Contacts of the strand formed by residues 437 - 441 (chain C) in PDB entry 1C7G


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 LEU 437 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33C  TYR*     4.2    17.9    -      -       +      +
    359C  ASP      4.5     0.7    -      -       -      +
    360C  GLN*     2.9    19.5    +      -       -      +
    361C  PHE*     3.7    16.5    -      -       +      +
    364C  GLN*     3.8    22.9    -      -       +      +
    365C  SER*     3.7    36.1    -      -       -      +
    368C  ALA*     5.4     0.9    -      -       +      -
    436C  GLY*     1.3    75.0    -      -       -      -
    438C  THR*     1.3    60.9    +      -       -      +
    453C  PHE*     4.0    20.4    -      -       +      -
    454C  ASP      3.6    15.0    -      -       -      -
    455C  PHE*     3.5    33.4    -      -       +      +
    456C  ILE*     2.9    17.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 438 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    361C  PHE*     4.1     5.4    -      -       -      -
    437C  LEU*     1.3    76.8    -      -       -      +
    439C  PHE*     1.3    70.8    +      -       -      +
    440C  VAL*     4.7     2.7    -      -       +      -
    453C  PHE*     3.1     9.6    -      -       -      -
    454C  ASP*     3.0    45.7    +      -       +      +
    455C  PHE      4.5     5.6    -      -       -      +
    456C  ILE*     4.0    11.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 439 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    361C  PHE*     3.5    29.9    -      +       -      -
    384C  VAL*     4.4     5.2    -      -       +      -
    388C  ARG*     4.8     2.0    -      -       -      -
    395C  ASN*     4.7     2.9    -      -       -      -
    438C  THR*     1.3    82.4    +      -       -      +
    440C  VAL*     1.3    60.9    +      -       -      +
    441C  TYR      4.0     7.2    -      -       -      +
    442C  GLU*     3.6    33.9    -      -       +      +
    447C  ARG*     3.5    42.8    -      -       -      -
    451C  ALA*     3.4    25.8    -      -       +      -
    452C  ARG      3.7     2.2    -      -       -      -
    453C  PHE*     3.2    28.9    -      +       -      -
----------------------------------------------------------
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Residues in contact with VAL 440 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    438C  THR*     4.1     4.0    -      -       +      +
    439C  PHE*     1.3    77.7    -      -       -      +
    441C  TYR*     1.3    63.3    +      -       +      +
    452C  ARG*     2.8    50.6    +      -       +      +
    453C  PHE      3.7     6.7    -      -       -      +
    454C  ASP*     3.4    35.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 441 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    439C  PHE*     3.4     2.6    -      -       -      +
    440C  VAL*     1.3    85.0    -      -       +      +
    442C  GLU*     1.3    62.6    +      -       -      +
    443C  PRO*     3.7    37.7    -      -       +      +
    450C  THR*     3.8    15.1    +      -       -      -
    451C  ALA*     3.4     4.2    -      -       -      +
    452C  ARG*     3.0    58.4    +      -       +      +
----------------------------------------------------------
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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