Contacts of the strand formed by residues 536 - 548 (chain C) 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 GLU 536 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    532C  VAL      4.2     0.3    -      -       -      +
    533C  ALA      5.2     0.2    -      -       -      +
    534C  GLY*     4.2     5.1    -      -       -      +
    535C  LEU*     1.3    96.6    +      -       -      +
    537C  ASN*     1.3    71.2    +      -       -      +
    538C  TRP*     4.0    13.2    -      -       +      -
    591C  SER*     3.7    14.2    +      -       -      -
    592C  ASN*     4.2     5.7    +      -       +      -
    593C  HIS*     6.5     1.1    -      -       +      -
    671C  GLY*     3.4    30.2    -      -       -      +
    672C  LYS*     3.4     8.8    -      -       -      -
    673C  ASP      4.9     0.5    +      -       -      -
      1J  NAG      5.9     2.0    -      -       -      -
      2J  NAG      6.1     5.1    -      -       +      +
      3J  FUC      4.8    11.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 537 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    530C  LEU      3.6    15.0    -      -       -      +
    532C  VAL*     3.0    54.6    +      -       -      +
    534C  GLY      3.5     3.8    +      -       -      +
    535C  LEU      3.0    13.5    -      -       -      +
    536C  GLU*     1.3    88.2    +      -       -      +
    538C  TRP*     1.3    65.4    +      -       -      +
    589C  LEU*     4.5    11.7    -      -       +      +
    590C  ALA      2.7    18.0    +      -       -      +
    671C  GLY      3.5    14.4    +      -       -      -
    672C  LYS      3.0     8.3    +      -       -      +
    674C  LEU*     3.1    25.9    +      -       +      +
   1737C   CA      4.1     1.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with TRP 538 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    536C  GLU*     4.0    14.4    -      -       +      -
    537C  ASN*     1.3    76.5    -      -       -      +
    539C  VAL*     1.3    66.1    +      -       -      +
    540C  TRP*     4.0    11.6    +      +       -      +
    568C  LEU*     3.9    30.1    -      -       +      +
    569C  LEU      5.2     0.4    -      -       -      -
    588C  TYR      3.6     0.3    -      -       -      +
    589C  LEU*     3.0     8.5    -      -       -      +
    590C  ALA      2.6    40.3    +      -       -      +
    591C  SER      3.9     6.5    -      -       -      -
    592C  ASN*     3.4    52.5    -      -       +      -
    669C  ILE      4.1     4.3    -      -       -      -
    670C  ALA*     3.1    33.9    -      -       +      +
    671C  GLY*     2.9    35.1    -      -       -      +
    674C  LEU*     4.3     0.9    -      -       -      -
      1J  NAG      4.6     0.4    -      -       -      -
      3J  FUC      4.6    10.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 539 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    538C  TRP*     1.3    79.9    -      -       -      +
    540C  TRP*     1.3    62.6    +      -       -      +
    568C  LEU*     2.9    11.2    -      -       -      +
    569C  LEU*     2.8    67.5    +      -       +      +
    575C  ALA*     4.7     4.9    -      -       +      -
    587C  LEU*     3.5    20.4    -      -       +      -
    588C  TYR      3.5     3.1    -      -       -      +
    589C  LEU*     3.8    17.3    -      -       +      -
    634C  VAL*     4.3    10.1    -      -       +      -
    669C  ILE*     3.9    23.1    +      -       +      +
    674C  LEU*     4.2    13.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 540 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    538C  TRP*     4.2    10.8    -      +       +      +
    539C  VAL*     1.3    76.7    -      -       -      +
    541C  ALA*     1.3    59.9    -      -       -      +
    542C  GLU*     4.0     2.7    -      -       +      -
    566C  ARG*     4.0    29.8    -      -       +      -
    567C  LYS      3.6    10.1    -      -       -      -
    568C  LEU*     3.4    51.6    -      -       +      +
    586C  TYR      3.8     1.0    -      -       -      +
    587C  LEU*     2.9    23.3    -      -       -      +
    588C  TYR*     2.9    59.5    +      +       +      +
    590C  ALA*     3.6    20.5    -      -       +      +
    591C  SER      5.3     0.8    +      -       -      -
    600C  PRO*     4.5    18.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 541 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    540C  TRP*     1.3    75.9    -      -       -      +
    542C  GLU*     1.3    62.6    +      -       -      +
    543C  ASP*     5.2     0.3    -      -       -      +
    565C  THR*     3.3     4.7    +      -       -      +
    567C  LYS*     2.9    39.4    +      -       +      +
    569C  LEU*     4.2    19.7    -      -       +      -
    577C  PHE*     5.9     0.4    -      -       +      -
    584C  PRO*     3.5    30.5    -      -       +      -
    586C  TYR      3.6     3.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 542 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    540C  TRP*     4.7     0.2    -      -       +      -
    541C  ALA*     1.3    77.7    -      -       -      +
    543C  ASP*     1.3    65.0    +      -       -      +
    564C  VAL*     4.9     6.3    -      -       +      +
    565C  THR      2.9     8.3    -      -       -      +
    566C  ARG*     2.8    44.6    +      -       +      -
    584C  PRO*     4.0     0.7    -      -       -      +
    585C  ARG      3.8     1.9    +      -       -      -
    586C  TYR*     2.7    43.8    +      -       +      +
    588C  TYR*     2.3    42.3    +      -       +      +
    708C  TYR*     2.9    23.3    +      -       -      -
    509D  ASN*     4.7     0.7    -      -       -      +
    685D  ILE*     3.6    15.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 543 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    541C  ALA      5.2     0.4    -      -       -      +
    542C  GLU*     1.3    75.3    -      -       -      +
    544C  MET*     1.3    78.5    +      -       -      +
    564C  VAL*     4.3     3.1    -      -       -      -
    565C  THR*     2.6    50.8    +      -       -      +
    583C  THR      4.1     2.9    -      -       -      +
    584C  PRO*     3.7    11.0    -      -       +      +
    585C  ARG*     2.8    64.3    +      -       -      +
    683D  LEU*     4.6     7.9    -      -       -      -
    685D  ILE*     4.9     2.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with MET 544 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    543C  ASP*     1.3    96.8    +      -       -      +
    545C  VAL*     1.3    70.2    +      -       -      +
    546C  PHE*     4.0    12.8    -      -       +      -
    562C  LEU*     4.2    15.5    -      -       +      -
    563C  GLN      3.3    11.9    -      -       -      +
    564C  VAL*     4.4     2.2    -      -       -      +
    565C  THR*     4.2     2.8    +      -       -      +
    585C  ARG*     4.0     7.8    +      -       -      +
    519D  VAL*     5.6     1.1    -      -       +      -
    521D  THR*     4.0     5.6    -      -       +      -
    612D  GLY*     3.5    13.7    -      -       -      -
    613D  GLU*     3.0    67.4    -      -       +      +
    683D  LEU*     3.9    31.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 545 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    544C  MET*     1.3    87.2    -      -       -      +
    546C  PHE*     1.3    76.0    +      -       -      +
    547C  VAL*     4.4    10.5    -      -       +      -
    561C  ARG      3.7     0.9    -      -       -      +
    562C  LEU*     3.6     2.9    -      -       -      +
    563C  GLN*     2.9    45.5    +      -       +      +
    565C  THR*     3.7    21.1    -      -       +      -
    613D  GLU*     4.4    10.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 546 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    544C  MET*     4.0     9.0    -      -       +      -
    545C  VAL*     1.3    80.8    -      -       -      +
    547C  VAL*     1.3    60.4    +      -       -      +
    548C  PRO*     3.7     9.0    -      -       -      +
    560C  GLN*     3.9    20.1    -      -       +      +
    561C  ARG      3.8     0.4    -      -       -      -
    562C  LEU*     3.1    38.6    -      -       +      -
    371D  ILE*     4.2    12.6    -      -       +      -
    383D  ARG*     5.0     0.4    -      -       -      -
    521D  THR*     5.7     2.0    -      -       +      -
    613D  GLU*     3.0    34.0    +      -       +      -
    614D  PRO      3.3    12.8    -      -       -      -
    615D  LEU*     3.4    31.4    -      -       +      -
    616D  PRO*     3.1    33.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 547 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    545C  VAL*     4.4    14.6    -      -       +      -
    546C  PHE*     1.3    74.5    -      -       -      +
    548C  PRO*     1.3    70.8    -      -       +      +
    549C  MET*     3.2    20.2    -      -       +      +
    560C  GLN      4.5     0.2    -      -       -      -
    561C  ARG*     2.8    40.8    +      -       -      +
    563C  GLN*     3.3    33.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with PRO 548 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    546C  PHE      3.7     9.2    -      -       -      +
    547C  VAL*     1.3    91.3    -      -       +      +
    549C  MET*     1.3    60.6    +      -       -      +
    558C  GLN*     3.4    17.5    -      -       +      +
    559C  LEU      3.0     8.7    -      -       -      +
    560C  GLN*     3.6    22.2    -      -       -      +
----------------------------------------------------------
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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