Contacts of the strand formed by residues 346 - 354 (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 GLY 346 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    341D  LEU*     3.7     3.4    -      -       -      -
    342D  GLY*     2.8    41.3    +      -       -      -
    344D  PHE      3.4     2.2    -      -       -      -
    345D  SER*     1.3    82.1    +      -       -      +
    347D  PRO*     1.3    74.0    -      -       -      +
    348D  ARG*     3.7     4.7    +      -       -      +
    364D  SER*     5.5     0.2    -      -       -      -
    365D  LEU      4.8     0.7    -      -       -      +
    391D  MET*     3.6    12.6    -      -       -      -
    392D  GLY      3.9     3.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 347 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    340D  GLY      3.6    10.3    -      -       -      +
    341D  LEU*     3.3    16.1    -      -       +      -
    346D  GLY*     1.3    83.7    -      -       -      +
    348D  ARG*     1.3    57.6    +      -       -      +
    364D  SER*     3.5     0.3    -      -       -      -
    365D  LEU*     2.8    46.8    +      -       +      -
    391D  MET*     4.6     2.9    -      -       +      +
    429D  PHE*     5.7     1.8    -      -       +      -
    464D  SER*     4.0     8.3    -      -       -      +
    466D  SER*     5.3     0.2    -      -       -      +
    475D  TRP*     3.5    43.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 348 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60D  PHE      5.2     1.8    +      -       -      -
     62D  ASP*     2.7    28.5    +      -       -      -
    100D  GLU*     4.7     6.7    +      -       -      -
    101D  LEU*     4.2    24.9    +      -       -      +
    103D  LEU*     3.9    29.4    -      -       -      +
    339D  PHE*     3.5     1.0    -      -       -      +
    340D  GLY*     3.2    38.5    +      -       -      +
    341D  LEU      3.8     6.9    +      -       -      +
    342D  GLY*     3.6    27.2    -      -       -      +
    345D  SER*     5.0     5.0    +      -       -      -
    346D  GLY      4.2     2.5    -      -       -      +
    347D  PRO*     1.3    77.5    -      -       -      +
    349D  ILE*     1.3    69.8    +      -       -      +
    350D  PHE*     3.6    27.1    -      -       +      -
    362D  GLU*     5.6     0.2    -      -       -      -
    363D  ILE      3.3     6.5    -      -       -      +
    364D  SER*     3.5    20.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 349 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    337D  PHE*     4.0    18.4    -      -       +      -
    338D  SER      3.3     4.3    -      -       -      +
    339D  PHE*     4.3    14.4    -      -       +      -
    348D  ARG*     1.3    80.9    -      -       -      +
    350D  PHE*     1.3    68.2    +      -       -      +
    352D  VAL*     3.3    29.3    -      -       +      +
    362D  GLU*     3.4     4.0    -      -       -      +
    363D  ILE*     2.7    44.7    +      -       +      +
    462D  VAL*     4.8     8.3    -      -       +      -
    477D  THR*     3.5    43.1    -      -       +      +
    479D  PHE*     3.7    14.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 350 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60D  PHE*     3.5    57.9    -      +       +      -
    103D  LEU*     3.6    32.8    -      -       +      -
    337D  PHE*     3.5     1.6    -      -       -      +
    338D  SER*     2.7    37.9    +      -       -      +
    339D  PHE      5.9     1.8    -      -       -      -
    348D  ARG*     3.6    34.3    -      -       +      -
    349D  ILE*     1.3    78.0    -      -       -      +
    351D  ASP*     1.3    69.7    +      -       -      +
    352D  VAL*     3.3     4.1    +      -       -      -
    361D  TYR*     3.4    21.3    -      +       -      +
    362D  GLU*     3.5    37.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 351 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60D  PHE*     4.1    17.0    -      -       +      -
    113D  LEU*     3.9    12.5    -      -       +      +
    329D  ARG*     3.1    25.9    +      -       -      +
    336D  THR      3.1    11.4    -      -       -      +
    337D  PHE*     3.5     4.2    -      -       -      -
    350D  PHE*     1.3    74.6    -      -       -      +
    352D  VAL*     1.3    62.8    +      -       -      +
    353D  ARG*     2.8    42.7    +      -       -      +
    358D  ARG*     3.2    26.1    +      -       -      +
    360D  VAL      3.5     6.4    +      -       -      -
    361D  TYR*     3.0    15.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 352 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    335D  TRP*     3.7    23.8    -      -       +      -
    336D  THR      3.2     7.4    -      -       -      +
    337D  PHE*     3.9     4.3    -      -       +      -
    349D  ILE*     3.3    33.7    -      -       +      -
    350D  PHE      4.2     2.2    -      -       -      +
    351D  ASP*     1.3    71.5    -      -       -      +
    353D  ARG*     1.3    61.1    +      -       -      +
    358D  ARG*     3.2     4.7    -      -       -      +
    359D  LEU*     2.8    27.5    +      -       +      -
    360D  VAL*     3.1    32.0    +      -       +      +
    363D  ILE*     5.5     2.5    -      -       +      -
    479D  PHE*     3.6    26.5    -      -       +      -
    485D  ILE*     4.2     7.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 353 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113D  LEU*     4.1    25.3    +      -       -      +
    329D  ARG*     4.5     6.7    -      -       -      +
    334D  LEU      3.7     0.3    -      -       -      +
    335D  TRP*     3.4    10.8    -      -       -      -
    336D  THR*     2.6    51.4    +      -       +      +
    351D  ASP*     2.8    40.7    +      -       -      +
    352D  VAL*     1.3    78.8    -      -       -      +
    354D  PHE*     1.3    58.8    +      -       -      +
    355D  GLN      4.0     0.4    +      -       -      -
    356D  GLY*     3.8    27.3    +      -       -      +
    357D  GLU      3.0     9.9    -      -       -      +
    358D  ARG*     3.7    29.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 354 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    334D  LEU*     3.3    21.8    -      -       +      -
    335D  TRP*     3.4    47.1    -      +       +      -
    353D  ARG*     1.3    70.9    -      -       -      +
    355D  GLN*     1.3    96.9    +      -       -      +
    356D  GLY      3.0     0.4    -      -       -      -
    357D  GLU*     2.7    28.4    +      -       -      +
    359D  LEU*     3.8    15.3    -      -       +      +
    480D  HIS      4.1     1.6    -      -       -      -
    481D  PRO      3.8    19.3    -      -       -      -
    483D  GLY*     3.8    19.3    -      -       -      -
    710D  PHE*     6.2     0.2    -      -       +      -
    711D  PHE*     3.5    34.6    -      +       -      -
    715D  PRO*     3.7    14.8    -      -       +      -
----------------------------------------------------------
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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