Contacts of the strand formed by residues 72 - 80 (chain I) 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 LYS 72 (chain I).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63A    C      3.4    47.6    +      -       -      +
     31I  SER      3.2     6.4    +      -       -      +
     32I  VAL*     3.5    45.0    -      -       +      +
     33I  VAL      3.7     0.5    +      -       -      -
     70I  PRO      3.7     5.1    +      -       -      +
     71I  ILE*     1.3    68.7    -      -       -      +
     73I  ILE*     1.3    61.4    +      -       -      +
     74I  LEU*     3.7     9.5    +      -       +      +
    229I  LEU*     5.4    12.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 73 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22I  VAL*     4.9    17.9    -      -       +      -
     33I  VAL*     3.4    17.5    -      -       +      +
     35I  ILE*     5.2     7.0    -      -       +      -
     54I  VAL*     3.8    42.8    -      -       +      -
     58I  PHE*     5.1    13.2    -      -       +      -
     62I  PRO*     5.2     6.1    -      -       +      -
     71I  ILE*     3.2    29.2    +      -       +      +
     72I  LYS*     1.3    70.2    -      -       -      +
     74I  LEU*     1.3    71.5    -      -       -      +
     75I  THR*     5.4     1.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 74 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32I  VAL*     4.0    15.7    -      -       +      -
     33I  VAL      3.5     5.1    +      -       -      -
     34I  ALA*     3.4    28.8    -      -       +      -
     35I  ILE*     3.5     6.1    +      -       -      +
     72I  LYS*     3.7    15.4    +      -       +      +
     73I  ILE*     1.3    85.8    -      -       -      +
     75I  THR*     1.3    69.8    +      -       -      +
     76I  ARG*     4.0    26.7    -      -       +      +
    101I  ASP*     4.9    11.4    -      -       +      +
    102I  VAL*     5.3     2.2    -      -       +      -
    229I  LEU*     3.8    39.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 75 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35I  ILE*     4.2     6.1    -      -       +      +
     37I  HIS*     5.5     4.7    -      -       -      +
     51I  PRO*     5.4     7.4    -      -       +      -
     52I  VAL*     6.3     1.6    -      -       +      -
     54I  VAL*     5.3    12.6    -      -       +      -
     73I  ILE*     5.4     1.6    -      -       +      +
     74I  LEU*     1.3    80.4    -      -       -      +
     76I  ARG*     1.3    64.0    +      -       -      +
    100I  TYR*     3.6    44.1    +      -       +      -
    101I  ASP*     3.7    11.5    +      -       -      +
    102I  VAL      4.3     0.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 76 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6I  ASP*     5.7     3.4    +      -       -      +
      8I  ASP*     2.4    50.3    +      -       -      -
     32I  VAL*     5.1     5.9    -      -       -      +
     34I  ALA*     4.0    11.6    -      -       +      +
     35I  ILE      3.0    20.3    +      -       -      +
     36I  ASN*     3.3    25.1    -      -       -      +
     37I  HIS*     3.6    10.4    +      -       -      -
     74I  LEU*     4.0    24.0    -      -       +      +
     75I  THR*     1.3    78.8    -      -       -      +
     77I  LEU*     1.3    62.4    +      -       -      +
    100I  TYR*     4.9     2.5    -      -       -      -
    102I  VAL*     3.5    47.9    -      -       +      +
    104I  ALA*     6.2     2.0    -      -       +      -
    124I  LEU*     4.6     9.1    -      -       -      +
    225I  CYS      4.8     4.6    +      -       -      -
    228I  ALA*     3.9    25.4    -      -       -      +
    229I  LEU*     4.6     5.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 77 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36I  ASN*     4.7     0.6    -      -       -      +
     37I  HIS*     3.7    24.7    -      -       +      +
     39I  VAL*     3.8    22.0    -      -       +      -
     48I  ILE*     5.7     4.3    -      -       +      -
     76I  ARG*     1.3    75.6    -      -       -      +
     78I  THR*     1.3    67.5    +      -       -      +
     79I  ILE*     3.7    29.8    -      -       +      -
    100I  TYR*     3.6    43.2    -      -       +      +
    102I  VAL      3.5     6.1    +      -       -      +
    103I  VAL*     5.1     6.1    -      -       +      -
    104I  ALA*     3.0    32.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 78 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10I  ARG*     4.0    19.9    +      -       -      +
     36I  ASN*     3.5    27.6    +      -       -      +
     37I  HIS      2.9    30.3    +      -       -      +
     38I  ILE*     3.9     6.5    -      -       +      -
     39I  VAL*     3.2    14.6    +      -       -      +
     77I  LEU*     1.3    74.6    +      -       -      +
     79I  ILE*     1.3    67.7    +      -       -      +
     80I  ILE*     3.9    10.5    +      -       +      +
    104I  ALA*     3.4     5.8    -      -       -      +
    106I  PHE*     5.1     1.3    -      -       +      -
    126I  CYS*     3.7    28.1    -      -       +      -
    153I  GLU*     5.1     1.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 79 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39I  VAL*     3.5    15.0    -      -       +      +
     77I  LEU*     3.7    32.8    -      -       +      +
     78I  THR*     1.3    72.7    -      -       -      +
     80I  ILE*     1.3    60.2    +      -       -      +
     81I  VAL*     3.5    12.7    +      -       +      -
     86I  HIS*     3.6    29.2    -      -       +      -
     90I  LEU*     3.8    25.1    -      -       +      -
    103I  VAL*     3.8    20.9    -      -       +      -
    104I  ALA      3.1    21.0    +      -       -      +
    105I  VAL*     3.6     7.0    -      -       +      +
    106I  PHE*     2.7    33.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 80 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38I  ILE*     3.9    27.4    -      -       +      -
     39I  VAL      2.8    19.2    +      -       -      +
     40I  ASP*     3.9    24.7    -      -       +      +
     41I  PHE*     4.3    10.5    +      -       +      -
     78I  THR*     4.9    10.3    -      -       +      +
     79I  ILE*     1.3    71.0    -      -       -      +
     81I  VAL*     1.3    64.2    +      -       -      +
     82I  SER      4.2     1.0    +      -       -      -
     86I  HIS*     3.9     8.3    +      -       -      -
    106I  PHE*     3.7    31.0    -      -       +      -
    108I  LYS*     4.1    19.1    -      -       -      +
----------------------------------------------------------
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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