Contacts of the strand formed by residues 600 - 608 (chain C) 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 PRO 600 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    540C  TRP*     4.5    20.4    -      -       +      +
    566C  ARG*     4.0    19.9    +      -       -      +
    588C  TYR*     5.3     3.8    -      -       +      +
    590C  ALA*     4.0    14.3    -      -       +      +
    591C  SER      4.0    16.2    -      -       -      +
    592C  ASN      5.2     3.6    -      -       -      +
    593C  HIS      3.8     6.7    -      -       -      +
    594C  SER*     4.1     6.1    -      -       -      +
    598C  GLY      4.3     3.4    -      -       -      +
    599C  HIS*     1.3    87.8    -      -       +      +
    601C  ARG*     1.3    63.7    +      -       -      +
    602C  GLY*     3.3     3.6    +      -       -      -
    708C  TYR*     3.8     2.8    -      -       -      +
    709C  ASN*     3.4    15.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 601 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    357C  GLU*     3.2    34.2    +      -       -      -
    532C  VAL*     3.0     8.7    -      -       +      +
    533C  ALA*     3.5    16.6    -      -       -      +
    590C  ALA*     4.2     0.7    -      -       -      -
    591C  SER*     2.8    33.6    +      -       -      +
    593C  HIS*     2.9    26.5    +      -       +      +
    594C  SER      3.6    14.4    -      -       -      -
    595C  ASN*     3.7    18.3    -      -       -      +
    600C  PRO*     1.3    69.5    -      -       -      +
    602C  GLY*     1.3    58.7    +      -       -      +
    709C  ASN      3.3     8.7    -      -       -      +
    710C  PHE*     2.5    53.9    +      -       +      +
    711C  PHE*     4.7     3.4    -      -       -      +
    712C  ASP*     5.5     2.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 602 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    532C  VAL*     4.0     3.4    -      -       -      -
    588C  TYR*     4.4     4.9    -      -       -      -
    589C  LEU      3.3    11.7    -      -       -      -
    590C  ALA*     3.9     6.3    -      -       -      -
    600C  PRO      3.3     2.2    +      -       -      -
    601C  ARG*     1.3    75.7    -      -       -      +
    603C  TYR*     1.3    65.9    +      -       -      -
    708C  TYR*     2.8    41.2    +      -       -      +
    710C  PHE*     3.3    12.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 603 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    359C  LEU*     3.2    36.9    -      -       +      +
    483C  GLY*     2.3    36.9    +      -       -      -
    485C  ILE*     5.0     1.8    -      -       +      -
    530C  LEU*     4.2    25.0    -      -       +      +
    532C  VAL*     4.6     7.1    -      -       +      +
    588C  TYR*     2.7    23.2    -      -       -      +
    589C  LEU*     2.9    19.9    +      -       -      +
    602C  GLY*     1.3    80.8    -      -       -      -
    604C  ARG*     1.3    55.9    +      -       -      +
    605C  ILE*     4.8     3.6    -      -       -      +
    705C  LEU*     3.2    40.2    -      -       +      -
    706C  ARG      3.2     5.4    -      -       -      -
    707C  PRO*     3.6    15.5    -      -       +      +
    710C  PHE*     3.5    33.4    -      +       -      -
    711C  PHE*     4.0     4.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 604 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    585C  ARG      2.6    34.1    +      -       -      -
    586C  TYR*     3.4    45.8    +      -       -      +
    587C  LEU      3.2    10.5    +      -       -      +
    588C  TYR*     3.0    17.5    -      -       +      -
    603C  TYR*     1.3    75.4    -      -       -      +
    605C  ILE*     1.3    62.6    +      -       -      +
    606C  GLN*     4.7    29.3    -      -       -      +
    704C  PHE      3.3     4.2    -      -       -      +
    705C  LEU*     3.4     4.3    -      -       -      +
    706C  ARG*     2.9    77.3    +      -       +      +
    707C  PRO      5.4     0.4    -      -       -      -
    708C  TYR*     4.4    10.6    -      -       +      +
    683D  LEU      5.5     0.2    +      -       -      -
    687D  HIS*     5.7     2.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 605 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    528C  VAL*     5.6     2.0    -      -       +      -
    530C  LEU*     5.0     6.3    -      -       +      -
    585C  ARG      5.7     0.2    -      -       -      +
    587C  LEU*     2.9    22.2    +      -       +      +
    588C  TYR*     5.3     1.8    -      -       -      -
    589C  LEU*     4.8    17.3    -      -       +      -
    603C  TYR      4.8     4.7    -      -       -      +
    604C  ARG*     1.3    75.6    +      -       -      +
    606C  GLN*     1.3    62.5    +      -       -      +
    607C  MET*     3.4    17.0    +      -       +      +
    632C  LEU*     4.5    19.8    -      -       +      +
    634C  VAL*     5.9     0.4    -      -       +      -
    676C  ALA*     3.7    30.1    -      -       +      -
    678C  VAL*     4.1    21.8    -      -       +      -
    703C  PHE*     4.7     3.8    -      -       +      -
    704C  PHE      3.5     6.3    -      -       -      +
    705C  LEU*     3.7    21.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 606 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    604C  ARG*     3.7    25.1    +      -       -      +
    605C  ILE*     1.3    72.5    -      -       -      +
    607C  MET*     1.3    66.6    +      -       -      +
    608C  LEU*     4.3     8.3    -      -       +      -
    703C  PHE*     3.1     7.2    -      -       -      +
    704C  PHE*     2.8    47.9    +      -       +      +
    706C  ARG*     3.2    32.9    +      -       -      +
    610D  PHE*     3.1    37.5    -      -       +      -
    698D  GLY*     3.5    26.1    +      -       -      +
    699D  ASN*     5.5     1.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 607 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    583C  THR*     6.0     3.4    -      -       -      -
    605C  ILE*     3.4    14.8    +      -       +      +
    606C  GLN*     1.3    79.3    -      -       -      +
    608C  LEU*     1.3    68.1    +      -       -      +
    609C  SER*     3.3    21.4    +      -       -      +
    631C  GLN*     3.5    46.2    -      -       +      +
    632C  LEU*     4.2    11.2    -      -       -      -
    678C  VAL*     3.8    19.7    -      -       +      -
    679C  THR      3.3    26.5    -      -       -      +
    702C  GLY      5.5     0.4    -      -       -      +
    703C  PHE*     4.1     2.7    -      -       +      -
    610D  PHE*     4.4    10.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 608 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    488C  ARG*     3.6    30.5    -      -       +      +
    606C  GLN*     4.3    10.3    -      -       +      -
    607C  MET*     1.3    83.6    -      -       -      +
    609C  SER*     1.3    63.0    +      -       -      +
    610C  PHE*     5.0     4.3    -      -       +      -
    701C  VAL*     3.3    11.4    -      -       +      +
    702C  GLY      3.2    29.8    +      -       -      +
    703C  PHE*     4.0    17.5    -      -       -      +
    704C  PHE*     3.1    42.6    -      -       +      -
    610D  PHE*     4.4    15.7    -      -       +      -
    698D  GLY      5.9     0.4    -      -       -      +
----------------------------------------------------------
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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