Contacts of the strand formed by residues 485 - 493 (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 ILE 485 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    335B  TRP*     3.6    18.6    -      -       +      -
    352B  VAL*     3.8    29.6    -      -       +      -
    359B  LEU*     4.5     5.6    -      -       +      -
    360B  VAL*     4.4    12.3    -      -       +      -
    363B  ILE*     4.4     7.2    -      -       +      -
    477B  THR*     4.6     3.4    -      -       +      -
    478B  VAL      3.5     8.7    -      -       -      +
    479B  PHE*     3.9    13.5    -      -       +      -
    483B  GLY      4.5     1.8    -      -       -      +
    484B  ALA*     1.3    77.0    -      -       -      +
    486B  GLU*     1.3    69.4    +      -       -      +
    487B  ILE*     4.3    13.0    +      -       +      -
    603B  TYR*     5.5     0.9    -      -       +      -
    703B  PHE      4.0     0.3    -      -       -      +
    704B  PHE*     3.4     6.2    -      -       -      -
    705B  LEU*     2.8    67.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 486 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    436B  GLN*     5.6     0.5    +      -       -      -
    476B  ASP      3.8     0.2    -      -       -      +
    477B  THR*     3.5     4.3    -      -       -      +
    478B  VAL*     2.7    52.8    +      -       +      +
    480B  HIS*     3.1    27.4    +      -       -      +
    485B  ILE*     1.3    74.1    -      -       -      +
    487B  ILE*     1.3    67.8    +      -       -      +
    488B  ARG*     3.1    50.6    +      -       +      +
    703B  PHE      3.6     5.2    -      -       -      +
    704B  PHE*     3.4    30.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 487 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    363B  ILE*     4.0    21.3    -      -       +      -
    476B  ASP      3.5     3.4    -      -       -      +
    477B  THR*     3.6    29.2    -      -       +      +
    485B  ILE*     4.3    11.2    -      -       +      +
    486B  GLU*     1.3    83.9    -      -       -      +
    488B  ARG*     1.3    69.5    +      -       -      +
    526B  PHE*     3.8    32.8    -      -       +      -
    702B  GLY*     3.1     4.7    -      -       -      -
    703B  PHE*     3.0    68.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 488 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    488A  ARG*     5.1    11.1    -      -       -      +
    474B  VAL      4.1     0.4    -      -       -      -
    475B  TRP*     3.8     1.6    -      -       -      -
    476B  ASP*     2.8    39.8    +      -       +      +
    478B  VAL*     5.1     2.9    -      -       +      -
    486B  GLU*     3.1    36.7    +      -       +      +
    487B  ILE*     1.3    88.4    -      -       -      +
    489B  PHE*     1.3    64.3    +      -       -      +
    490B  TYR*     3.8    31.9    +      -       +      +
    526B  PHE*     5.6     0.6    -      -       -      -
    608B  LEU*     2.8    39.7    -      -       -      +
    700B  GLY*     3.2    26.2    +      -       -      -
    701B  VAL      3.2    10.8    -      -       -      +
    702B  GLY*     4.4     0.7    -      -       -      -
    704B  PHE*     4.4     4.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 489 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    473B  TYR*     3.6    38.4    -      +       -      -
    474B  VAL      3.0     7.4    -      -       -      +
    475B  TRP*     3.4    30.1    -      +       +      -
    488B  ARG*     1.3    76.4    -      -       -      +
    490B  TYR*     1.3    72.6    +      -       -      +
    491B  ALA*     4.4     6.3    -      -       +      -
    522B  HIS*     4.6    17.9    -      -       +      -
    523B  SER      5.0     1.1    -      -       -      -
    524B  ALA*     3.9    28.3    -      -       +      -
    526B  PHE*     4.4    11.0    -      +       +      -
    680B  ALA*     4.3    11.2    -      -       +      -
    682B  PHE*     4.6     6.3    -      +       -      -
    699B  ASN      3.9     1.2    -      -       -      +
    700B  GLY*     3.6     0.9    -      -       -      -
    701B  VAL*     3.0    57.7    +      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 490 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    438A  LEU*     3.6    39.1    -      -       +      +
    472B  ASP      3.7     1.6    -      -       -      +
    473B  TYR*     3.4     7.3    -      -       -      -
    474B  VAL*     3.0    46.6    +      -       +      +
    476B  ASP*     4.3     9.4    +      -       +      -
    488B  ARG*     3.8    41.5    +      -       +      +
    489B  PHE*     1.3    84.5    -      -       -      +
    491B  ALA*     1.3    61.7    +      -       -      +
    492B  THR      3.9     0.2    -      -       -      -
    696B  THR*     3.6    43.5    -      -       +      -
    699B  ASN      4.0     5.2    -      -       -      +
    700B  GLY*     3.4    24.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 491 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    471B  PAQ      5.0     7.6    -      -       +      +
    472B  ASP      4.0     3.1    -      -       -      -
    473B  TYR*     4.7     7.2    -      -       +      -
    489B  PHE*     4.4    10.0    -      -       +      -
    490B  TYR*     1.3    74.3    -      -       -      +
    492B  THR*     1.3    60.2    +      -       -      +
    522B  HIS*     4.0    33.0    -      -       +      +
    682B  PHE*     4.5    14.3    -      -       +      -
    684B  HIS*     6.0     0.4    -      -       +      +
    694B  THR*     4.0    18.0    -      -       +      +
    695B  VAL      4.0     6.4    -      -       -      +
    696B  THR*     5.3     0.2    -      -       -      -
    699B  ASN*     4.4    10.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 492 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    439A  PRO*     5.9     0.7    -      -       +      -
    441A  ARG*     3.5     3.6    -      -       -      -
    442A  ARG*     3.3    34.8    +      -       +      +
    471B  PAQ      2.9     9.8    -      -       -      +
    472B  ASP*     2.7    46.9    +      -       +      +
    474B  VAL*     3.9    21.3    -      -       +      -
    491B  ALA*     1.3    73.0    -      -       -      +
    493B  GLY*     1.3    65.1    +      -       -      +
    694B  THR*     2.7    25.7    +      -       -      -
    696B  THR*     4.0    17.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 493 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    442A  ARG      3.4     1.1    -      -       -      -
    443A  HIS*     4.2     1.3    -      -       -      -
    472B  ASP*     3.3    16.2    -      -       -      -
    492B  THR*     1.3    85.3    +      -       -      +
    494B  TYR*     1.3    61.4    +      -       -      -
    692B  PRO      3.9     0.3    -      -       -      +
    693B  ASN*     2.9    47.2    +      -       -      -
    694B  THR*     2.9    10.1    +      -       -      -
----------------------------------------------------------
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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