Contacts of the strand formed by residues 335 - 342 (chain D) in PDB entry 2C11


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 TRP 335 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    330D  VAL      4.6     0.4    -      -       -      -
    331D  ALA*     3.6     0.7    -      -       -      -
    332D  SER*     2.8    44.7    +      -       -      +
    334D  LEU*     1.3    89.4    -      -       +      +
    336D  THR*     1.3    61.3    +      -       -      +
    337D  PHE*     4.2    17.7    -      -       +      -
    352D  VAL*     3.6    15.0    -      -       +      -
    353D  ARG      3.4     5.6    -      -       -      -
    354D  PHE*     3.7    31.6    -      +       +      -
    359D  LEU*     3.7    13.9    -      -       +      -
    460D  LEU*     4.3     8.2    -      -       +      +
    479D  PHE*     3.4    37.4    +      +       +      +
    480D  HIS      3.0    30.7    +      -       -      -
    481D  PRO      4.6     0.2    -      -       -      -
    483D  GLY*     3.2    37.2    -      -       -      -
    484D  ALA      3.7     6.7    -      -       -      -
    485D  ILE*     3.6    18.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 336 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    329D  ARG*     3.0    18.3    +      -       -      +
    330D  VAL      3.2     6.5    -      -       -      -
    331D  ALA*     3.5    24.0    -      -       +      -
    332D  SER      4.5     4.9    -      -       -      +
    335D  TRP*     1.3    79.9    -      -       -      +
    337D  PHE*     1.3    68.3    +      -       -      +
    351D  ASP      3.3     1.2    -      -       -      +
    352D  VAL*     3.4     0.5    -      -       -      +
    353D  ARG*     3.0    52.4    +      -       -      +
    356D  GLY*     5.2     2.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 337 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    329D  ARG*     3.0    18.2    -      -       -      +
    330D  VAL*     2.6    75.2    +      -       +      -
    335D  TRP*     4.2     5.2    -      -       +      -
    336D  THR*     1.3    83.3    -      -       -      +
    338D  SER*     1.3    68.0    +      -       -      +
    339D  PHE*     4.1     5.8    -      +       -      -
    349D  ILE*     3.9    18.8    -      -       +      -
    350D  PHE      3.8     9.9    -      -       -      +
    351D  ASP      3.5     5.6    -      -       -      +
    352D  VAL*     4.0     5.2    -      -       +      -
    460D  LEU*     3.9    15.0    -      -       +      -
    462D  VAL*     3.5    29.4    -      -       +      -
    479D  PHE*     3.3    38.4    -      +       -      -
----------------------------------------------------------
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Residues in contact with SER 338 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     58D  GLN*     4.4     3.0    +      -       -      +
     60D  PHE*     3.6    33.1    +      -       -      +
    328D  SER*     3.0    26.1    -      -       -      -
    329D  ARG*     3.6    19.0    -      -       -      +
    337D  PHE*     1.3    75.3    -      -       -      +
    339D  PHE*     1.3    63.1    +      -       -      +
    349D  ILE*     3.4     9.0    -      -       -      +
    350D  PHE*     3.1    34.3    +      -       -      -
    351D  ASP*     5.8     1.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 339 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60D  PHE      4.2     4.3    -      -       -      +
     62D  ASP*     3.8     4.5    -      -       -      +
    325D  VAL*     3.7    21.5    -      -       +      -
    327D  GLY      3.8    11.0    -      -       -      -
    328D  SER*     2.8    42.8    +      -       -      -
    330D  VAL*     3.3    33.9    -      -       +      -
    337D  PHE*     4.1     7.6    -      +       +      -
    338D  SER*     1.3    75.8    +      -       -      +
    340D  GLY*     1.3    60.2    +      -       -      +
    348D  ARG*     3.4    11.2    -      -       -      +
    349D  ILE*     3.9    14.1    -      -       +      -
    350D  PHE*     5.5     2.9    -      -       -      -
    411D  VAL*     3.9    16.2    -      -       +      -
    429D  PHE*     4.0    39.9    -      +       +      -
    431D  VAL*     4.3     7.6    -      -       +      -
    462D  VAL*     4.6    12.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 340 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60D  PHE      5.4     0.4    -      -       -      -
     62D  ASP*     3.0    15.9    -      -       -      -
    339D  PHE*     1.3    78.7    -      -       -      +
    341D  LEU*     1.3    62.1    +      -       -      -
    347D  PRO*     3.7     2.1    -      -       -      +
    348D  ARG*     2.9    40.0    +      -       -      +
    350D  PHE*     5.8     0.4    -      -       -      -
    429D  PHE*     3.5    19.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 341 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     62D  ASP*     2.7    25.0    +      -       -      +
    100D  GLU*     4.0     1.2    -      -       -      +
    340D  GLY*     1.3    74.3    -      -       -      -
    342D  GLY*     1.3    64.0    +      -       -      +
    343D  ALA      3.4     0.9    +      -       -      -
    346D  GLY      4.1     1.3    -      -       -      -
    347D  PRO*     3.6    28.7    -      -       +      -
    348D  ARG*     3.4     5.3    +      -       -      +
    392D  GLY*     3.5    17.3    -      -       -      -
    395D  THR*     3.2    28.3    -      -       +      +
    413D  TRP*     3.2    50.5    -      -       +      +
    428D  ALA*     4.9     0.7    -      -       +      -
    429D  PHE*     3.7    14.3    -      -       +      -
    464D  SER*     3.5    23.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 342 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    100D  GLU*     3.8     3.1    -      -       -      -
    341D  LEU*     1.3    72.0    -      -       -      +
    343D  ALA*     1.3    67.7    +      -       -      -
    344D  PHE      3.0     3.7    +      -       -      -
    345D  SER*     3.3    22.4    -      -       -      -
    346D  GLY      3.1    22.1    +      -       -      -
    348D  ARG*     3.7    17.9    -      -       -      +
    392D  GLY*     3.1    16.2    -      -       -      -
----------------------------------------------------------
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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