Contacts of the strand formed by residues 64 - 68 (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 LEU 64 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33H  LEU*     5.1     9.0    -      -       +      -
     34H  PHE      3.2    11.2    -      -       -      +
     35H  ARG*     5.1     0.7    -      -       -      -
     36H  LYS*     3.8     6.4    -      -       -      -
     41H  LEU*     3.4    32.8    -      -       +      -
     59H  LEU*     3.3    28.9    -      -       +      -
     60H  THR*     3.9    25.1    -      -       +      -
     61H  GLU      3.0    10.3    +      -       -      +
     63H  ASP*     1.3    86.4    -      -       -      +
     65H  LEU*     1.3    78.0    +      -       -      +
     66H  VAL*     5.8     0.7    -      -       +      -
     83H  SER      5.0     0.2    -      -       -      +
     84H  MET*     5.0     3.3    -      -       -      +
     85H  LEU*     3.7    22.8    +      -       +      +
     88H  ILE*     3.7     7.4    -      -       +      -
    106H  MET*     3.7    17.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 65 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33H  LEU*     3.5     4.3    -      -       -      +
     34H  PHE*     2.7    47.1    +      -       +      +
     36H  LYS*     3.8    17.9    -      -       +      -
     64H  LEU*     1.3    85.2    -      -       -      +
     66H  VAL*     1.3    64.8    +      -       -      +
     67H  ARG*     5.1     0.9    -      -       +      -
     82H  ILE*     4.2    15.9    -      -       +      -
     83H  SER      3.8    13.9    -      -       -      +
     84H  MET*     4.3    11.4    -      -       +      +
     85H  LEU*     5.8     0.2    -      -       -      -
     59I  ILE*     3.6    31.0    -      -       +      -
     63I  TYS      3.3    28.3    -      -       -      +
     64I  LEU*     3.7    12.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 66 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31H  VAL*     3.2    26.0    -      -       +      -
     32H  MET      3.5     3.1    -      -       -      -
     33H  LEU*     3.7    20.9    -      -       +      -
     52H  VAL*     4.0    12.6    -      -       +      -
     64H  LEU*     5.8     0.2    -      -       +      -
     65H  LEU*     1.3    76.7    -      -       -      +
     67H  ARG*     1.3    60.5    +      -       -      +
     68H  ILE*     3.7    19.8    +      -       +      +
     81H  LYS      3.4     1.7    -      -       -      +
     82H  ILE*     3.4     4.3    -      -       -      -
     83H  SER*     3.1    35.0    +      -       -      +
     85H  LEU*     3.6    32.1    -      -       +      -
    106H  MET*     4.9     0.9    -      -       -      -
    108H  LEU*     4.2    10.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 67 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30H  GLN      4.8     0.2    -      -       -      +
     31H  VAL*     3.7     1.2    -      -       -      -
     32H  MET*     2.8    45.8    +      -       +      +
     34H  PHE*     3.2    65.2    -      -       +      -
     65H  LEU*     4.9     0.7    -      -       +      -
     66H  VAL*     1.3    76.5    -      -       -      +
     68H  ILE*     1.3    61.9    -      -       -      +
     70H  LYS*     3.4    28.1    -      -       +      +
     73H  ARG      5.0     0.6    +      -       -      -
     74H  THR      5.3     1.0    -      -       -      -
     75H  ARG      3.6    23.0    +      -       -      +
     76H  TYR*     3.8    11.3    -      -       -      +
     80H  GLU*     2.9    28.5    +      -       -      +
     81H  LYS      3.4     4.7    -      -       -      -
     82H  ILE*     4.0    16.5    -      -       +      +
    141H  TRP*     5.3     0.3    -      -       -      -
     56I  PHE*     4.2    10.7    -      -       -      +
     57I  GLU      5.2     1.0    +      -       -      -
     59I  ILE*     3.9    16.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 68 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28H  PRO      4.5     7.0    -      -       -      +
     30H  GLN      4.3     6.5    -      -       -      +
     31H  VAL*     4.2    19.1    -      -       +      -
     46H  LEU*     4.4    15.0    -      -       +      -
     52H  VAL*     4.9     0.7    -      -       +      -
     66H  VAL*     3.7    27.1    -      -       +      +
     67H  ARG*     1.3    77.6    -      -       -      +
     69H  GLY*     1.3    62.4    +      -       -      +
     70H  LYS      3.3     2.7    -      -       -      -
     80H  GLU*     3.0     6.1    -      -       -      +
     81H  LYS*     2.9    37.1    +      -       +      +
     83H  SER*     4.9     4.9    -      -       -      +
    108H  LEU*     4.5    11.4    -      -       +      -
    112H  VAL*     4.3    27.1    -      -       +      -
    118H  ILE*     3.9    29.5    -      -       +      +
----------------------------------------------------------
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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