Contacts of the strand formed by residues 27 - 34 (chain B) in PDB entry 6P7B


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 ILE 27 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18B  PHE*     4.9     9.6    -      -       +      -
     19B  ASN      3.8     1.6    -      -       -      -
     20B  TYR*     3.4    33.9    -      -       +      -
     25B  ASN      3.9     6.0    +      -       -      +
     26B  THR*     1.3    73.5    -      -       -      +
     28B  LYS*     1.3    67.1    +      -       -      +
     29B  LEU      4.2     0.4    -      -       -      +
    115B  GLU      4.5     2.1    -      -       -      +
    116B  TYR*     3.6    58.4    -      -       +      +
    141B  LEU*     4.4     6.1    -      -       +      -
    144B  MET*     3.5    38.6    -      -       +      -
    148B  LEU*     6.5     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 28 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18B  PHE*     4.6     1.8    -      -       -      -
     19B  ASN*     2.8    68.3    +      -       +      +
     21B  ASP*     4.4    11.9    +      -       -      +
     26B  THR*     3.8    30.0    +      -       +      +
     27B  ILE*     1.3    80.5    -      -       -      +
     29B  LEU*     1.3    64.1    +      -       -      +
     30B  ILE*     3.2     0.9    +      -       -      +
    116B  TYR      4.0     4.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 29 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18B  PHE*     3.3    37.7    -      -       +      -
     27B  ILE*     4.2     0.8    -      -       -      +
     28B  LYS*     1.3    70.3    -      -       -      +
     30B  ILE*     1.3    65.3    +      -       -      +
     31B  ALA*     4.0    18.6    -      -       -      +
     32B  ILE*     4.1    27.4    -      -       +      -
    113B  ILE*     6.3     0.4    -      -       +      -
    116B  TYR*     3.0    33.1    +      -       +      +
    117B  THR*     3.5    29.6    -      -       +      +
    119B  TYR*     6.2     1.3    -      -       +      -
    123B  ILE*     5.8     3.6    -      -       +      -
    137B  PHE*     4.3    15.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 30 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2B  ILE*     3.7    20.0    -      -       +      -
     17B  ILE*     2.8    31.1    +      -       +      +
     18B  PHE      3.6    11.9    -      -       -      +
     19B  ASN*     3.6    35.2    -      -       +      +
     28B  LYS*     3.2     1.5    +      -       +      +
     29B  LEU*     1.3    78.1    -      -       -      +
     31B  ALA*     1.3    64.4    +      -       +      +
     52B  TYR*     4.7    14.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 31 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15B  TYR*     5.4     1.1    -      -       +      -
     16B  ALA*     3.7     0.3    -      -       -      -
     17B  ILE*     2.8    34.6    +      -       +      +
     29B  LEU*     3.7    11.0    -      -       -      +
     30B  ILE*     1.3    82.6    -      -       +      +
     32B  ILE*     1.3    66.1    +      -       -      +
     33B  GLU*     5.0     7.9    -      -       +      +
     52B  TYR*     3.6    31.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 32 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15B  TYR      3.6    11.4    -      -       -      +
     16B  ALA*     4.2     9.2    -      -       +      -
     29B  LEU*     4.1    22.2    -      -       +      +
     31B  ALA*     1.3    78.7    -      -       -      +
     33B  GLU*     1.3    79.0    +      -       -      +
    109B  PHE*     3.8    20.9    -      -       +      -
    123B  ILE*     4.1    30.7    -      -       +      +
    127B  TYR*     4.1     8.0    +      -       -      -
    133B  ILE*     3.5    45.1    -      -       +      +
    136B  SER*     4.5     0.7    -      -       -      +
    137B  PHE*     4.1    13.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 33 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14B  ALA*     3.5     4.5    -      -       -      +
     15B  TYR*     2.9    63.1    +      -       +      +
     31B  ALA*     5.0     7.2    -      -       +      +
     32B  ILE*     1.3    92.4    +      -       -      +
     34B  LYS*     1.3    65.5    +      -       -      +
     52B  TYR*     5.2     2.7    -      -       -      +
    123B  ILE*     5.4     5.2    -      -       -      +
    127B  TYR*     2.6    26.5    +      -       -      -
    133B  ILE*     3.9     8.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 34 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12B  ASN*     5.7     1.6    -      -       +      -
     13B  PRO      3.4    14.4    -      -       -      +
     14B  ALA*     3.9    11.0    -      -       +      +
     15B  TYR*     5.0     2.0    -      -       -      -
     33B  GLU*     1.3    82.7    +      -       -      +
     35B  SER*     1.3    62.6    +      -       -      +
    126B  LYS*     6.0     0.4    -      -       -      +
    127B  TYR*     3.4    42.0    +      -       +      +
    129B  LYS*     3.3    34.4    +      -       -      +
    132B  ASP*     3.2    23.4    +      -       -      +
    133B  ILE*     4.2     5.2    -      -       +      -
----------------------------------------------------------
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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