Contacts of the strand formed by residues 395 - 399 (chain X) in PDB entry 3Q0F


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 ILE 395 (chain X).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5C  5CM      4.3     5.2    -      -       +      -
    388X  HIS*     3.7     1.3    -      -       -      -
    390X  PRO*     3.9     9.4    -      -       -      +
    393X  SER*     3.4    14.4    +      -       -      -
    394X  GLY*     1.3    81.0    -      -       -      +
    396X  ASP*     1.3    71.5    +      -       -      +
    397X  TYR*     4.4     8.7    -      -       +      -
    407X  ALA*     4.6     5.6    -      -       +      -
    409X  SER      3.8     5.2    -      -       -      +
    410X  ILE*     4.5     2.9    -      -       +      -
    428X  TYR*     3.8    20.9    -      -       +      +
    430X  GLY*     4.8     1.3    -      -       -      -
    431X  GLN*     4.0    17.8    +      -       +      +
    452X  GLY*     3.5    36.1    -      -       -      +
    453X  ASN*     3.7    22.7    -      -       -      +
    455X  ALA*     5.0     0.2    -      -       +      -
    456X  LEU*     3.8    28.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 396 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    362X  GLN*     3.9     4.9    +      -       -      +
    387X  ILE      4.7     0.7    -      -       -      +
    388X  HIS*     3.3    25.7    -      -       +      +
    389X  ARG*     3.0    39.5    +      -       -      +
    390X  PRO*     3.4    20.2    -      -       +      +
    395X  ILE*     1.3    73.4    -      -       -      +
    397X  TYR*     1.3    71.9    +      -       -      +
    407X  ALA*     3.4     4.2    -      -       -      +
    408X  THR*     2.7    39.7    +      -       -      -
    409X  SER*     2.9    19.0    +      -       -      +
    467X  ARG*     5.2     0.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 397 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10B    A      4.4     5.6    +      -       -      -
     11B    T      3.2    28.0    +      -       -      -
    362X  GLN*     3.2     4.1    +      -       -      -
    389X  ARG*     3.1    24.8    +      -       -      -
    395X  ILE*     4.4     5.6    -      -       +      -
    396X  ASP*     1.3    84.2    +      -       -      +
    398X  MET*     1.3    66.2    +      -       -      +
    405X  LEU*     3.8    32.5    -      -       +      +
    406X  VAL      3.1    17.0    -      -       -      +
    408X  THR*     3.9     3.1    -      -       -      -
    431X  GLN*     5.5     1.3    -      -       -      -
    451X  THR*     3.6    23.9    -      -       -      +
    452X  GLY*     3.5    30.5    -      -       -      -
    455X  ALA*     3.4    17.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 398 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    362X  GLN*     3.8    41.7    -      -       +      +
    364X  ILE*     3.8    31.0    -      -       +      -
    389X  ARG*     4.9     2.0    -      -       -      +
    397X  TYR*     1.3    81.0    -      -       -      +
    399X  LYS*     1.3    81.9    +      -       -      +
    400X  ASP*     5.4     1.3    -      -       -      -
    405X  LEU*     3.1     8.3    -      -       -      +
    406X  VAL*     2.9    43.6    +      -       +      +
    408X  THR*     4.1     5.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 399 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11B    T      4.2    20.3    +      -       -      -
    398X  MET*     1.3    99.4    -      -       -      +
    400X  ASP*     1.3    64.4    +      -       -      +
    401X  ASP      4.0     0.5    +      -       -      -
    403X  GLY*     4.0    16.4    -      -       -      +
    404X  GLU      3.2     4.5    -      -       -      +
    405X  LEU*     3.9    22.7    -      -       +      -
----------------------------------------------------------
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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