Contacts of the strand formed by residues 520 - 530 (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 HIS 520 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    370C  ALA*     5.4     0.2    -      -       +      -
    371C  ILE      3.1    12.3    -      -       -      +
    372C  TYR*     3.2    41.0    -      +       +      -
    471C  PAQ      5.0     1.1    -      -       -      -
    495C  ILE*     4.6     9.0    -      -       +      -
    496C  SER      5.7     0.2    -      -       -      -
    518C  THR*     2.9    22.9    +      -       -      -
    519C  VAL*     1.3    75.4    -      -       -      +
    521C  THR*     1.3    69.2    +      -       -      +
    522C  HIS*     2.9    26.2    +      +       -      -
    683C  LEU*     3.8     3.5    -      -       -      +
    684C  HIS*     2.9    49.4    +      +       +      +
    686C  PRO*     4.0     9.2    -      -       +      -
   1738C   CU      2.1    30.2    -      -       -      -
    562D  LEU*     4.1     2.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 521 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    370C  ALA*     2.8     9.9    -      -       -      +
    371C  ILE*     2.8    55.1    +      -       +      +
    520C  HIS*     1.3    80.5    -      -       -      +
    522C  HIS*     1.3    64.8    +      -       -      +
    523C  SER*     4.3     3.5    +      -       -      -
    612C  GLY*     4.8     7.9    -      -       -      -
    613C  GLU      4.8     3.3    +      -       -      +
    628C  GLU*     4.1    12.0    +      -       -      -
    682C  PHE      3.7     8.7    -      -       -      -
    683C  LEU*     4.0     9.2    -      -       +      -
    544D  MET*     3.7    36.3    -      -       +      -
    546D  PHE*     5.5     0.8    -      -       +      -
    562D  LEU*     4.4     4.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 522 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    369C  LEU      3.5     3.4    -      -       -      +
    370C  ALA*     4.3     5.8    -      -       +      +
    471C  PAQ      3.0    40.9    -      +       -      -
    473C  TYR*     4.3    13.5    +      -       +      -
    489C  PHE*     4.9     8.5    -      -       +      -
    491C  ALA*     4.2    14.4    -      -       +      +
    520C  HIS*     2.9    17.7    +      +       -      -
    521C  THR*     1.3    73.1    -      -       -      +
    523C  SER*     1.3    67.3    +      -       -      +
    611C  ALA*     5.5     0.2    -      -       -      -
    612C  GLY      5.3     0.5    +      -       -      -
    681C  GLY*     3.0     3.0    -      -       -      -
    682C  PHE*     2.9    69.5    +      +       +      +
    684C  HIS*     4.2     2.7    -      -       +      -
   1738C   CU      2.0    29.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 523 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    368C  ALA*     3.5     1.9    -      -       -      +
    369C  LEU*     2.8    39.8    +      -       -      +
    473C  TYR*     6.1     0.5    -      -       -      -
    489C  PHE*     4.7     3.1    -      -       -      -
    521C  THR*     4.3     6.4    +      -       -      -
    522C  HIS*     1.3    80.1    +      -       -      +
    524C  ALA*     1.3    61.9    +      -       -      +
    611C  ALA*     6.0     2.0    -      -       -      +
    612C  GLY      5.7     1.4    +      -       -      -
    627C  TRP*     3.6    20.6    -      -       -      -
    628C  GLU*     3.7    27.0    +      -       -      +
    679C  THR*     4.7     5.4    -      -       -      -
    680C  ALA      3.5     8.5    -      -       -      -
    681C  GLY*     3.9     2.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 524 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    365C  LEU*     4.3     5.6    -      -       +      -
    367C  GLU      3.5    11.4    -      -       -      +
    368C  ALA*     4.8     3.1    -      -       +      -
    475C  TRP*     4.6     5.6    -      -       +      -
    489C  PHE*     3.4    31.2    -      -       +      -
    523C  SER*     1.3    75.8    -      -       -      +
    525C  HIS*     1.3    60.4    +      -       -      +
    526C  PHE*     3.6    17.4    -      -       +      -
    627C  TRP*     3.7     4.2    -      -       -      -
    679C  THR*     3.5     4.5    -      -       -      -
    680C  ALA      3.0    28.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 525 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    365C  LEU*     3.5     2.6    -      -       -      +
    366C  GLN*     2.9    27.7    +      -       +      +
    367C  GLU*     3.1    11.5    +      -       +      +
    524C  ALA*     1.3    73.3    -      -       -      +
    526C  PHE*     1.3    61.9    +      -       -      +
    627C  TRP*     3.3    44.2    +      +       +      +
    630C  TYR*     5.9     1.4    -      -       -      +
    644C  SER*     2.7    41.3    +      -       -      +
    660C  PHE*     3.6     9.6    -      +       -      -
    677C  TRP*     3.2    39.8    +      +       +      +
    678C  VAL      3.3    11.0    -      -       -      -
    679C  THR*     3.1    25.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 526 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    363C  ILE*     5.5     2.7    -      -       +      -
    364C  SER      3.4    16.4    -      -       -      +
    365C  LEU*     4.1    18.2    -      -       +      -
    366C  GLN*     4.2     2.2    -      -       -      -
    475C  TRP*     4.6     9.2    -      +       -      -
    487C  ILE*     3.8    28.7    -      -       +      -
    489C  PHE*     3.8    29.4    -      +       +      -
    524C  ALA*     3.6    29.4    -      -       +      -
    525C  HIS*     1.3    77.2    -      -       -      +
    527C  LYS*     1.3    61.4    +      -       -      +
    528C  VAL*     3.6     4.5    +      -       +      +
    677C  TRP*     3.4    11.0    -      -       -      +
    678C  VAL      2.9    32.6    +      -       -      +
    680C  ALA*     4.7    10.3    -      -       +      -
    702C  GLY*     5.3     4.0    -      -       -      -
    703C  PHE*     3.9    27.6    -      +       +      -
----------------------------------------------------------
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Residues in contact with LYS 527 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    362C  GLU*     3.4    34.3    +      -       -      +
    363C  ILE*     3.3     5.5    -      -       -      +
    364C  SER*     2.8    31.0    +      -       -      +
    366C  GLN*     3.5    24.1    -      -       +      +
    526C  PHE*     1.3    71.2    -      -       -      +
    528C  VAL*     1.3    60.3    +      -       -      +
    529C  ASP*     4.4     5.4    -      -       -      +
    637C  ARG*     3.5    32.7    -      -       -      +
    641C  GLU      4.4     2.2    +      -       -      -
    642C  PRO*     3.6    35.9    +      -       -      +
    675C  VAL*     3.7    19.3    -      -       +      -
    676C  ALA      3.9     2.0    -      -       -      -
    677C  TRP*     3.7    24.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 528 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    362C  GLU      3.9     1.8    -      -       -      -
    363C  ILE*     4.0    14.1    -      -       +      -
    526C  PHE*     4.2     7.4    -      -       +      +
    527C  LYS*     1.3    76.4    -      -       -      +
    529C  ASP*     1.3    58.3    +      -       -      +
    530C  LEU*     3.6    16.0    +      -       +      +
    605C  ILE*     5.6     0.9    -      -       +      -
    675C  VAL*     3.4     1.5    -      -       -      -
    676C  ALA*     2.6    55.9    +      -       +      +
    678C  VAL*     4.2    10.1    -      -       +      -
    703C  PHE*     3.6    32.1    -      -       +      -
    705C  LEU*     3.8    33.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 529 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106C  LYS*     3.1    10.0    +      -       -      -
    360C  VAL*     2.8    17.3    -      -       -      +
    361C  TYR*     2.9    41.1    +      -       -      +
    362C  GLU*     2.9    17.1    +      -       +      +
    527C  LYS*     3.9    12.3    -      -       -      -
    528C  VAL*     1.3    70.9    -      -       -      +
    530C  LEU*     1.3    56.1    +      -       -      +
    637C  ARG*     4.0    12.9    +      -       -      +
    673C  ASP*     3.4     3.6    -      -       -      +
    674C  LEU      2.7     8.7    -      -       -      +
    675C  VAL*     3.8    16.9    -      -       +      +
   1737C   CA      2.4    29.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 530 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    359C  LEU*     3.4    12.3    -      -       +      +
    360C  VAL*     3.1    37.5    -      -       +      -
    528C  VAL*     3.6    13.0    +      -       +      +
    529C  ASP*     1.3    74.7    -      -       -      +
    531C  ASP*     1.3    57.8    +      -       -      +
    532C  VAL*     3.8    15.0    -      -       +      -
    537C  ASN*     3.6     5.1    -      -       -      +
    589C  LEU*     4.7    22.4    -      -       +      +
    603C  TYR*     4.2    29.2    -      -       +      +
    605C  ILE*     5.0     5.8    -      -       +      -
    674C  LEU      3.6     2.6    +      -       -      +
    675C  VAL*     4.9     0.6    -      -       -      +
    676C  ALA*     6.2     0.9    -      -       +      -
    705C  LEU*     3.7    30.7    -      -       +      -
   1737C   CA      2.1    34.1    -      -       -      -
----------------------------------------------------------
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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