Contacts of the strand formed by residues 151 - 156 (chain I) in PDB entry 3CII


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 ASN 151 (chain I).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    119I  LEU      4.9     0.7    -      -       -      +
    120I  SER*     5.0     2.4    -      -       -      -
    121I  TYR      5.2     0.5    +      -       -      -
    128I  TRP*     3.3    25.7    -      -       -      -
    148I  ASN*     2.9    44.5    +      -       +      +
    149I  THR      3.3     3.7    -      -       -      +
    150I  LYS*     1.3    81.5    -      -       -      +
    152I  CYS*     1.3    61.2    +      -       -      +
    163I  ASP*     4.0    20.4    +      -       +      -
    164I  GLU      3.0    18.9    -      -       -      +
    165I  SER*     3.2    17.0    +      -       -      -
    166I  CYS*     3.5     5.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 152 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     82I  TRP*     3.3    52.0    -      -       +      +
    116I  TRP*     3.5    14.9    -      -       +      -
    119I  LEU      4.2     6.1    -      -       -      -
    120I  SER*     5.5     3.8    -      -       -      -
    151I  ASN*     1.3    73.8    -      -       -      +
    153I  ILE*     1.3    62.9    +      -       -      +
    163I  ASP*     3.3     1.0    -      -       -      -
    164I  GLU      2.8    34.1    +      -       -      +
    166I  CYS*     2.0    46.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 153 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     82I  TRP*     4.4     0.4    +      -       -      +
    116I  TRP*     3.1    15.4    -      -       -      -
    117I  ILE*     3.3    21.7    +      -       +      +
    119I  LEU*     3.8    39.9    +      -       +      +
    128I  TRP*     3.5    36.3    -      -       +      -
    141I  PHE*     4.6     2.0    -      -       +      -
    147I  PHE*     3.7    29.8    -      -       +      -
    152I  CYS*     1.3    74.6    -      -       -      +
    154I  ALA*     1.3    66.1    +      -       -      +
    161I  ALA*     3.7    28.3    -      -       +      -
    162I  LEU      3.4     3.6    -      -       -      +
    163I  ASP*     3.8    13.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 154 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114I  PHE*     3.8    18.4    -      -       +      -
    115I  TYR      3.3    15.5    -      -       -      +
    116I  TRP*     3.8    16.4    -      -       +      +
    117I  ILE*     4.5     0.4    -      -       -      -
    153I  ILE*     1.3    75.6    -      -       -      +
    155I  TYR*     1.3    60.2    +      -       -      +
    161I  ALA*     3.1     6.8    -      -       -      +
    162I  LEU*     2.7    41.1    +      -       +      +
    164I  GLU*     4.7    11.0    -      -       -      +
    170I  ASN*     4.8     4.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 155 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99I  LEU*     3.6    31.5    -      -       +      +
    102I  THR*     4.0    23.2    +      -       -      +
    105I  LEU*     3.7    25.5    +      -       +      -
    114I  PHE*     3.4     7.2    -      -       -      -
    115I  TYR*     2.5    45.3    +      -       +      +
    117I  ILE*     3.3    30.5    -      -       +      +
    140I  LEU*     6.2     0.4    -      -       +      +
    141I  PHE*     3.6    23.3    -      +       -      -
    154I  ALA*     1.3    72.5    -      -       -      +
    156I  ASN*     1.3    64.2    -      -       -      +
    157I  PRO*     3.4    27.8    +      -       +      +
    159I  GLY*     3.4    35.1    +      -       -      -
    160I  ASN      3.5    10.1    -      -       -      -
    161I  ALA*     4.7     0.9    -      -       +      -
    173I  ILE*     6.0     0.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 156 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     73D  ILE*     4.5     1.4    -      -       -      +
      8F  PHE*     3.7    10.3    -      -       -      -
    111I  SER      3.1    27.5    +      -       -      +
    112I  GLN*     3.5     4.8    -      -       -      +
    113I  GLN      3.1    27.6    +      -       -      +
    114I  PHE*     3.6    17.2    -      -       +      -
    155I  TYR*     1.3    76.2    -      -       -      +
    157I  PRO*     1.3    59.2    -      -       -      +
    158I  ASN*     2.7    35.5    +      -       -      +
    159I  GLY*     2.7    16.1    +      -       -      -
    160I  ASN*     2.9    28.8    +      -       -      +
----------------------------------------------------------
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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