Contacts of the strand formed by residues 701 - 708 (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 VAL 701 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    488D  ARG*     3.8     4.4    -      -       -      -
    489D  PHE*     3.1    54.8    +      -       +      +
    608D  LEU*     3.1    25.4    -      -       -      +
    610D  PHE*     3.7    30.7    -      -       +      -
    680D  ALA*     4.3     1.6    -      -       +      -
    681D  GLY      3.8    17.5    -      -       -      +
    682D  PHE*     3.8    23.1    -      -       +      -
    699D  ASN      3.3     8.2    +      -       -      +
    700D  GLY*     1.3    79.2    -      -       -      +
    702D  GLY*     1.3    57.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 702 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    487D  ILE*     3.0    15.0    -      -       -      -
    488D  ARG*     4.3     0.9    -      -       -      -
    489D  PHE*     5.5     0.2    -      -       -      -
    526D  PHE*     5.6     1.8    -      -       -      -
    607D  MET*     3.9     2.8    -      -       -      +
    608D  LEU*     3.2    29.5    +      -       -      +
    609D  SER*     5.6     0.2    -      -       -      -
    678D  VAL*     4.7     0.5    -      -       -      +
    680D  ALA*     4.0    17.2    -      -       -      +
    701D  VAL*     1.3    77.0    -      -       -      +
    703D  PHE*     1.3    75.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 703 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    363D  ILE*     4.8     2.2    -      -       +      -
    485D  ILE      4.0     0.2    -      -       -      +
    486D  GLU*     3.6     3.8    -      -       -      +
    487D  ILE*     2.9    63.5    +      -       +      +
    488D  ARG*     4.8     0.2    -      -       -      +
    526D  PHE*     3.8    36.6    -      +       +      -
    528D  VAL*     4.1    18.6    -      -       +      -
    605D  ILE*     4.9     3.4    -      -       +      -
    606D  GLN      3.0    15.5    -      -       -      +
    607D  MET*     4.0    11.9    -      -       +      +
    608D  LEU*     4.2     8.7    -      -       -      +
    678D  VAL*     3.6    31.2    -      -       +      -
    680D  ALA*     5.4     0.4    -      -       +      -
    702D  GLY*     1.3    81.9    -      -       -      +
    704D  PHE*     1.3    68.8    +      -       -      +
    705D  LEU*     3.9    27.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 704 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    697C  VAL*     4.0    27.8    -      -       +      -
    698C  GLY*     3.8    20.4    -      -       -      -
    480D  HIS*     4.1     2.0    -      +       -      -
    484D  ALA*     5.0     1.6    -      -       +      -
    485D  ILE      3.4     7.0    -      -       -      -
    486D  GLU*     3.2    48.2    -      -       +      -
    488D  ARG*     4.4     2.9    -      -       -      -
    604D  ARG      3.2     4.6    -      -       -      +
    605D  ILE*     3.4     1.6    -      -       -      -
    606D  GLN*     2.6    48.3    +      -       +      +
    608D  LEU*     3.9    31.2    -      -       +      -
    703D  PHE*     1.3    80.4    -      -       -      +
    705D  LEU*     1.3    70.7    +      -       -      +
    706D  ARG*     3.7    23.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 705 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    360D  VAL*     4.4     7.6    -      -       +      -
    363D  ILE*     3.3    34.5    -      -       +      -
    484D  ALA*     3.1     6.3    -      -       -      -
    485D  ILE*     2.8    58.5    +      -       +      +
    487D  ILE*     5.3     0.2    -      -       +      -
    528D  VAL*     4.1    14.4    -      -       +      -
    530D  LEU*     4.4    11.2    -      -       +      -
    603D  TYR*     3.4    18.4    -      -       +      -
    604D  ARG      3.4     4.0    -      -       -      +
    605D  ILE*     4.3    18.4    -      -       +      -
    678D  VAL*     6.4     0.2    -      -       +      -
    703D  PHE*     3.9    22.2    -      -       +      -
    704D  PHE*     1.3    84.8    -      -       -      +
    706D  ARG*     1.3    59.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 706 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    687C  HIS*     4.8     4.0    +      -       +      -
    697C  VAL*     3.1    21.8    +      -       -      -
    698C  GLY      3.5     1.6    +      -       -      -
    699C  ASN*     2.8    29.3    +      -       -      +
   1747C   CU      3.1    25.5    -      -       -      -
    484D  ALA*     4.2     8.5    -      -       +      -
    586D  TYR*     4.5     0.6    +      -       -      -
    603D  TYR*     3.3     5.3    -      -       -      -
    604D  ARG*     2.6    78.0    +      -       +      +
    606D  GLN*     3.3    30.9    +      -       +      -
    704D  PHE*     3.7    22.0    -      -       +      -
    705D  LEU*     1.3    76.3    -      -       -      +
    707D  PRO*     1.3    72.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with PRO 707 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    687C  HIS*     3.5    20.3    +      -       +      -
    689C  GLU*     3.4    32.1    -      -       +      +
    482D  SER*     3.8    16.4    -      -       -      +
    483D  GLY      4.1     6.5    -      -       -      +
    484D  ALA*     4.2     8.7    -      -       +      +
    602D  GLY      3.9     1.1    -      -       -      +
    603D  TYR*     3.3    36.8    -      -       +      +
    604D  ARG*     5.5     0.2    -      -       -      +
    706D  ARG*     1.3    88.7    -      -       +      +
    708D  TYR*     1.3    59.6    +      -       -      +
    710D  PHE*     3.8     1.3    -      -       +      -
    711D  PHE*     3.6    12.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 708 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    509C  ASN*     2.9    22.1    +      -       -      -
    685C  ILE*     3.0    31.1    -      -       -      +
    687C  HIS*     3.6    20.0    -      +       -      -
    689C  GLU*     3.7     1.3    -      -       -      -
    542D  GLU*     2.5    37.1    +      -       -      -
    586D  TYR*     3.4    28.9    -      +       -      -
    588D  TYR*     3.9    28.3    -      +       +      -
    600D  PRO      3.8     1.1    -      -       -      +
    602D  GLY      2.9    32.0    +      -       -      +
    604D  ARG*     4.4    15.5    -      -       +      +
    706D  ARG      3.5     0.2    +      -       -      -
    707D  PRO*     1.3    74.0    -      -       -      +
    709D  ASN*     1.3    90.9    +      -       -      +
    710D  PHE      3.0     2.9    +      -       -      -
----------------------------------------------------------
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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