Contacts of the strand formed by residues 282 - 291 (chain C) in PDB entry 6C3P


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 GLU 282 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    326B  TYR*     4.2     6.4    +      -       -      -
     33C  ALA      4.9     0.2    -      -       -      +
     34C  ARG*     4.3     6.1    +      -       -      -
     35C  PHE*     3.2    42.8    +      -       -      +
     36C  VAL      3.5     0.5    +      -       -      +
    219C  VAL*     3.2     4.0    -      -       -      +
    220C  VAL*     2.5    48.8    +      -       +      +
    233C  LEU*     5.7     0.5    -      -       -      +
    281C  LEU*     1.3    82.7    -      -       -      +
    283C  ILE*     1.3    61.9    +      -       -      +
    284C  ILE*     3.3    15.2    -      -       +      +
    303C  SER*     3.1    27.5    +      -       -      -
    304C  TYR      3.2    21.1    -      -       -      +
    305C  LEU*     4.2     7.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 283 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    198C  PHE*     4.1    29.2    -      -       +      -
    217C  MET*     4.5     6.5    -      -       +      -
    218C  GLN      3.3    21.8    -      -       -      +
    219C  VAL*     3.8    15.7    -      -       +      +
    238C  ILE*     4.2    12.1    -      -       +      -
    267C  LEU*     3.7    30.7    -      -       +      -
    281C  LEU*     5.2     3.1    -      -       +      -
    282C  GLU*     1.3    78.9    -      -       -      +
    284C  ILE*     1.3    65.2    +      -       -      +
    285C  VAL*     3.6    11.2    +      -       +      +
    303C  SER*     3.8     0.9    -      -       -      -
    304C  TYR*     2.9    32.3    +      -       +      +
    309C  ILE*     4.0    22.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 284 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    250B  PHE*     3.8    21.5    -      -       +      -
     35C  PHE*     3.6    18.6    -      -       +      -
     36C  VAL*     4.6     8.3    -      -       +      +
    216C  HIS      3.2     5.2    -      -       -      +
    217C  MET*     3.3     0.5    -      -       -      -
    218C  GLN*     2.2    66.1    +      -       +      +
    220C  VAL*     3.6    22.2    -      -       +      -
    282C  GLU*     3.3    37.7    -      -       +      +
    283C  ILE*     1.3    66.4    -      -       -      +
    285C  VAL*     1.3    63.2    +      -       -      +
    286C  ILE*     3.6    18.2    -      -       +      -
    301C  ARG*     5.3     1.8    -      -       +      -
    302C  THR      4.0     5.4    -      -       -      +
    303C  SER*     3.8     6.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 285 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    183C  PHE*     4.7    11.5    -      -       +      -
    198C  PHE*     5.9     1.3    -      -       +      -
    200C  LEU*     4.2    27.8    -      -       +      -
    215C  ILE*     5.0    10.3    -      -       +      -
    216C  HIS      3.9     1.8    -      -       -      -
    217C  MET*     4.4    21.5    -      -       +      +
    257C  ILE*     6.0     1.3    -      -       +      -
    283C  ILE*     3.8    15.7    -      -       +      +
    284C  ILE*     1.3    76.5    -      -       -      +
    286C  ILE*     1.3    69.4    +      -       -      +
    300C  ALA      4.0     0.2    -      -       -      +
    301C  ARG*     3.6     6.9    -      -       -      +
    302C  THR*     2.8    53.0    +      -       +      +
    304C  TYR*     4.3     7.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 286 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    250B  PHE*     3.5    27.8    -      -       +      -
    214C  THR      3.4     0.2    -      -       -      +
    215C  ILE*     3.3    11.1    -      -       -      +
    216C  HIS*     3.0    57.8    +      -       +      +
    218C  GLN*     4.0     8.1    -      -       -      +
    284C  ILE*     3.6    31.2    -      -       +      +
    285C  VAL*     1.3    77.1    -      -       -      +
    287C  LEU*     1.3    62.7    +      -       -      +
    288C  GLU*     3.3    25.1    -      -       +      +
    299C  GLN*     3.3    30.3    -      -       -      +
    300C  ALA      3.9     2.5    -      -       -      -
    301C  ARG*     4.3     2.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 287 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    181C  LEU*     3.6    37.3    -      -       +      +
    183C  PHE*     3.9    30.1    -      -       +      -
    202C  VAL*     4.6     8.7    -      -       +      -
    210C  ILE*     6.0     4.7    -      -       +      -
    213C  ALA*     4.2    24.2    -      -       +      -
    214C  THR      3.4     6.7    -      -       -      +
    215C  ILE*     3.6    24.2    -      -       +      -
    249C  ILE*     4.7     5.4    -      -       +      -
    251C  LEU*     5.3     3.8    -      -       +      -
    286C  ILE*     1.3    74.4    -      -       -      +
    288C  GLU*     1.3    63.9    +      -       -      +
    298C  THR      3.9     0.7    -      -       -      +
    299C  GLN*     3.2     7.3    -      -       -      +
    300C  ALA*     3.0    34.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 288 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    210B  ILE      5.0     0.2    -      -       -      +
    211B  ILE*     3.5    21.2    -      -       +      -
    212B  SER*     3.1    33.8    +      -       -      -
    249B  ILE      5.5     2.1    -      -       -      +
    250B  PHE*     5.2     1.6    -      -       -      -
    212C  SER      3.1     5.2    -      -       -      +
    213C  ALA*     4.3     1.3    -      -       -      -
    214C  THR*     2.8    42.8    +      -       -      +
    216C  HIS*     4.5    12.4    -      -       -      +
    286C  ILE*     3.3    18.3    -      -       +      +
    287C  LEU*     1.3    83.1    -      -       -      +
    289C  GLY*     1.3    58.2    +      -       -      +
    297C  THR*     5.0     0.9    -      -       +      -
    298C  THR      3.5     3.6    -      -       -      -
    299C  GLN*     3.2    32.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 289 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    210C  ILE*     3.4    19.3    -      -       -      +
    211C  ILE      3.1    13.0    -      -       -      -
    212C  SER*     4.0     3.6    -      -       -      -
    287C  LEU*     5.6     0.4    -      -       -      +
    288C  GLU*     1.3    75.3    -      -       -      +
    290C  VAL*     1.3    65.3    +      -       -      -
    297C  THR*     3.1     9.0    -      -       -      +
    298C  THR      3.0    30.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 290 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    210C  ILE*     3.2     6.0    -      -       -      +
    211C  ILE*     2.7    55.9    +      -       +      +
    212C  SER*     5.4     3.8    -      -       -      -
    289C  GLY*     1.3    74.4    -      -       -      -
    291C  VAL*     1.3    76.8    +      -       -      +
    295C  GLY*     3.3    28.5    -      -       -      +
    296C  ILE      3.5     3.4    -      -       -      +
    297C  THR*     3.5    20.4    -      -       +      +
    297D  THR*     4.2    24.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 291 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    174C  ALA*     5.3     5.8    -      -       +      -
    177C  ARG*     4.6    26.2    -      -       +      +
    208C  SER*     5.9     1.8    -      -       -      +
    209C  MET      4.4     1.1    -      -       -      -
    210C  ILE*     4.2     6.3    -      -       +      -
    211C  ILE*     4.1     0.3    -      -       -      +
    289C  GLY      4.0     0.2    +      -       -      -
    290C  VAL*     1.3    82.0    -      -       -      +
    292C  GLU*     1.3    67.6    +      -       -      +
    293C  THR*     3.8    16.8    -      -       +      +
    294C  THR*     2.7    45.6    -      -       +      +
    295C  GLY*     4.0     0.7    -      -       -      -
    296C  ILE*     3.0    14.3    +      -       +      +
    298C  THR*     4.0    28.0    -      -       +      -
     61D  THR*     6.0     4.7    -      -       +      -
    297D  THR      5.2     0.3    -      -       -      +
----------------------------------------------------------
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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