Contacts of the strand formed by residues 630 - 636 (chain D) in PDB entry 2C10


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 TYR 630 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    525D  HIS*     6.0     0.9    -      -       -      +
    576D  ALA*     3.8    22.9    -      -       +      -
    577D  PHE      3.3    13.5    -      -       -      +
    578D  LEU*     3.6    20.0    -      -       +      -
    579D  VAL*     3.8     6.2    -      -       -      +
    626D  SER      3.6    20.4    -      -       -      -
    627D  TRP*     3.5     4.4    -      -       -      +
    628D  GLU      3.2     0.6    -      -       -      -
    629D  ARG*     1.3   106.7    +      -       +      +
    631D  GLN*     1.3    56.3    +      -       -      +
    632D  LEU      4.0    12.8    -      -       -      +
    633D  ALA*     4.9     0.4    -      -       +      -
    660D  PHE*     4.1    22.2    -      +       +      -
    661D  SER*     4.4    15.0    +      -       -      -
    664D  ILE*     3.6    33.7    -      -       +      +
    677D  TRP      5.8     0.4    -      -       -      +
    679D  THR*     2.6    34.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 631 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    577D  PHE      2.7    11.5    +      -       -      +
    578D  LEU      3.0    21.3    +      -       -      +
    579D  VAL*     3.8    16.3    -      -       +      +
    580D  GLY      4.0     3.4    -      -       -      +
    581D  SER*     2.9    30.1    +      -       -      +
    583D  THR*     3.5    23.2    +      -       +      +
    607D  MET*     3.6    31.4    -      -       +      +
    609D  SER*     6.2     1.9    -      -       -      -
    611D  ALA*     5.8     4.0    -      -       +      -
    630D  TYR*     1.3    73.3    -      -       -      +
    632D  LEU*     1.3    59.1    +      -       +      +
    677D  TRP      4.4     0.2    -      -       -      -
    678D  VAL*     3.6     1.7    -      -       -      -
    679D  THR*     3.0    30.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 632 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    575D  ALA      3.5     2.3    -      -       -      +
    576D  ALA*     3.6     0.2    -      -       -      -
    577D  PHE*     2.8    51.7    +      -       +      +
    583D  THR*     5.8     2.0    -      -       -      -
    587D  LEU*     3.2    35.0    -      -       +      -
    605D  ILE*     4.3    16.8    -      -       +      +
    607D  MET*     3.9    20.6    -      -       +      -
    630D  TYR*     3.3     6.4    -      -       -      +
    631D  GLN*     1.3    82.2    -      -       +      +
    633D  ALA*     1.3    67.7    -      -       -      +
    634D  VAL*     4.8     3.4    -      -       +      -
    676D  ALA*     4.3    14.8    -      -       +      -
    677D  TRP      3.2    15.3    -      -       -      +
    678D  VAL*     3.9    20.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 633 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    575D  ALA      3.3     7.4    -      -       -      +
    576D  ALA*     4.5     3.6    -      -       +      -
    630D  TYR*     4.9     3.1    -      -       +      -
    632D  LEU*     1.3    76.5    -      -       -      +
    634D  VAL*     1.3    64.2    +      -       -      +
    635D  THR*     4.1     1.3    -      -       +      -
    660D  PHE*     4.0    21.3    -      -       +      -
    664D  ILE*     3.9    31.2    -      -       +      -
    676D  ALA*     3.4     2.1    -      -       -      +
    677D  TRP*     2.7    42.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 634 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    539D  VAL*     3.8    24.7    -      -       +      -
    572D  GLU*     3.5    23.9    +      -       -      +
    575D  ALA*     3.4    26.8    +      -       +      +
    587D  LEU*     4.9     4.9    -      -       +      -
    589D  LEU*     4.0    20.9    -      -       +      -
    632D  LEU*     4.8     9.9    -      -       +      -
    633D  ALA*     1.3    78.8    -      -       -      +
    635D  THR*     1.3    64.6    +      -       -      +
    664D  ILE*     5.9     0.2    -      -       -      +
    669D  ILE*     3.7     6.1    -      -       +      +
    674D  LEU*     3.9    25.8    -      -       +      -
    675D  VAL      3.4    10.3    -      -       -      +
    676D  ALA*     4.3    10.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 635 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    572D  GLU*     3.4    14.8    -      -       -      +
    633D  ALA*     4.9     1.1    -      -       +      -
    634D  VAL*     1.3    79.3    -      -       -      +
    636D  GLN*     1.3    71.1    +      -       -      +
    641D  GLU*     4.6     2.5    +      -       -      -
    660D  PHE*     5.2     0.4    -      -       +      -
    663D  PHE*     3.9    27.0    -      -       +      +
    664D  ILE*     4.1    21.3    -      -       +      -
    669D  ILE*     4.2     0.9    -      -       -      -
    674D  LEU*     3.3    13.6    -      -       -      +
    675D  VAL*     2.9    31.5    +      -       -      +
    677D  TRP*     3.0    33.8    +      -       +      +
   1778D   CA      4.7     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 636 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    572D  GLU*     3.0    12.8    +      -       -      +
    635D  THR*     1.3    86.0    +      -       -      +
    637D  ARG*     1.3    67.2    +      -       -      +
    638D  LYS*     3.4    15.9    +      -       +      +
    641D  GLU*     3.7    11.6    -      -       -      +
    667D  GLU*     3.9    24.1    -      -       -      +
    668D  THR*     2.6    45.7    +      -       -      +
    669D  ILE*     4.4     1.5    -      -       +      +
    672D  LYS*     3.6    31.0    -      -       +      +
    673D  ASP      3.5     8.3    -      -       -      +
    674D  LEU*     4.5     0.9    -      -       -      -
    675D  VAL*     4.0     0.6    -      -       -      +
    677D  TRP*     5.8     0.2    -      -       -      -
----------------------------------------------------------
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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