Contacts of the strand formed by residues 100 - 108 (chain H) in PDB entry 6AHU


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 CYS 100 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26H  LEU*     5.1     5.8    -      -       -      -
     27H  GLU      3.3    17.9    -      -       -      -
     28H  PHE*     3.6    33.2    -      -       +      +
     43H  LEU*     6.4     1.6    -      -       -      -
     92H  LEU*     3.4    36.3    -      -       +      +
     93H  GLY      6.1     0.2    -      -       -      -
     94H  SER*     4.5    15.4    -      -       -      -
     98H  LYS      3.7     4.9    +      -       -      +
     99H  LYS*     1.3    75.7    -      -       -      +
    101H  ALA*     1.3    89.6    +      -       -      +
    195J  LEU*     4.2    11.0    +      -       -      +
    198J  ARG*     3.7     0.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 101 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26H  LEU*     4.3     4.0    -      -       -      +
     27H  GLU*     3.4    28.8    +      -       +      +
     92H  LEU*     5.0     1.3    -      -       -      -
    100H  CYS*     1.3    92.8    -      -       -      +
    102H  PHE*     1.3    61.7    +      -       -      +
    103H  ARG*     4.2    16.8    -      -       +      +
    195J  LEU*     4.2    21.8    -      -       +      -
    198J  ARG*     3.5    22.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 102 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22H  MET*     4.7    10.8    -      -       +      -
     24H  VAL*     3.6    41.1    -      -       +      -
     25H  CYS      3.9     7.4    -      -       -      -
     26H  LEU*     3.7    19.7    -      -       +      -
     40H  PHE*     5.0     4.3    -      +       -      -
     43H  LEU*     6.4     1.3    -      -       +      -
     75H  LEU*     5.5     0.7    -      -       +      -
     85H  LEU      5.4     1.1    -      -       -      -
     86H  TRP*     6.0     2.5    -      -       -      -
     89H  LEU*     3.3    63.3    -      -       +      +
     90H  THR*     5.6     0.4    -      -       -      -
     92H  LEU*     6.0     1.6    -      -       -      -
    100H  CYS*     6.0     0.2    -      -       -      -
    101H  ALA*     1.3    75.0    -      -       -      +
    103H  ARG*     1.3    62.1    +      -       -      +
    104H  VAL*     3.6    28.4    +      -       +      +
    198J  ARG*     3.3    26.5    +      -       -      +
    202J  ASP*     5.0     7.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 103 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25H  CYS*     3.1    41.4    +      -       +      +
     26H  LEU      6.0     0.2    -      -       -      -
     27H  GLU*     2.7    47.3    +      -       +      +
    101H  ALA*     4.2     8.1    +      -       +      +
    102H  PHE*     1.3    83.0    -      -       -      +
    104H  VAL*     1.3    62.2    +      -       -      +
    105H  ILE*     4.7     2.6    -      -       +      +
     24J  THR*     3.4    33.5    -      -       -      +
     27J  HIS*     4.7     5.7    -      -       -      -
     28J  LEU*     3.6    40.6    -      -       +      +
    195J  LEU*     3.4    19.3    -      -       -      +
    197J  ILE*     3.1    35.2    +      -       -      +
    198J  ARG*     4.7     3.8    -      -       -      -
    199J  GLY*     4.8     6.1    -      -       -      +
    202J  ASP*     6.3     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 104 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22H  MET*     4.4    11.2    -      -       +      -
     23H  LYS      4.0    11.9    -      -       -      +
     25H  CYS      5.3     0.2    -      -       -      +
     86H  TRP*     5.4     3.1    -      -       +      +
    102H  PHE*     3.6    31.0    -      -       +      -
    103H  ARG*     1.3    72.5    -      -       -      +
    105H  ILE*     1.3    67.9    +      -       -      +
    106H  GLN*     4.0     7.2    -      -       -      +
    107H  VAL*     3.7    29.8    -      -       +      -
    119H  ARG*     5.5     1.4    +      -       -      -
     28J  LEU*     6.1     0.7    -      -       -      +
    199J  GLY*     6.0     1.2    -      -       -      +
    201J  TYR*     5.8     8.0    -      -       +      +
    202J  ASP*     4.1    29.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 105 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23H  LYS*     3.8    44.1    +      -       +      +
     25H  CYS*     3.8    34.1    -      -       +      +
    103H  ARG*     3.8     2.9    +      -       +      +
    104H  VAL*     1.3    80.6    -      -       -      +
    106H  GLN*     1.3    68.6    +      -       +      +
    117H  ASN*     4.9     2.5    -      -       -      +
    118H  SER*     5.4     0.5    -      -       -      -
    119H  ARG*     3.8    56.7    -      -       +      +
    201J  TYR*     5.3     8.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 106 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22H  MET*     4.0     0.2    -      -       -      -
     23H  LYS*     3.1    62.7    +      -       +      +
    104H  VAL*     3.8     2.1    -      -       -      +
    105H  ILE*     1.3    84.5    -      -       +      +
    107H  VAL*     1.3    67.6    +      -       -      +
    108H  SER*     4.3     0.7    -      -       -      -
    114H  LEU*     2.4    43.5    +      -       +      +
    115H  SER      4.9     1.0    +      -       -      -
    116H  GLY      5.1     0.2    -      -       -      -
    117H  ASN*     3.2     8.5    -      -       -      +
    118H  SER*     2.8    51.4    +      -       -      +
    119H  ARG      5.0     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 107 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20H  HIS*     5.4     2.0    -      -       +      +
     21H  TYR      3.7    12.3    -      -       -      +
     22H  MET*     3.8    17.7    -      -       +      -
     82H  LEU*     4.3    13.0    -      -       +      -
     86H  TRP*     3.6    37.0    -      -       +      +
    104H  VAL*     3.7    20.6    -      -       +      -
    106H  GLN*     1.3    80.2    -      -       -      +
    108H  SER*     1.3    66.9    +      -       -      +
    109H  PRO*     5.9     0.4    -      -       +      -
    333L  LYS      4.2     9.1    -      -       -      +
    334L  GLY*     3.8    22.9    -      -       -      -
    335L  GLY      4.4     0.5    +      -       -      -
    336L  GLU*     4.5     3.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 108 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20H  HIS*     5.0     0.7    -      -       -      -
     21H  TYR*     2.9    26.3    +      -       -      +
    106H  GLN*     6.4     0.7    -      -       -      -
    107H  VAL*     1.3    78.6    -      -       -      +
    109H  PRO*     1.3    68.7    -      -       -      +
    110H  PHE      3.0    23.8    +      -       -      -
    113H  ALA*     4.0    11.0    -      -       -      -
    114H  LEU*     3.3    22.1    +      -       -      +
    118H  SER*     5.8     0.4    -      -       -      -
    335L  GLY      5.4     0.7    -      -       -      +
    336L  GLU*     3.5    24.5    -      -       -      -
----------------------------------------------------------
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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