Contacts of the strand formed by residues 397 - 401 (chain D) in PDB entry 2R2N


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 397 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    357D  TRP*     3.2    50.5    -      +       +      -
    358D  ILE      3.2     7.4    -      -       -      -
    359D  LYS*     3.3    43.3    +      -       +      +
    366D  VAL*     3.1    11.3    -      -       -      +
    384D  GLY      2.9    23.1    +      -       -      -
    388D  TYR*     3.9    21.3    -      +       -      -
    395D  SER*     3.3     7.8    -      -       -      +
    396D  PRO*     1.3   103.3    -      -       +      +
    398D  LEU*     1.3    60.9    +      -       -      +
    428D  GOL      3.3    27.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 398 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    356D  LEU      3.6     1.2    -      -       -      +
    357D  TRP*     3.5     8.3    -      -       -      -
    358D  ILE*     2.9    38.6    +      -       +      +
    360D  VAL*     4.0    19.1    -      -       +      -
    366D  VAL*     3.6    22.2    -      -       +      -
    370D  ILE*     3.2    41.3    -      -       +      -
    381D  MET*     2.9    37.2    -      -       +      -
    382D  LEU      3.3    13.2    -      -       -      +
    397D  TYR*     1.3    74.7    -      -       -      +
    399D  ARG*     1.3    59.1    +      -       -      +
    400D  ALA      4.0     0.2    -      -       -      -
    417D  LEU*     3.9    16.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 399 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19C  ILE*     4.4     0.2    -      -       -      +
     36C  LEU      3.7     4.6    -      -       -      +
     37C  ALA      3.2    25.1    +      -       -      -
     38C  GLY*     3.6    15.4    +      -       -      -
     39C  GLY      3.8     0.4    -      -       -      +
    427C  KYN      3.0    35.0    +      -       -      -
    202D  ASN*     2.9    23.7    +      -       -      +
    203D  PRO*     3.5    27.6    -      -       +      +
    355D  PHE*     3.5    35.4    -      -       +      -
    356D  LEU      3.5     2.7    -      -       -      +
    357D  TRP*     4.1    12.2    -      -       +      -
    381D  MET*     3.7     2.3    -      -       -      +
    382D  LEU*     2.6    54.2    +      -       +      +
    387D  PHE*     3.4    16.9    -      -       +      -
    398D  LEU*     1.3    73.5    -      -       -      +
    400D  ALA*     1.3    61.7    +      -       -      +
    401D  SER      5.5     1.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 400 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36C  LEU*     3.4    11.2    -      -       +      -
    333D  ILE*     4.0    18.9    -      -       +      +
    355D  PHE*     3.6     3.3    -      -       -      -
    356D  LEU*     2.7    44.8    +      -       +      +
    358D  ILE*     4.1    13.0    -      -       +      -
    381D  MET*     3.9    25.1    -      -       -      -
    398D  LEU      4.0     0.4    +      -       -      -
    399D  ARG*     1.3    75.0    -      -       -      +
    401D  SER*     1.3    62.0    +      -       -      +
    402D  PHE      3.7     0.3    +      -       -      -
    414D  PHE*     4.5     0.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 401 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36C  LEU*     2.8    40.1    +      -       -      +
     38C  GLY      3.4    26.0    +      -       -      -
     40C  LEU      4.6     1.6    +      -       -      -
    333D  ILE*     4.1     4.8    -      -       -      +
    354D  MET*     3.5     8.9    +      -       -      +
    355D  PHE*     3.8    14.1    -      -       -      -
    399D  ARG*     4.3     0.8    -      -       -      +
    400D  ALA*     1.3    73.4    -      -       -      +
    402D  PHE*     1.3    58.4    +      -       -      +
    403D  SER*     3.0    31.4    +      -       -      -
    404D  SER      4.7     0.9    +      -       -      -
    405D  ALA*     5.2     1.7    +      -       -      +
    410D  MET*     5.2     0.2    -      -       -      +
----------------------------------------------------------
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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