Contacts of the strand formed by residues 334 - 339 (chain C) in PDB entry 1L6O


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 ILE 334 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    256C  THR*     3.6     0.9    -      -       -      -
    257C  LEU*     2.9    38.2    +      -       +      +
    259C  MSE      3.5    31.6    -      -       +      -
    265C  LEU*     3.7    24.0    -      -       +      -
    307C  VAL*     4.4    11.2    -      -       +      -
    308C  ASN*     3.6     5.4    -      -       -      +
    327C  ILE*     4.6    11.7    -      -       +      +
    328C  VAL*     4.0    28.3    -      -       +      +
    330C  LYS      4.9     2.0    -      -       -      +
    332C  GLY      3.6     8.1    -      -       -      +
    333C  PRO*     1.3    81.9    -      -       -      +
    335C  VAL*     1.3    64.3    +      -       -      +
    336C  LEU*     4.2    22.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 335 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    254C  THR*     3.9    26.9    -      -       +      -
    255C  VAL      3.5     4.9    -      -       -      +
    256C  THR*     3.7    21.3    -      -       -      +
    306C  GLN      4.0     0.2    -      -       -      +
    307C  VAL*     3.4     9.9    -      -       -      +
    308C  ASN*     2.7    46.5    +      -       -      +
    309C  ASP      6.0     0.4    -      -       -      +
    333C  PRO*     5.6     2.0    -      -       +      -
    334C  ILE*     1.3    75.6    -      -       -      +
    336C  LEU*     1.3    66.2    +      -       -      +
    337C  THR*     4.9     4.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 336 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    253C  ILE      3.9     0.5    -      -       -      +
    254C  THR*     3.2     2.7    -      -       -      -
    255C  VAL*     2.8    40.5    +      -       +      +
    257C  LEU*     4.3    19.5    -      -       +      -
    265C  LEU*     4.7     7.0    -      -       +      -
    267C  ILE*     4.7    17.3    -      -       +      -
    283C  ILE*     5.3     1.1    -      -       +      -
    292C  VAL*     5.0     1.8    -      -       +      -
    298C  ILE*     3.9    25.8    -      -       +      -
    304C  LEU*     4.1    21.5    -      -       +      -
    306C  GLN      3.8     1.1    -      -       -      -
    307C  VAL*     4.1    26.5    -      -       +      -
    324C  LEU*     4.6     8.5    -      -       +      -
    334C  ILE*     4.2     9.9    -      -       +      -
    335C  VAL*     1.3    83.6    -      -       -      +
    337C  THR*     1.3    65.3    +      -       -      +
    338C  VAL*     4.0     2.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with THR 337 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    252C  ILE*     4.2    17.3    -      -       +      -
    253C  ILE      3.4     9.6    -      -       -      +
    254C  THR*     3.7    17.2    +      -       -      +
    304C  LEU*     4.0     4.7    -      -       -      +
    305C  LEU*     3.1    33.8    +      -       +      -
    306C  GLN*     3.0    38.9    +      -       +      +
    335C  VAL*     4.9     4.5    -      -       -      +
    336C  LEU*     1.3    76.9    -      -       -      +
    338C  VAL*     1.2    66.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 338 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    252C  ILE*     3.6     2.9    -      -       -      -
    253C  ILE*     2.8    44.6    +      -       +      +
    255C  VAL*     5.7     1.3    -      -       +      -
    283C  ILE*     5.4     2.5    -      -       +      -
    298C  ILE*     4.7    24.2    -      -       +      -
    302C  ASP*     3.6    22.0    -      -       +      +
    303C  MSE      2.6    36.6    -      -       -      +
    304C  LEU*     4.3     6.5    -      -       +      -
    305C  LEU*     4.0     7.2    -      -       -      +
    336C  LEU*     5.2     2.5    -      -       +      +
    337C  THR*     1.2    81.2    -      -       -      +
    339C  ALA*     1.3    67.0    +      -       -      +
    340C  LYS*     3.9     4.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 339 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    251C  MSE      3.8     5.2    -      -       -      +
    252C  ILE*     4.3     7.9    -      -       +      -
    302C  ASP*     3.3     3.6    -      -       -      -
    303C  MSE      2.7    49.4    +      -       +      +
    305C  LEU*     3.9    17.3    -      -       +      +
    338C  VAL*     1.3    84.2    -      -       -      +
    340C  LYS*     1.3    66.6    +      -       -      +
    341C  LEU*     3.4     0.9    +      -       -      -
----------------------------------------------------------
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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