Contacts of the strand formed by residues 145 - 150 (chain A) in PDB entry 1CT8


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 145 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    144A  ILE*     1.3    76.5    +      -       -      +
    146A  VAL*     1.3    78.3    +      -       -      +
    147A  LYS*     4.9     7.8    -      -       -      +
    196A  ALA*     3.4     4.3    -      -       -      -
    197A  THR*     2.8    51.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 146 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136A  LEU*     3.5    34.8    -      -       +      -
    144A  ILE*     5.2     0.2    -      -       +      -
    145A  ASN*     1.3    90.0    +      -       -      +
    147A  LYS*     1.3    72.8    +      -       -      +
    148A  TRP*     4.2     9.2    -      -       +      +
    159A  VAL*     6.1     1.2    -      -       +      +
    161A  ASN*     4.9     7.1    +      -       -      +
    175A  MET*     3.8    23.6    -      -       +      -
    177A  SER*     4.0    20.6    -      -       -      +
    194A  CYS*     3.6    30.5    -      -       -      -
    195A  GLU      3.4     3.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 147 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    145A  ASN*     4.9     7.4    -      -       -      +
    146A  VAL*     1.3    83.9    +      -       -      +
    148A  TRP*     1.3    91.3    +      -       -      +
    149A  LYS*     5.0     3.4    -      -       +      -
    154A  GLU*     3.2    36.6    -      -       +      +
    155A  ARG      2.9    32.9    +      -       -      +
    156A  GLN*     4.1    16.4    -      -       +      +
    159A  VAL*     5.1     1.6    -      -       -      +
    193A  THR      3.5     0.9    -      -       -      +
    194A  CYS*     3.4     5.5    -      -       -      -
    195A  GLU*     2.9    51.1    +      -       +      +
    197A  THR*     5.2     4.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 148 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117A  ILE*     3.8    15.9    -      -       +      -
    132A  VAL*     3.5    45.8    -      -       +      -
    133A  VAL      4.1     0.4    -      -       -      -
    134A  CYS*     3.5    33.7    -      -       +      -
    146A  VAL*     4.2     5.6    -      -       +      +
    147A  LYS*     1.3    86.8    +      -       -      +
    149A  LYS*     1.3    64.2    +      -       -      +
    150A  ILE*     6.3     0.2    -      -       +      -
    154A  GLU*     3.1    25.1    -      -       -      +
    155A  ARG*     3.1    20.1    +      -       +      +
    159A  VAL*     3.7    28.0    -      -       +      +
    177A  SER*     2.9    36.7    +      -       -      -
    179A  LEU*     4.0    29.3    -      -       +      +
    192A  TYR*     5.4     2.2    -      +       +      -
    193A  THR      3.2    22.7    -      -       -      -
    194A  CYS*     4.1     4.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 149 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    147A  LYS*     5.0     2.0    -      -       +      -
    148A  TRP*     1.3    80.8    -      -       -      +
    150A  ILE*     1.3    63.3    +      -       -      +
    151A  ASP      4.0     0.2    -      -       -      -
    152A  GLY*     3.8    25.5    +      -       -      +
    153A  SER      3.2     7.6    -      -       -      +
    154A  GLU*     3.3    39.6    +      -       +      +
    191A  SER      3.6     3.3    -      -       -      +
    192A  TYR*     3.7     1.4    -      -       -      -
    193A  THR*     2.9    44.4    +      -       +      -
    195A  GLU*     3.4    36.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 150 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    148A  TRP      5.6     0.2    -      -       -      -
    149A  LYS*     1.3    76.3    -      -       -      +
    151A  ASP*     1.3    72.0    +      -       -      +
    152A  GLY      3.0     0.2    -      -       -      -
    153A  SER*     2.8    25.8    +      -       -      +
    155A  ARG*     3.8    36.1    -      -       +      -
    179A  LEU*     4.0    20.0    -      -       +      -
    181A  LEU*     4.1    11.2    -      -       +      -
    189A  HIS*     3.4    47.2    -      -       +      +
    191A  SER      3.4     2.9    -      -       -      -
    192A  TYR*     3.6    26.7    -      -       +      -
----------------------------------------------------------
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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