Contacts of the strand formed by residues 236 - 243 (chain A) in PDB entry 3CL0


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 236 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    232A  CYS*     3.2     1.6    -      -       -      -
    233A  VAL      2.7    41.1    +      -       -      +
    234A  ASN      4.1     4.5    +      -       -      -
    235A  GLY*     1.3    78.3    -      -       -      +
    237A  CYS*     1.3    61.1    +      -       -      +
    238A  PHE*     3.5    18.0    -      -       -      -
    256A  LYS*     3.5    16.9    +      -       -      -
    257A  MET      3.5     8.5    -      -       -      -
    258A  GLU*     2.8    27.3    +      -       -      +
    308A  GLN*     5.3     3.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 237 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    183A  CYS*     3.8    14.6    -      -       -      -
    185A  ASP*     3.6    21.1    -      -       -      -
    190A  LEU*     3.8    21.1    -      -       +      -
    231A  ALA      3.2     3.8    -      -       -      +
    232A  CYS*     2.0    45.8    -      -       -      -
    235A  GLY      5.2     0.4    -      -       -      -
    236A  SER*     1.3    74.3    -      -       -      +
    238A  PHE*     1.3    66.4    +      -       -      +
    256A  LYS*     3.7     0.3    -      -       -      -
    257A  MET*     2.9    40.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 238 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    226A  GLN*     3.8     1.0    +      -       -      -
    230A  CYS*     3.1    21.1    -      -       -      +
    231A  ALA*     2.8    27.7    +      -       -      +
    233A  VAL*     4.3    11.2    -      -       +      -
    236A  SER*     3.5    34.5    -      -       -      -
    237A  CYS*     1.3    75.7    -      -       -      +
    239A  THR*     1.3    61.8    +      -       -      +
    255A  PHE      3.3     5.6    -      -       -      +
    256A  LYS*     3.5    27.6    -      -       +      -
    257A  MET*     4.1     1.1    -      -       -      -
    280A  CYS*     5.3     2.6    -      -       -      +
    287A  ILE*     3.6    22.7    -      -       +      -
    305A  PHE*     3.7    33.0    -      +       +      -
    306A  ASN      4.2     2.2    -      -       -      -
    308A  GLN*     3.8    26.5    -      -       +      -
    310A  LEU*     3.6    22.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 239 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    181A  SER*     3.7     6.2    +      -       -      -
    192A  ILE*     3.9    13.1    -      -       +      +
    215A  ILE*     5.8     0.2    -      -       +      -
    225A  THR*     3.6    10.2    +      -       -      -
    226A  GLN*     2.5    26.0    +      -       -      +
    230A  CYS*     4.3     0.9    -      -       -      -
    238A  PHE*     1.3    75.6    -      -       -      +
    240A  VAL*     1.3    66.3    +      -       -      +
    241A  MET*     4.3    12.8    -      -       +      -
    254A  ILE*     3.4     7.0    -      -       -      +
    255A  PHE*     2.9    53.1    +      -       +      -
    257A  MET*     3.6    22.2    -      -       +      +
    280A  CYS*     5.8     1.3    -      -       -      -
    305A  PHE*     5.6     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 240 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    225A  THR*     3.0    25.8    +      -       -      -
    226A  GLN*     4.0     8.5    +      -       +      +
    239A  THR*     1.3    80.8    +      -       -      +
    241A  MET*     1.3    73.5    +      -       -      +
    242A  THR*     4.8     5.8    -      -       -      +
    252A  TYR*     5.0     7.2    -      -       +      -
    253A  LYS      3.3    13.0    -      -       -      +
    254A  ILE*     4.4    16.2    -      -       +      -
    268A  LEU*     5.6     3.6    -      -       +      -
    275A  TYR*     5.1     4.0    -      -       +      -
    276A  GLU*     6.3     0.2    -      -       -      -
    278A  CYS*     4.0    29.1    -      -       +      +
    280A  CYS*     4.3     1.6    -      -       -      -
    289A  CYS*     4.0    27.4    -      -       +      -
    303A  VAL*     5.1     5.6    -      -       +      -
    305A  PHE*     4.7     3.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 241 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    192A  ILE*     3.6    31.4    -      -       +      -
    194A  ILE*     4.3     6.1    -      -       +      -
    203A  ALA*     3.7    13.5    -      -       +      -
    215A  ILE*     3.7    26.7    -      -       +      -
    218A  TRP*     3.9    10.1    -      -       +      -
    223A  LEU*     3.9    20.6    -      -       +      -
    224A  ARG      3.3     6.1    -      -       -      +
    225A  THR*     3.8    14.6    -      -       -      +
    239A  THR*     4.3    13.9    -      -       +      -
    240A  VAL*     1.3    81.1    -      -       -      +
    242A  THR*     1.3    64.6    +      -       -      +
    251A  SER      3.9     0.5    -      -       -      +
    252A  TYR*     3.5     3.5    -      -       -      -
    253A  LYS      2.9    32.2    +      -       -      -
    255A  PHE*     3.7    23.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 242 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    218A  TRP*     4.3     2.5    -      -       -      -
    223A  LEU*     3.5     3.6    -      -       -      +
    224A  ARG*     2.9    68.5    +      -       -      +
    240A  VAL*     4.8     3.6    -      -       -      +
    241A  MET*     1.3    76.2    +      -       -      +
    243A  ASP*     1.3    64.1    +      -       -      +
    250A  ALA*     3.8     9.4    -      -       +      -
    251A  SER      3.4    11.0    -      -       -      +
    252A  TYR*     3.7    10.9    -      -       +      +
    274A  TYR*     4.8     1.3    -      -       -      +
    275A  TYR*     2.6    33.7    +      -       -      +
    276A  GLU*     4.0     7.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 243 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    217A  SER*     2.4    28.6    +      -       -      -
    218A  TRP*     3.0    37.7    +      -       +      -
    219A  ARG*     3.0    17.5    +      -       +      +
    221A  ASN      2.9    36.9    +      -       -      +
    223A  LEU*     4.2     8.4    -      -       -      +
    224A  ARG*     4.3     1.6    -      -       -      +
    242A  THR*     1.3    74.5    -      -       -      +
    244A  GLY*     1.3    61.1    +      -       -      +
    250A  ALA*     3.4     3.4    -      -       -      +
    251A  SER*     2.8    35.2    +      -       -      +
----------------------------------------------------------
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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