Contacts of the strand formed by residues 394 - 402 (chain F) in PDB entry 6M17


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 ASN 394 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    357F  ARG*     3.0    35.1    +      -       -      +
    358F  ILE      3.4    14.6    -      -       -      +
    359F  SER*     4.3     6.5    -      -       -      +
    392F  PHE*     3.8     2.8    -      -       -      +
    393F  THR*     1.3    89.4    -      -       -      +
    395F  VAL*     1.3    64.3    +      -       -      +
    396F  TYR*     3.7    20.7    +      -       +      -
    515F  PHE*     3.6     2.6    -      -       -      -
    516F  GLU*     2.9    51.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 395 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    338F  PHE*     6.0     1.6    -      -       +      -
    357F  ARG      3.6     1.6    -      -       -      -
    358F  ILE*     2.9    51.8    +      -       +      +
    359F  SER*     5.6     0.2    -      -       -      +
    365F  TYR*     4.0    15.5    -      -       +      +
    392F  PHE*     5.2     6.5    -      -       +      -
    394F  ASN*     1.3    77.5    -      -       -      +
    396F  TYR*     1.3    76.6    +      -       -      +
    513F  LEU*     3.9    19.7    -      -       +      -
    514F  SER      3.6     4.5    -      -       -      +
    515F  PHE*     3.7    32.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 396 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    355F  ARG*     3.6    47.6    -      -       +      +
    356F  LYS      3.5     3.4    -      -       -      +
    357F  ARG*     3.1    54.1    +      -       +      -
    358F  ILE*     5.2     0.2    -      -       -      -
    394F  ASN*     3.7    15.9    +      -       +      -
    395F  VAL*     1.3    80.3    -      -       -      +
    397F  ALA*     1.3    61.8    +      -       -      +
    398F  ASP*     4.2     1.1    -      -       -      +
    512F  VAL      3.6     0.7    -      -       -      +
    513F  LEU*     3.3     4.0    -      -       -      -
    514F  SER*     2.9    48.7    +      -       -      +
    516F  GLU*     3.5    33.8    +      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 397 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    341F  VAL*     3.8    28.7    -      -       +      -
    354F  ASN*     5.6     0.2    -      -       -      +
    355F  ARG*     3.7     0.9    +      -       -      -
    356F  LYS*     2.8    40.4    +      -       +      +
    358F  ILE*     4.5    10.5    -      -       +      +
    396F  TYR*     1.3    74.5    -      -       -      +
    398F  ASP*     1.3    64.7    +      -       -      +
    399F  SER*     4.2     3.3    +      -       -      -
    511F  VAL*     4.7     5.8    -      -       +      -
    512F  VAL      3.5     4.7    -      -       -      +
    513F  LEU*     4.2    15.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 398 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    353F  TRP*     3.9    14.0    -      -       +      -
    354F  ASN      3.5    10.5    -      -       -      +
    355F  ARG*     3.1    38.8    +      -       -      -
    396F  TYR*     4.3     0.6    -      -       -      +
    397F  ALA*     1.3    79.5    +      -       -      +
    399F  SER*     1.3    64.4    +      -       -      +
    400F  PHE*     4.5     5.0    -      -       +      -
    423F  TYR*     2.5    38.1    +      -       +      +
    464F  PHE*     4.0     3.3    -      -       -      -
    510F  VAL      3.8     0.5    -      -       -      +
    511F  VAL*     3.2     7.1    -      -       -      +
    512F  VAL*     2.9    37.7    +      -       +      +
    514F  SER*     5.7     1.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 399 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    341F  VAL*     4.5    12.7    +      -       -      +
    347F  PHE*     4.0    20.4    -      -       -      -
    348F  ALA*     3.9     6.2    -      -       -      +
    353F  TRP*     3.6     0.7    -      -       -      -
    354F  ASN*     3.1    41.3    +      -       -      +
    356F  LYS*     6.0     0.7    -      -       -      +
    397F  ALA      4.3     5.4    +      -       -      -
    398F  ASP*     1.3    79.8    +      -       -      +
    400F  PHE*     1.3    69.6    +      -       -      +
    510F  VAL      3.4     4.7    -      -       -      -
    511F  VAL*     4.3     8.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 400 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    347F  PHE*     3.2    11.3    -      -       -      -
    348F  ALA      3.1     9.9    -      -       -      -
    349F  SER      3.1    20.6    -      -       -      +
    350F  VAL*     3.9    20.2    -      -       +      -
    353F  TRP*     3.7    15.5    -      +       +      -
    398F  ASP*     4.7     2.5    -      -       +      -
    399F  SER*     1.3    86.3    -      -       -      +
    401F  VAL*     1.3    66.0    +      -       -      +
    402F  ILE*     4.1    12.3    -      -       +      -
    410F  ILE*     4.0    20.2    -      -       +      -
    423F  TYR*     4.0    42.6    -      +       +      -
    510F  VAL*     3.0    53.6    +      -       +      -
    512F  VAL*     4.5     9.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 401 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    347F  PHE*     3.6    25.6    -      -       +      -
    348F  ALA      3.3     3.6    +      -       -      +
    350F  VAL*     3.6    15.8    +      -       -      +
    400F  PHE*     1.3    81.0    -      -       -      +
    402F  ILE*     1.3    76.1    +      -       -      +
    442F  ASP*     4.3     3.6    -      -       -      +
    451F  TYR*     4.0    40.2    -      -       +      +
    495F  TYR*     4.4     5.9    -      -       -      -
    497F  PHE*     4.5     5.2    -      -       +      -
    507F  PRO*     4.2    17.3    -      -       +      -
    508F  TYR      3.4     8.7    -      -       -      +
    509F  ARG*     3.6    17.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 402 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    350F  VAL*     3.2    35.0    -      -       +      -
    400F  PHE*     4.1     6.3    -      -       +      -
    401F  VAL*     1.3    73.8    -      -       -      +
    403F  ARG*     1.3    70.3    +      -       -      +
    406F  GLU*     3.7    43.3    -      -       -      +
    407F  VAL*     4.1     8.7    -      -       +      -
    410F  ILE*     4.2    12.8    -      -       +      -
    418F  ILE*     4.2     6.5    -      -       +      -
    495F  TYR*     4.3     6.1    -      -       -      +
    497F  PHE*     4.5     5.6    -      -       -      -
    507F  PRO*     3.5     6.2    -      -       -      +
    508F  TYR      2.9    27.2    +      -       -      +
    510F  VAL*     3.7    29.6    -      -       +      -
----------------------------------------------------------
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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