Contacts of the strand formed by residues 390 - 396 (chain A) in PDB entry 2Q0N


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 GLU 390 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    351A  LYS*     4.1    12.2    -      -       -      +
    352A  MET      3.3    12.1    -      -       -      +
    353A  ASP*     4.3    18.0    -      -       +      +
    386A  LEU*     3.3     9.9    -      -       -      +
    387A  VAL*     2.8    39.8    +      -       -      +
    388A  GLY      3.3     0.2    -      -       -      -
    389A  ASP*     1.3    82.3    -      -       -      +
    391A  LEU*     1.3    59.5    +      -       -      +
    392A  TRP*     2.8    34.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 391 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    308A  LEU*     4.4     9.2    -      -       +      -
    312A  VAL*     3.7    25.6    -      -       +      -
    350A  LYS      3.5     1.9    -      -       -      +
    351A  LYS*     3.4     4.2    -      -       -      -
    352A  MET*     2.8    64.6    +      -       +      +
    354A  LEU*     3.7    15.2    -      -       +      +
    363A  LEU*     3.8    24.7    -      -       +      +
    366A  GLU*     5.8     0.4    -      -       +      +
    367A  VAL*     3.8    24.9    -      -       +      -
    384A  SER*     4.4     0.9    -      -       -      -
    385A  TYR      3.4    16.2    -      -       -      +
    386A  LEU*     4.0     3.8    -      -       +      -
    390A  GLU*     1.3    72.1    -      -       -      +
    392A  TRP*     1.3    66.6    +      -       -      +
    393A  VAL*     4.0     4.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 392 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    317A  PRO*     3.4    28.0    -      -       +      -
    318A  ARG*     3.8    27.6    -      -       +      -
    321A  LEU*     5.4     1.6    -      -       +      -
    324A  PHE*     3.6    29.2    -      +       -      -
    349A  VAL*     4.0    17.5    -      -       +      -
    350A  LYS      3.2     4.5    -      -       -      +
    351A  LYS*     3.7    32.6    -      -       +      +
    384A  SER*     3.1     6.4    -      -       -      -
    385A  TYR*     2.8    50.6    +      -       +      +
    387A  VAL*     3.6    28.0    -      -       +      +
    390A  GLU*     2.8    36.0    +      -       +      +
    391A  LEU*     1.3    79.3    -      -       -      +
    393A  VAL*     1.3    60.9    +      -       -      +
    394A  VAL*     4.1     2.0    +      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 393 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    348A  ALA      3.8     0.5    -      -       -      +
    349A  VAL*     3.3     4.1    -      -       -      -
    350A  LYS*     2.8    45.6    +      -       +      +
    352A  MET*     4.0    11.9    -      -       +      -
    366A  GLU*     5.2    10.1    -      -       -      +
    367A  VAL*     4.1    15.9    -      -       +      -
    370A  MET*     5.5     1.3    -      -       +      -
    381A  MET*     3.6    19.1    -      -       -      -
    383A  ASN      3.8     2.5    -      -       -      -
    384A  SER*     4.2     3.8    -      -       -      -
    391A  LEU*     4.0    22.4    -      -       +      -
    392A  TRP*     1.3    75.9    -      -       -      +
    394A  VAL*     1.3    62.1    +      -       -      +
    395A  MET*     3.0    32.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 394 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    317A  PRO*     5.1     1.1    -      -       +      -
    321A  LEU*     4.1    21.5    -      -       +      -
    340A  VAL*     6.0     0.2    -      -       +      -
    347A  VAL*     4.0    34.1    -      -       +      -
    348A  ALA      3.5     3.4    -      -       -      +
    349A  VAL*     4.4     9.4    -      -       +      +
    381A  MET*     3.6     2.6    -      -       -      -
    382A  TYR*     2.8    39.8    +      -       +      -
    383A  ASN*     2.8    24.4    +      -       +      +
    385A  TYR*     3.8    31.0    -      -       +      -
    392A  TRP*     4.9     2.0    -      -       +      +
    393A  VAL*     1.3    75.2    -      -       -      +
    395A  MET*     1.3    56.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 395 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    347A  VAL*     3.6     8.5    -      -       -      +
    348A  ALA*     2.8    34.9    +      -       +      +
    350A  LYS*     4.2    22.4    -      -       +      +
    366A  GLU*     5.4     2.7    -      -       -      +
    370A  MET*     3.9    13.7    -      -       -      +
    379A  VAL*     3.5    35.0    -      -       +      -
    380A  GLU      3.4    22.2    -      -       -      +
    381A  MET*     3.9     7.4    -      -       -      -
    382A  TYR*     3.9     5.1    -      -       -      -
    393A  VAL*     3.0    40.8    -      -       +      +
    394A  VAL*     1.3    75.6    -      -       -      +
    396A  GLU*     1.3    72.8    +      -       -      +
    397A  PHE      3.5     0.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 396 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    348A  ALA*     4.0     1.4    -      -       -      +
    378A  VAL      4.3     0.5    -      -       -      +
    379A  VAL*     3.5    23.5    -      -       +      +
    380A  GLU*     2.8    42.5    +      -       -      +
    382A  TYR*     3.4    33.2    +      -       +      +
    395A  MET*     1.3    82.6    -      -       -      +
    397A  PHE*     1.3    61.0    +      -       -      +
    398A  LEU*     3.8    23.1    +      -       +      +
    455A  LYS*     4.0    17.2    +      -       -      +
    597A  EDO      3.6     8.7    +      -       -      -
----------------------------------------------------------
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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