Contacts of the strand formed by residues 172 - 178 (chain J) 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 SER 172 (chain J).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    151D  SER*     5.4     1.6    +      -       -      -
    154D  GLU*     5.4     5.0    -      -       -      +
    155D  HIS*     2.9    28.8    +      -       -      -
    170J  SER*     4.2     5.2    -      -       -      +
    171J  PRO*     1.3    79.4    -      -       -      +
    173J  SER*     1.3    65.5    +      -       -      +
    210J  VAL*     6.2     0.2    -      -       -      -
    211J  LEU      3.3     6.7    -      -       -      -
    212J  GLN*     4.3    13.0    -      -       -      -
    225J  ILE*     4.3    15.9    -      -       -      +
    226J  ILE*     3.6    26.9    -      -       -      +
    228J  HIS*     4.2     3.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 173 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    155J  LEU*     3.8    10.9    -      -       -      +
    172J  SER*     1.3    76.5    -      -       -      +
    174J  TRP*     1.3    74.9    +      -       -      +
    210J  VAL*     3.4     6.8    -      -       -      +
    211J  LEU*     2.8    45.9    +      -       -      +
    225J  ILE*     4.5     2.3    -      -       -      +
    226J  ILE      3.0     9.8    +      -       -      -
    228J  HIS*     3.3    42.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with TRP 174 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    138J  ARG      3.3    18.8    +      -       -      -
    140J  TRP*     3.3    42.1    -      +       +      +
    143J  SER*     3.3    22.0    -      -       -      -
    154J  LEU*     4.3    17.8    -      -       +      +
    155J  LEU*     3.9     9.9    -      -       -      +
    173J  SER*     1.3    85.9    +      -       -      +
    175J  ILE*     1.3    61.1    +      -       -      +
    208J  CYS*     3.6    20.0    -      -       +      -
    209J  ALA      3.3     8.1    -      -       -      -
    210J  VAL*     3.3    26.7    -      -       +      +
    219J  ALA*     4.0    13.7    -      -       +      -
    220J  GLN      3.3    23.6    -      -       -      -
    221J  CYS*     3.9     7.4    -      -       -      -
    223J  SER      3.2    21.8    -      -       -      -
    225J  ILE*     3.4    23.3    -      -       +      +
    226J  ILE      3.2    15.7    +      -       -      +
    227J  TYR*     4.9     1.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 175 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    140J  TRP*     3.3    14.2    +      -       -      -
    154J  LEU*     3.8     4.7    -      -       -      -
    155J  LEU*     3.3    18.6    -      -       +      +
    156J  SER*     5.3     1.1    -      -       -      -
    157J  ILE*     4.2    19.5    -      -       +      +
    173J  SER      3.5     8.3    +      -       -      +
    174J  TRP*     1.3    79.1    -      -       -      +
    176J  GLY*     1.3    53.7    +      -       -      +
    177J  VAL*     2.5    47.8    +      -       +      +
    194J  PHE*     4.6     1.8    -      -       +      -
    209J  ALA*     3.4    29.2    +      -       +      +
    210J  VAL      4.4     0.2    -      -       -      +
    211J  LEU*     4.2    16.6    -      -       +      -
    216J  LEU*     3.4    33.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 176 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    140J  TRP*     4.4     0.9    -      -       -      -
    154J  LEU*     3.6    17.6    -      -       -      +
    155J  LEU      2.9    15.5    +      -       -      -
    156J  SER*     4.9     7.0    -      -       -      +
    175J  ILE*     1.3    66.4    -      -       -      +
    177J  VAL*     1.3    65.9    +      -       -      +
    188J  THR*     3.4    20.4    -      -       -      +
    189J  MET*     3.5    34.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 177 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    140J  TRP*     4.6     1.8    +      -       -      -
    156J  SER*     6.4     1.1    -      -       -      -
    157J  ILE      6.3     0.7    -      -       -      +
    175J  ILE*     2.5    29.2    +      -       +      +
    176J  GLY*     1.3    80.4    -      -       -      +
    178J  PHE*     1.3    64.5    +      -       -      +
    186J  TRP*     3.5    24.2    -      -       +      -
    187J  VAL      3.3     9.0    -      -       -      +
    188J  THR*     4.5     2.5    -      -       +      -
    194J  PHE*     3.7    57.0    -      -       +      -
    198J  ILE*     4.9     1.6    -      -       +      -
    208J  CYS*     3.9     1.0    -      -       -      +
    209J  ALA*     3.1    31.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 178 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    140J  TRP*     3.7    29.2    -      +       +      -
    177J  VAL*     1.3    74.3    -      -       -      +
    179J  ARG*     1.3    78.6    +      -       -      +
    180J  ASN*     3.5    23.6    -      -       -      -
    186J  TRP*     3.9     7.4    -      -       -      -
    187J  VAL*     2.9    45.1    +      -       +      +
    188J  THR      4.2    11.9    -      -       -      -
    189J  MET*     3.9    25.6    -      -       +      -
    207J  ASN      3.2    12.6    -      -       -      +
    208J  CYS*     4.4    11.2    -      -       -      -
----------------------------------------------------------
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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