Contacts of the strand formed by residues 104 - 108 (chain H) in PDB entry 1C1V


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 ALA 104 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53H  LEU*     3.4     9.6    -      -       -      +
     54H  THR*     3.1    42.6    +      -       +      -
     56H  ALA*     3.8    21.5    -      -       -      +
     59H  LEU*     4.2     6.3    -      -       +      -
     89H  TYR      3.2    14.6    -      -       -      +
     90H  ILE*     4.0    11.7    -      -       +      -
    103H  ILE*     1.3    76.9    -      -       -      +
    105H  LEU*     1.3    65.9    +      -       -      +
    243H  TRP*     4.3     2.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 105 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47H  ILE*     3.9    20.9    -      -       +      -
     51H  TRP*     4.1    21.1    -      -       +      -
     52H  VAL      3.7    11.0    -      -       -      +
     53H  LEU*     3.4    24.7    -      -       +      -
     88H  ILE*     3.4     2.6    -      -       -      +
     89H  TYR*     2.8    42.7    +      -       +      -
    104H  ALA*     1.3    79.3    -      -       -      +
    106H  MET*     1.3    63.7    +      -       -      +
    243H  TRP*     3.8    19.9    -      -       +      -
    244H  ILE*     4.0    18.8    -      -       +      +
    247H  VAL*     3.6    28.7    -      -       +      -
    248H  ILE*     4.4     2.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 106 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33H  LEU*     3.9    26.9    -      -       +      -
     50H  ARG      3.7     0.2    -      -       -      +
     51H  TRP*     3.3    10.9    -      -       -      -
     52H  VAL*     2.9    48.4    +      -       +      +
     54H  THR*     4.0    22.7    -      -       +      -
     59H  LEU*     3.8    13.5    -      -       +      -
     64H  LEU*     3.7    11.9    -      -       +      -
     85H  LEU*     3.4    47.3    -      -       +      -
     87H  LYS      3.4     6.7    -      -       -      +
     88H  ILE*     3.5    21.5    -      -       +      -
    105H  LEU*     1.3    79.3    -      -       -      +
    107H  LYS*     1.3    60.7    +      -       -      +
    108H  LEU*     4.0     0.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 107 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50H  ARG*     3.6    14.7    -      -       +      +
     51H  TRP*     3.6    36.7    -      -       +      -
     85H  LEU*     3.4     5.7    -      -       -      +
     86H  GLU*     2.7    52.9    +      -       +      +
     87H  LYS*     2.8    23.8    +      -       +      +
     89H  TYR*     4.6     5.6    -      -       -      +
    106H  MET*     1.3    74.1    -      -       -      +
    108H  LEU*     1.3    72.4    +      -       -      +
    251H  PHE      2.6    26.7    +      -       -      +
    252H  GLY*     3.8     8.3    -      -       -      -
    253H  GLU      5.0     6.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 108 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46H  LEU*     5.1     1.1    -      -       +      -
     49H  ASP      4.2    14.8    -      -       -      +
     50H  ARG*     2.9    31.3    +      -       -      +
     52H  VAL*     3.8    30.3    -      -       +      -
     66H  VAL*     4.2    10.8    -      -       +      -
     68H  ILE*     4.5    13.2    -      -       +      -
     83H  SER*     4.1    18.8    -      -       -      +
     84H  MET      3.4     9.2    -      -       -      +
     85H  LEU*     3.7    24.9    -      -       +      -
     86H  GLU*     3.8    10.0    -      -       -      +
    106H  MET      4.7     1.1    -      -       -      +
    107H  LYS*     1.3    84.3    -      -       -      +
    109H  LYS*     1.3    69.4    +      -       -      +
    110H  LYS*     3.7    14.8    -      -       -      +
    112H  VAL*     4.8     4.9    -      -       +      -
----------------------------------------------------------
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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