Contacts of the strand formed by residues 157 - 162 (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 THR 157 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133A  PHE      3.5     0.5    -      -       -      +
    134A  LEU*     3.5     2.8    -      -       -      -
    135A  THR*     2.7    52.5    +      -       -      +
    137A  GLY*     5.3     0.9    -      -       -      -
    154A  PRO      5.6     0.2    -      -       -      +
    155A  HIS      3.7    10.0    +      -       -      +
    156A  ARG*     1.3    80.9    -      -       -      +
    158A  LEU*     1.3    63.5    +      -       -      +
    159A  MET*     3.9    12.8    -      -       -      +
    173A  PHE*     3.7    26.9    -      -       +      -
    175A  SER      3.4     8.7    -      -       -      +
    176A  VAL*     4.3    11.2    -      -       +      -
    177A  ALA      3.9     5.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 158 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121A  PHE*     4.4     5.6    -      -       +      -
    132A  PHE*     3.9    27.1    -      -       +      -
    133A  PHE      3.4    19.7    -      -       -      +
    134A  LEU*     4.1    11.5    -      -       +      +
    157A  THR*     1.3    70.3    -      -       -      +
    159A  MET*     1.3    64.1    +      -       -      +
    173A  PHE*     4.3     0.9    -      -       -      -
    174A  GLU*     3.0    41.1    +      -       +      -
    175A  SER*     2.7    28.7    +      -       -      +
    177A  ALA*     4.3     6.5    -      -       +      +
    180A  ALA*     3.8    27.4    -      -       +      -
    181A  SER      4.3     4.3    -      -       -      +
    182A  ALA*     4.9     0.4    -      -       +      -
    191A  THR*     4.0    23.1    -      -       +      -
    192A  ILE      4.3     5.6    -      -       -      +
    193A  GLY*     5.4     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with MET 159 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    115A  PHE*     3.7    31.4    -      -       +      -
    132A  PHE*     3.3     5.0    -      -       -      +
    133A  PHE*     3.0    51.1    +      -       +      -
    135A  THR*     3.9    11.0    -      -       +      -
    157A  THR*     3.9    15.3    -      -       -      +
    158A  LEU*     1.3    80.6    -      -       -      +
    160A  SER*     1.3    60.7    +      -       -      +
    169A  PRO*     5.5     2.5    -      -       +      +
    171A  SER*     3.8    29.4    -      -       -      +
    172A  ARG      3.2    11.0    -      -       -      +
    173A  PHE*     4.0    27.6    -      -       +      +
    174A  GLU*     3.8     5.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 160 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    130A  ARG*     2.9    31.5    +      -       -      -
    131A  THR      3.1    12.8    -      -       -      -
    132A  PHE*     3.7    17.7    -      -       -      -
    133A  PHE*     3.8     4.5    -      -       -      -
    159A  MET*     1.3    76.7    -      -       -      +
    161A  CYS*     1.3    62.3    +      -       -      +
    171A  SER*     3.3     2.9    -      -       -      -
    172A  ARG*     2.7    39.2    +      -       -      +
    174A  GLU*     2.5    27.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 161 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    130A  ARG*     3.5    11.5    -      -       -      +
    131A  THR*     2.9    37.6    +      -       -      +
    133A  PHE*     3.7    19.3    -      -       -      -
    160A  SER*     1.3    75.8    -      -       -      +
    162A  PRO*     1.3    83.5    -      -       +      +
    165A  GLU      3.8    18.2    -      -       -      -
    167A  PRO*     4.1    12.6    -      -       -      -
    170A  ASN*     3.5    21.1    -      -       -      +
    171A  SER*     4.0     7.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 162 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128A  GLU*     5.3     3.6    -      -       -      +
    129A  CYS      4.1     7.9    -      -       -      +
    130A  ARG*     4.4    16.1    -      -       +      +
    131A  THR*     4.4     0.3    +      -       -      -
    161A  CYS*     1.3    94.9    -      -       +      +
    163A  VAL*     1.3    68.2    +      -       +      +
    164A  GLY      3.5     0.2    +      -       -      -
    165A  GLU*     3.3    50.1    +      -       +      +
    170A  ASN      4.0     8.7    -      -       -      +
----------------------------------------------------------
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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