0    22.4    +      -       -      -
    265C  GLY      3.2    11.1    +      -       -      +
    268C  ILE*     1.3    77.1    -      -       -      +
    270C  VAL*     1.3    62.3    +      -       -      +
    328C  THR      2.9    10.8    -      -       -      -
    329C  THR*     3.7     9.4    -      -       -      -
    330C  LEU      2.8    26.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 270 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    242C  MET*     3.6    10.5    -      -       +      +
    244C  VAL*     4.1    21.8    -      -       +      -
    250C  ALA*     4.2     9.0    -      -       +      +
    253C  ALA*     5.2     2.5    -      -       +      -
    254C  MET*     4.4    11.9    -      -       +      -
    257C  ILE*     3.8    21.3    -      -       +      -
    264C  VAL*     4.2     9.4    -      -       +      -
    268C  ILE*     3.7    10.3    -      -       +      +
    269C  SER*     1.3    81.6    -      -       -      +
    271C  VAL*     1.3    70.9    +      -       -      +
    286C  LEU*     4.1    13.2    -      -       +      -
    287C  THR*     4.0     0.2    -      -       -      -
    328C  THR*     2.7    39.9    +      -       -      -
    329C  THR*     3.2    12.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 271 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    170C  GLY*     4.8     7.6    -      -       -      +
    173C  HIS*     4.6     5.2    -      -       +      -
    174C  LEU*     4.2    20.6    -      -       +      -
    242C  MET      3.1    10.1    +      -       -      +
    243C  LEU*     3.8    13.9    -      -       +      -
    244C  VAL*     2.9    31.2    +      -       -      +
    270C  VAL*     1.3    86.7    -      -       -      +
    272C  GLY*     1.3    72.1    +      -       -      +
    287C  THR*     3.4    15.5    -      -       +      +
    288C  THR*     4.2     5.6    -      -       -      -
    289C  ILE*     4.7    12.1    -      -       +      -
    323C  LEU*     5.1     1.8    -      -       +      -
    329C  THR*     3.3    22.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 272 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    244C  VAL      3.8     6.6    -      -       -      +
    247C  ASP*     3.5     7.9    -      -       -      -
    250C  ALA*     4.3     9.2    -      -       -      -
    271C  VAL*     1.3    82.3    -      -       -      +
    273C  TYR*     1.3    64.1    +      -       -      +
    286C  LEU*     3.9    10.6    -      -       -      +
    287C  THR      2.9    12.1    +      -       -      -
    288C  THR*     2.7    15.5    +      -       -      -
    289C  ILE*     3.2    14.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 273 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    161C  PHE*     5.7     0.3    -      -       -      +
    162C  SER      4.3     1.4    +      -       -      -
    163C  HIS*     3.8    19.1    +      -       -      -
    166C  GLY*     3.5    27.3    -      -       -      -
    167C  THR*     4.4     6.3    -      -       +      -
    197C  ARG*     3.4    37.3    +      -       +      -
    201C  TRP*     5.1     9.2    -      +       -      -
    244C  VAL      3.9     3.8    -      -       -      +
    245C  ALA      3.4    23.6    -      -       -      +
    246C  ASN*     3.2     1.8    -      -       -      -
    247C  ASP*     2.8    23.0    +      -       -      +
    272C  GLY*     1.3    73.9    -      -       -      -
    274C  ASP*     1.3    76.4    +      -       -      +
    288C  THR*     2.7     3.8    +      -       -      -
    289C  ILE*     3.5    34.3    -      -       +      +
    291C  GLN*     3.4    41.0    +      -       +      -
    321C  VAL*     4.9     3.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 274 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74C  HIS*     4.8     2.3    -      -       -      -
    246C  ASN*     3.9     3.1    +      -       -      +
    247C  ASP*     3.7     6.3    +      -       -      +
    248C  GLN*     5.2     1.7    +      -       -      +
    273C  TYR*     1.3    81.7    -      -       -      +
    275C  ASP*     1.3    73.7    +      -       -      +
    276C  THR*     3.7    19.5    -      -       +      +
    289C  ILE      2.7    15.6    +      -       -      -
    290C  LYS*     4.6     0.3    -      -       -      +
    291C  GLN*     2.7    51.6    +      -       -      +
    293C  PHE*     3.9    19.8    -      -       +      -
    334C  NPF      2.2    36.0    +      -       -      -
----------------------------------------------------------
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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