Contacts of the strand formed by residues 599 - 607 (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 HIS 599 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    504C  THR*     5.0    10.1    -      -       +      +
    505C  GLY*     6.4     0.4    -      -       -      -
    508C  GLY      4.8     1.6    -      -       -      -
    509C  ASN*     3.4    32.9    +      -       +      -
    510C  GLN*     2.8    38.2    +      -       -      +
    566D  ARG*     5.6     4.0    +      -       -      -
    594D  SER*     3.0     5.1    +      -       -      -
    595D  ASN*     2.6    42.3    +      -       -      +
    597D  TRP*     3.3    25.3    +      -       +      -
    598D  GLY*     1.3    80.2    +      -       -      +
    600D  PRO*     1.3    74.1    -      -       +      +
    709D  ASN*     3.7    23.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with PRO 600 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    540D  TRP*     4.3    22.2    -      -       +      +
    588D  TYR*     4.7    13.7    -      -       -      +
    590D  ALA*     4.2     8.6    -      -       +      +
    591D  SER      3.6    19.1    -      -       -      +
    592D  ASN      5.1     3.4    -      -       -      +
    593D  HIS      3.5     9.2    -      -       -      +
    594D  SER*     4.0     5.1    -      -       -      +
    598D  GLY      4.7     1.1    -      -       -      +
    599D  HIS*     1.3    90.1    -      -       +      +
    601D  ARG*     1.3    60.5    +      -       -      +
    602D  GLY*     3.1     8.7    +      -       -      -
    708D  TYR      3.8     0.9    -      -       -      +
    709D  ASN*     3.8    14.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 601 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    357D  GLU*     2.8    31.9    +      -       -      -
    532D  VAL*     3.2    11.8    -      -       -      +
    533D  ALA*     3.4    24.4    -      -       +      +
    591D  SER*     2.9    25.8    +      -       -      +
    593D  HIS*     3.1    22.8    +      -       -      +
    594D  SER      4.3     9.2    -      -       -      -
    595D  ASN*     3.6    25.1    -      -       +      +
    600D  PRO*     1.3    68.2    -      -       -      +
    602D  GLY*     1.3    58.5    +      -       -      +
    709D  ASN      3.3     9.9    -      -       -      +
    710D  PHE*     2.9    48.9    +      -       +      +
    711D  PHE*     5.4     0.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 602 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    532D  VAL*     3.8     1.6    -      -       -      -
    588D  TYR*     4.1     5.4    -      -       -      -
    589D  LEU      3.1    13.0    -      -       -      -
    590D  ALA*     3.3    10.3    -      -       -      -
    600D  PRO      3.1     8.3    +      -       -      -
    601D  ARG*     1.3    75.3    -      -       -      +
    603D  TYR*     1.3    64.3    +      -       -      -
    604D  ARG      4.2     0.2    -      -       -      -
    708D  TYR*     2.9    33.7    +      -       -      +
    710D  PHE*     3.5    10.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 603 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    359D  LEU*     3.7    25.2    -      -       +      +
    483D  GLY*     2.5    28.3    +      -       -      -
    485D  ILE*     5.2     1.1    -      -       +      -
    530D  LEU*     4.5    18.2    -      -       +      +
    532D  VAL*     4.0    17.7    -      -       +      +
    588D  TYR*     3.1    13.8    -      -       -      +
    589D  LEU*     2.7    21.0    +      -       -      +
    602D  GLY*     1.3    73.0    -      -       -      -
    604D  ARG*     1.3    62.4    +      -       -      +
    605D  ILE*     3.9     4.9    +      -       -      +
    705D  LEU*     3.4    31.9    -      -       +      -
    706D  ARG      3.3    13.9    -      -       -      -
    707D  PRO*     3.3    20.3    -      -       +      +
    710D  PHE*     3.4    45.8    -      +       -      -
    711D  PHE*     3.6    14.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 604 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    610C  PHE*     6.2     2.4    -      -       -      +
    682C  PHE*     6.4     0.4    -      -       -      +
    683C  LEU      4.8     3.6    +      -       -      -
    699C  ASN*     4.8     0.8    +      -       -      -
    585D  ARG*     2.8    27.1    +      -       -      +
    586D  TYR*     3.3    51.0    +      -       +      -
    587D  LEU      3.4    13.0    -      -       -      +
    588D  TYR*     3.3    12.7    -      -       +      +
    602D  GLY      4.2     0.4    -      -       -      -
    603D  TYR*     1.3    73.4    -      -       -      +
    605D  ILE*     1.3    66.8    +      -       -      +
    606D  GLN*     3.9    26.3    +      -       -      +
    704D  PHE      3.2     5.2    -      -       -      +
    705D  LEU*     3.4     4.2    -      -       -      +
    706D  ARG*     2.6    80.9    +      -       +      +
    707D  PRO      5.5     0.2    -      -       -      +
    708D  TYR*     4.4    12.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 605 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    528D  VAL*     5.6     1.1    -      -       +      -
    530D  LEU*     4.9     6.3    -      -       +      -
    587D  LEU*     2.9    28.0    +      -       +      +
    588D  TYR*     5.2     1.8    -      -       -      -
    589D  LEU*     4.7    16.6    -      -       +      -
    603D  TYR      4.5     7.0    -      -       -      +
    604D  ARG*     1.3    78.6    +      -       -      +
    606D  GLN*     1.3    62.8    +      -       -      +
    607D  MET*     4.0    25.8    +      -       +      +
    632D  LEU*     4.5    20.8    -      -       +      +
    634D  VAL*     5.6     0.9    -      -       +      -
    676D  ALA*     3.6    30.3    -      -       +      -
    678D  VAL*     4.4    14.8    -      -       +      -
    703D  PHE*     4.9     5.4    -      -       +      -
    704D  PHE      3.4     5.6    -      -       -      +
    705D  LEU*     4.3    13.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 606 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    610C  PHE*     3.7    38.0    -      -       +      -
    682C  PHE*     6.3     0.8    -      -       -      +
    698C  GLY      3.1    25.3    +      -       -      +
    699C  ASN*     4.6     3.2    +      -       -      -
    604D  ARG*     3.9    28.0    -      -       -      +
    605D  ILE*     1.3    74.9    -      -       -      +
    607D  MET*     1.3    63.9    +      -       -      +
    608D  LEU*     4.8     3.6    -      -       +      -
    703D  PHE*     3.0     5.4    -      -       -      +
    704D  PHE*     2.6    53.6    +      -       +      -
    706D  ARG*     3.3    28.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 607 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    610C  PHE*     3.5    18.4    -      -       -      -
    583D  THR*     4.4    15.3    -      -       +      +
    587D  LEU*     5.9     1.8    -      -       +      -
    605D  ILE*     4.0    15.4    +      -       +      +
    606D  GLN*     1.3    77.8    -      -       -      +
    608D  LEU*     1.3    74.1    +      -       -      +
    609D  SER*     3.8    11.2    -      -       -      +
    631D  GLN*     3.6    48.0    -      -       +      +
    632D  LEU*     4.1    22.0    -      -       +      -
    678D  VAL*     4.0    20.2    -      -       +      -
    679D  THR      5.3     2.0    -      -       -      +
    702D  GLY      3.9     6.5    -      -       -      +
    703D  PHE*     4.3     0.7    -      -       +      -
----------------------------------------------------------
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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