Contacts of the strand formed by residues 104 - 108 (chain F) in PDB entry 1C9T


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 MET 104 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33F  LEU*     4.6     1.6    -      -       +      -
     53F  VAL*     3.6     6.2    -      -       -      +
     54F  SER*     2.7    45.0    +      -       -      +
     55F  ALA      3.3    18.6    -      -       -      +
     56F  ALA*     3.5    13.7    -      -       +      +
     58F  CYS*     3.9     6.3    -      -       +      +
     59F  TYR*     3.5    49.6    -      -       -      +
     63F  ILE*     4.6     1.8    -      -       +      -
     88F  SER*     4.9     2.7    -      -       -      -
     89F  ILE      3.5    21.3    -      -       -      +
     90F  VAL*     3.9     2.7    -      -       +      -
    103F  ILE*     1.3    74.7    -      -       -      +
    105F  LEU*     1.3    71.9    +      -       -      +
    106F  ILE*     4.0    26.9    -      -       +      -
    237F  TRP*     4.6     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 105 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47F  ILE*     4.5     3.1    -      -       +      -
     51F  TRP*     3.8    18.4    -      -       +      -
     52F  VAL      3.7     2.0    -      -       -      +
     53F  VAL*     3.9    24.5    -      -       +      +
     87F  LYS      3.9     0.9    -      -       -      +
     88F  SER*     3.6     1.0    -      -       -      -
     89F  ILE*     2.8    47.5    +      -       +      +
    104F  MET*     1.3    78.1    -      -       -      +
    106F  ILE*     1.3    61.3    +      -       -      +
    237F  TRP*     3.7    17.0    -      -       +      -
    238F  ILE*     3.7    42.6    -      -       +      +
    241F  THR*     3.7    31.0    -      -       +      -
    242F  ILE*     4.5     8.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 106 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33F  LEU*     3.7    39.5    -      -       +      -
     51F  TRP*     3.2     8.9    -      -       -      -
     52F  VAL*     2.7    54.3    +      -       +      +
     54F  SER*     4.6     4.5    -      -       -      -
     63F  ILE*     4.4    10.5    -      -       +      -
     65F  VAL*     4.4    12.1    -      -       +      -
     85F  ALA*     3.4    29.8    -      -       +      -
     87F  LYS      3.6     4.5    -      -       -      +
     88F  SER*     4.5     8.3    -      -       -      +
    104F  MET*     4.0    22.4    -      -       +      -
    105F  LEU*     1.3    77.7    -      -       -      +
    107F  LYS*     1.3    65.7    +      -       -      +
    108F  LEU*     4.1     1.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 107 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50B  GLN*     2.8    37.9    +      -       -      +
    111B  ALA*     4.5     4.6    -      -       -      +
     50F  GLN*     3.5    30.1    -      -       -      +
     51F  TRP*     3.6    29.3    -      -       +      +
     85F  ALA*     3.3     4.7    -      -       -      -
     86F  SER*     2.6    38.0    +      -       -      -
     87F  LYS*     2.8    39.9    +      -       +      +
    106F  ILE*     1.3    74.5    -      -       -      +
    108F  LEU*     1.3    61.5    +      -       -      +
    245F  ASN      2.9    28.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 108 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46F  LEU*     4.5     3.1    -      -       +      -
     49F  SER      3.5    23.6    -      -       -      +
     50F  GLN*     2.9    31.3    +      -       -      +
     52F  VAL*     4.0    20.9    -      -       +      -
     65F  VAL*     3.4    39.3    -      -       +      -
     67F  LEU*     4.5     4.3    -      -       +      -
     83F  ILE*     3.8    17.9    -      -       +      -
     84F  SER      3.7     3.8    -      -       -      +
     85F  ALA*     5.1     0.2    -      -       -      -
     86F  SER*     4.1     1.4    -      -       -      -
    106F  ILE*     4.7     2.0    -      -       +      -
    107F  LYS*     1.3    77.2    -      -       -      +
    109F  LYS*     1.3    68.4    +      -       -      +
    110F  SER      2.9    21.6    +      -       -      +
    112F  ALA*     3.9    17.0    -      -       +      -
----------------------------------------------------------
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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