Contacts of the strand formed by residues 905 - 910 (chain A) in PDB entry 3MP6


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 TYR 905 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    896A  TRP*     3.5    15.2    -      -       -      -
    903A  GLY      3.5    13.2    -      -       -      -
    904A  GLY*     1.3    73.3    -      -       -      +
    906A  ALA*     1.3    60.4    +      -       -      +
    907A  PHE      3.9     3.1    -      -       -      +
    908A  LYS*     3.7    50.3    +      -       +      +
    918A  ASP*     2.5    39.3    +      -       -      -
    919A  VAL      4.2     1.0    +      -       -      -
    920A  GLY*     2.9    52.1    +      -       -      -
    921A  VAL*     3.4     2.3    +      -       -      +
    923A  ASN*     3.5    18.2    -      -       -      -
    994A  LYS*     6.3     0.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 906 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    896A  TRP*     3.5     3.6    -      -       -      -
    905A  TYR*     1.3    73.4    -      -       -      +
    907A  PHE*     1.3    76.2    +      -       +      +
    919A  VAL*     3.2    13.9    -      -       -      +
    920A  GLY      3.1    21.7    +      -       -      -
    996A  PHE*     3.8    20.8    -      -       +      -
   1069A  PRO*     4.9     5.6    -      -       +      -
   1074A  MET*     5.1     0.4    -      -       -      -
   1077A  PHE*     3.5    40.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 907 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    905A  TYR*     3.9     6.8    -      -       -      +
    906A  ALA*     1.3    90.1    +      -       +      +
    908A  LYS*     1.3    63.2    +      -       -      +
    909A  TYR*     3.5     1.0    +      -       -      +
    914A  TYR*     3.5    34.8    -      -       +      -
    915A  ASP      3.7     5.2    -      -       -      +
    916A  ILE*     3.7    25.6    -      -       +      -
    918A  ASP      3.5     1.8    -      -       -      -
    919A  VAL*     3.7    22.4    -      -       +      -
   1069A  PRO*     4.5     5.0    -      -       +      +
   1071A  ILE*     3.8    17.7    -      -       +      -
   1073A  GLN*     3.5    33.9    -      -       +      -
   1074A  MET*     3.8    25.4    -      -       -      -
   1077A  PHE*     3.8    22.0    -      +       +      -
   1106A  ALA      3.8    10.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 908 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    905A  TYR*     3.7    37.1    +      -       +      -
    907A  PHE*     1.3    71.3    -      -       -      +
    909A  TYR*     1.3    68.2    +      -       -      +
    910A  GLU*     3.6     7.8    +      -       +      +
    914A  TYR*     3.4     2.2    -      -       -      -
    915A  ASP*     2.8    30.7    +      -       +      +
    918A  ASP*     3.1    41.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 909 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    907A  PHE      3.5     2.2    +      -       -      -
    908A  LYS*     1.3    76.9    -      -       -      +
    910A  GLU*     1.3    60.3    +      -       -      +
    911A  ASN      5.4     0.2    -      -       -      -
    912A  GLY*     3.2    46.4    +      -       -      -
    913A  LYS*     3.5    11.9    -      -       -      -
    914A  TYR*     3.6    42.8    -      +       +      -
----------------------------------------------------------
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Residues in contact with GLU 910 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    908A  LYS*     3.6     9.9    +      -       +      +
    909A  TYR*     1.3    76.3    -      -       -      +
    911A  ASN*     1.3    93.9    +      -       -      +
    912A  GLY      3.3     2.5    -      -       -      -
    913A  LYS*     2.9    25.2    +      -       -      +
    915A  ASP*     4.7    16.4    -      -       +      +
----------------------------------------------------------
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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