Contacts of the helix formed by residues 541 - 547 (chain J) in PDB entry 6H25


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 PRO 541 (chain J).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    444J  PHE*     3.6    44.9    -      -       +      -
    448J  VAL*     4.8     4.5    -      -       +      +
    449J  LEU*     5.3     7.2    -      -       +      -
    452J  LEU*     4.7    22.0    -      -       +      -
    519J  LEU*     4.0    26.9    -      -       +      -
    522J  GLU*     6.5     0.2    -      -       +      -
    539J  MET      4.1     1.3    -      -       -      +
    540J  VAL*     1.3    95.9    -      -       +      +
    542J  GLU*     1.3    65.8    +      -       -      +
    543J  LEU*     3.2     4.7    +      -       +      +
    544J  LEU*     3.3     5.0    +      -       +      +
    545J  SER*     3.2    18.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 542 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    444J  PHE*     4.7     4.2    -      -       +      -
    538J  ASP*     5.2     8.3    -      -       -      +
    540J  VAL      3.8     0.6    +      -       -      -
    541J  PRO*     1.3    72.4    -      -       -      +
    543J  LEU*     1.3    55.5    +      -       -      +
    545J  SER*     3.9     5.6    -      -       -      -
    546J  SER*     2.3    50.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 543 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    449J  LEU*     5.6     5.2    -      -       +      -
    452J  LEU*     3.8    36.8    -      -       +      -
    453J  PRO      4.5     5.6    -      -       -      +
    455J  MET*     4.6    21.8    -      -       +      -
    541J  PRO*     3.2     1.1    -      -       +      -
    542J  GLU*     1.3    77.0    -      -       -      +
    544J  LEU*     1.3    60.1    +      -       -      +
    547J  ASN*     3.0    41.2    +      -       +      +
    548J  LEU*     3.7    26.7    +      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 544 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    452J  LEU*     4.1    27.1    -      -       +      +
    453J  PRO*     4.5     4.3    -      -       +      -
    509J  VAL*     5.1    12.3    -      -       +      -
    512J  PHE*     3.6    31.6    -      -       +      -
    513J  ILE*     5.7     3.4    -      -       +      -
    519J  LEU*     5.8     3.6    -      -       +      -
    540J  VAL*     3.7    26.0    -      -       +      -
    541J  PRO*     3.3     4.2    +      -       -      +
    543J  LEU*     1.3    80.5    -      -       -      +
    545J  SER*     1.3    59.4    +      -       -      +
    548J  LEU*     2.9    47.4    +      -       +      -
    549J  CYS*     3.1    35.7    +      -       +      -
----------------------------------------------------------
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Residues in contact with SER 545 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    484J  THR*     5.8     0.2    -      -       -      -
    485J  ASP*     3.3    18.7    -      -       -      +
    536J  ARG*     5.6     0.9    +      -       -      -
    538J  ASP*     4.2    12.1    +      -       -      -
    540J  VAL*     3.8    24.7    +      -       -      -
    541J  PRO      3.2    14.1    +      -       -      -
    542J  GLU*     3.9     6.6    -      -       -      -
    544J  LEU*     1.3    80.5    -      -       -      +
    546J  SER*     1.3    62.0    +      -       -      +
    549J  CYS*     5.1     2.7    -      -       -      +
    550J  SER*     3.3    21.3    +      -       -      +
    779J  ILE*     4.2    21.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 546 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    484J  THR*     3.8    25.7    -      -       -      +
    542J  GLU*     2.3    36.4    +      -       -      +
    545J  SER*     1.3    81.0    +      -       -      +
    547J  ASN*     1.3    74.7    +      -       -      +
    550J  SER*     3.4    17.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 547 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    543J  LEU*     3.0    19.9    +      -       +      +
    546J  SER*     1.3    92.8    +      -       -      +
    548J  LEU*     1.3    75.2    +      -       +      +
    549J  CYS      3.4     2.9    +      -       -      -
    550J  SER      3.8    12.2    -      -       -      +
    552J  LYS*     5.8     1.7    -      -       -      +
----------------------------------------------------------
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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