Contacts of the strand formed by residues 46 - 52 (chain H) in PDB entry 6PB4


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 SER 46 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45H  GLY*     1.3    73.7    -      -       -      -
     47H  VAL*     1.3    62.6    +      -       -      +
     63H  TYR*     5.5     2.9    -      -       -      -
     64H  LEU      3.5     5.8    -      -       -      -
     65H  ASN*     2.8    21.0    +      -       -      -
     89H  LYS*     3.2    33.1    +      -       -      -
     90H  THR*     2.8    31.5    +      -       -      +
     92H  CYS*     3.1    11.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 47 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29H  LEU*     5.3     6.5    -      -       +      -
     42H  ILE*     4.2    22.2    -      -       +      -
     46H  SER*     1.3    81.3    -      -       -      +
     48H  ALA*     1.3    64.3    +      -       -      +
     49H  VAL*     4.8     2.2    -      -       +      -
     63H  TYR*     3.0     8.9    -      -       -      +
     64H  LEU*     2.8    35.7    +      -       +      +
     86H  VAL*     3.3    34.1    -      -       +      +
     87H  ARG      3.4    19.5    -      -       -      +
     88H  ALA*     3.9    11.9    -      -       +      +
     89H  LYS*     4.0     4.7    -      -       -      +
     92H  CYS*     3.9    13.0    -      -       +      -
     94H  VAL*     5.8     3.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 48 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47H  VAL*     1.3    72.6    -      -       -      +
     49H  VAL*     1.3    62.5    +      -       -      +
     50H  LEU*     3.2    11.3    -      -       +      +
     60H  ILE*     4.5    13.0    -      -       +      -
     62H  SER      3.7     7.9    -      -       -      +
     63H  TYR*     4.2     4.5    -      -       +      +
     86H  VAL*     3.4     1.0    -      -       -      -
     87H  ARG*     2.9    69.1    +      -       -      +
     89H  LYS*     4.9     4.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 49 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47H  VAL*     4.8     2.7    -      -       +      -
     48H  ALA*     1.3    74.8    -      -       -      +
     50H  LEU*     1.3    62.8    +      -       -      +
     60H  ILE*     3.8     0.2    -      -       -      +
     61H  LEU*     3.0     9.0    +      -       +      +
     62H  SER*     2.9    42.9    +      -       -      +
     64H  LEU*     3.6    28.5    -      -       +      -
     70H  ILE*     4.6     7.6    -      -       +      -
     84H  ALA*     4.1    11.0    -      -       +      -
     85H  TRP      3.3     9.6    -      -       -      +
     86H  VAL*     3.9    25.4    -      -       +      -
    301H  CMP      3.2    32.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 50 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48H  ALA*     3.2    26.0    -      -       +      +
     49H  VAL*     1.3    76.1    -      -       -      +
     51H  ILE*     1.3    69.2    +      -       -      +
     58H  GLU*     3.1    25.8    -      -       +      +
     59H  MET      3.2    13.7    -      -       -      +
     60H  ILE*     3.6    21.5    -      -       +      -
     61H  LEU*     4.1     2.5    -      -       -      +
     84H  ALA*     3.4     0.3    -      -       -      +
     85H  TRP*     3.0    55.6    +      -       +      +
     87H  ARG*     4.0    26.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 51 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128G  SER*     5.6     7.9    -      -       -      +
     32H  GLN*     4.4     6.1    -      -       -      +
     50H  LEU*     1.3    81.2    -      -       -      +
     52H  LYS*     1.3    64.9    +      -       -      +
     58H  GLU*     3.0     8.8    -      -       -      +
     59H  MET*     2.7    47.0    +      -       +      +
     61H  LEU*     3.6    37.5    -      -       +      -
     83H  SER      4.3     7.0    -      -       -      +
     84H  ALA*     3.6    20.0    -      -       +      -
     85H  TRP*     4.1     8.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 52 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32H  GLN*     4.5    10.4    +      -       -      +
     51H  ILE*     1.3    81.5    -      -       -      +
     53H  ASP*     1.3    78.4    +      -       -      +
     54H  GLU*     3.5    35.5    +      -       -      +
     56H  GLY*     3.8    15.0    -      -       -      +
     57H  LYS      3.4    10.1    -      -       -      +
     58H  GLU*     3.8     5.6    -      -       +      +
     85H  TRP*     3.4    36.8    -      -       +      -
----------------------------------------------------------
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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