Contacts of the strand formed by residues 520 - 530 (chain B) 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 B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    562A  LEU*     4.0     3.4    -      -       -      -
    370B  ALA*     5.5     0.4    -      -       +      -
    371B  ILE      2.9    15.7    -      -       -      +
    372B  TYR*     3.5    38.5    +      +       +      -
    471B  PAQ      4.7     0.4    +      -       -      -
    495B  ILE*     4.8     8.5    -      -       +      -
    496B  SER      5.5     0.9    -      -       -      -
    518B  THR*     2.7    26.5    +      -       -      -
    519B  VAL*     1.3    79.5    -      -       -      +
    521B  THR*     1.3    66.5    +      -       -      +
    522B  HIS*     3.0    25.0    +      +       -      -
    683B  LEU*     3.9     3.3    -      -       -      +
    684B  HIS*     2.9    44.8    +      +       -      -
    686B  PRO*     3.9     8.1    -      -       +      -
   1742B   CU      2.2    28.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 521 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    544A  MET*     4.2    30.1    -      -       +      -
    546A  PHE*     5.7     0.8    -      -       +      -
    562A  LEU*     4.8     8.3    -      -       +      -
    369B  LEU*     4.3     0.5    -      -       -      +
    370B  ALA*     2.9    29.3    +      -       -      +
    371B  ILE*     2.9    26.7    +      -       +      +
    520B  HIS*     1.3    78.5    -      -       -      +
    522B  HIS*     1.3    65.9    +      -       -      +
    523B  SER*     4.4     3.3    +      -       -      -
    612B  GLY*     4.4    12.8    -      -       -      -
    613B  GLU      4.9     4.4    +      -       -      +
    628B  GLU*     3.8    14.2    +      -       -      -
    682B  PHE      3.8     7.9    -      -       -      -
    683B  LEU*     4.2     8.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 522 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    369B  LEU      3.7     4.9    -      -       -      +
    370B  ALA*     4.7     3.6    -      -       +      +
    471B  PAQ      3.5    27.5    -      +       -      -
    473B  TYR*     4.4    14.8    +      -       +      +
    489B  PHE*     4.6    10.1    -      -       +      -
    491B  ALA*     4.0    15.4    -      -       +      +
    520B  HIS*     3.0    18.7    +      +       -      -
    521B  THR*     1.3    74.9    +      -       -      +
    523B  SER*     1.3    69.4    +      -       -      +
    612B  GLY      5.4     0.7    +      -       -      -
    681B  GLY*     3.2     2.2    -      -       -      -
    682B  PHE*     3.2    61.5    +      +       +      +
    684B  HIS*     3.4     8.9    +      -       +      -
   1742B   CU      2.0    32.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 523 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    368B  ALA*     3.4     2.0    -      -       -      -
    369B  LEU*     2.8    38.1    +      -       -      +
    489B  PHE*     5.0     3.5    -      -       -      -
    521B  THR*     4.4     4.5    +      -       -      -
    522B  HIS*     1.3    83.3    +      -       -      +
    524B  ALA*     1.3    59.3    +      -       -      +
    611B  ALA*     5.5     4.5    -      -       -      +
    612B  GLY      5.6     1.4    +      -       -      -
    627B  TRP*     3.3    22.8    -      -       -      -
    628B  GLU*     3.5    27.4    +      -       -      +
    679B  THR*     4.6     4.3    -      -       -      -
    680B  ALA      3.3    10.8    -      -       -      -
    681B  GLY*     4.7     1.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 524 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    365B  LEU*     4.1     5.6    -      -       +      -
    367B  GLU      3.3    11.4    -      -       -      +
    368B  ALA*     4.9     1.8    -      -       +      -
    473B  TYR*     6.4     0.2    -      -       +      -
    475B  TRP*     4.4     8.5    -      -       +      -
    489B  PHE*     3.9    20.6    -      -       +      -
    523B  SER*     1.3    74.4    -      -       -      +
    525B  HIS*     1.3    60.3    +      -       -      +
    526B  PHE*     3.6    26.3    -      -       +      -
    627B  TRP*     3.8     3.1    -      -       -      -
    678B  VAL      3.6     0.7    -      -       -      +
    679B  THR*     3.3     6.9    -      -       -      +
    680B  ALA      3.0    28.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 525 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    365B  LEU*     3.2     6.9    -      -       -      +
    366B  GLN*     2.8    33.6    +      -       +      +
    367B  GLU      3.0    11.6    +      -       -      +
    524B  ALA*     1.3    74.1    -      -       -      +
    526B  PHE*     1.3    66.0    +      -       -      +
    627B  TRP*     3.4    40.2    -      +       +      +
    644B  SER*     2.6    35.0    +      -       -      +
    660B  PHE*     3.5    17.1    -      +       -      -
    677B  TRP*     3.2    26.8    -      +       -      +
    678B  VAL      3.2    17.9    -      -       -      -
    679B  THR*     3.4    18.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 526 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    363B  ILE*     5.5     4.0    -      -       +      -
    364B  SER      3.4     7.4    -      -       -      +
    365B  LEU*     3.4    37.2    -      -       +      -
    366B  GLN*     4.3     3.4    -      -       -      +
    475B  TRP*     4.2    14.8    -      +       -      -
    487B  ILE*     3.8    26.2    -      -       +      -
    488B  ARG      5.6     1.1    -      -       -      -
    489B  PHE*     4.4    11.0    -      +       +      -
    524B  ALA*     3.6    26.0    -      -       +      -
    525B  HIS*     1.3    77.0    -      -       -      +
    527B  LYS*     1.3    64.6    +      -       -      +
    528B  VAL*     3.8     1.2    +      -       +      +
    676B  ALA      3.7     0.3    -      -       -      +
    677B  TRP*     3.4    10.7    -      -       -      -
    678B  VAL*     2.7    43.3    +      -       +      +
    680B  ALA*     4.6    13.5    -      -       +      -
    702B  GLY*     5.6     2.0    -      -       -      -
    703B  PHE*     3.8    31.4    -      +       +      -
----------------------------------------------------------
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Residues in contact with LYS 527 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    362B  GLU*     3.3    32.6    +      -       -      +
    363B  ILE*     3.2     6.4    -      -       -      +
    364B  SER*     2.8    36.3    +      -       -      +
    366B  GLN*     3.5    17.6    -      -       -      +
    526B  PHE*     1.3    73.3    -      -       -      +
    528B  VAL*     1.3    62.2    +      -       -      +
    529B  ASP*     4.5     7.4    -      -       -      +
    637B  ARG*     3.4    23.7    -      -       -      +
    641B  GLU      3.6     5.9    +      -       -      -
    642B  PRO*     3.0    43.8    +      -       -      +
    675B  VAL*     3.7    21.5    -      -       +      -
    676B  ALA      3.8     3.1    -      -       -      -
    677B  TRP*     3.6    20.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 528 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    362B  GLU      3.7     2.0    -      -       -      -
    363B  ILE*     3.9    23.8    -      -       +      -
    526B  PHE      4.0     4.3    -      -       -      +
    527B  LYS*     1.3    75.2    -      -       -      +
    529B  ASP*     1.3    60.3    +      -       -      +
    530B  LEU*     2.9    19.1    +      -       +      +
    589B  LEU*     5.3     0.2    -      -       -      +
    605B  ILE*     5.7     0.4    -      -       +      -
    675B  VAL*     3.7     0.8    -      -       -      -
    676B  ALA*     2.8    45.1    +      -       +      +
    678B  VAL*     3.9    26.5    -      -       +      -
    703B  PHE*     4.1    14.1    -      -       +      -
    705B  LEU*     3.9    31.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 529 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106B  LYS*     2.7    25.3    +      -       -      +
    360B  VAL*     4.0     1.8    -      -       -      -
    361B  TYR*     3.0    41.4    +      -       -      +
    362B  GLU*     2.6    35.4    +      -       +      +
    527B  LYS*     3.7     4.6    -      -       -      -
    528B  VAL*     1.3    67.9    -      -       -      +
    530B  LEU*     1.3    59.7    +      -       -      +
    637B  ARG*     3.9    15.5    +      -       -      +
    673B  ASP*     3.4     2.4    -      -       -      +
    674B  LEU      3.2     5.4    -      -       -      +
    675B  VAL*     4.1    12.8    -      -       +      +
   1741B   CA      2.8    23.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 530 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    359B  LEU*     3.4    16.4    -      -       +      +
    360B  VAL*     3.3    29.8    -      -       +      +
    528B  VAL*     2.9    20.7    +      -       +      +
    529B  ASP*     1.3    72.4    -      -       -      +
    531B  ASP*     1.3    53.8    +      -       -      +
    532B  VAL*     3.7    17.9    -      -       +      -
    537B  ASN*     3.7     5.5    -      -       -      +
    589B  LEU*     4.1    29.2    -      -       +      +
    603B  TYR*     4.5    27.1    -      -       +      +
    605B  ILE*     4.8     6.7    -      -       +      -
    674B  LEU      3.4     4.0    +      -       -      +
    705B  LEU*     4.3    24.5    -      -       +      -
   1741B   CA      2.2    31.0    -      -       -      -
----------------------------------------------------------
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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