Contacts of the strand formed by residues 293 - 297 (chain A) in PDB entry 1RS0


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 PRO 293 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    287A  VAL*     3.9    17.5    -      -       +      -
    288A  THR      3.3     6.7    -      -       -      +
    289A  TYR*     3.9     2.7    -      -       +      -
    292A  TYR*     1.3    95.8    -      -       +      +
    294A  LYS*     1.3    60.6    +      -       -      +
    295A  ILE*     4.1     5.0    +      -       +      +
    322A  HIS*     3.9     0.4    -      -       -      -
    332A  LYS*     3.7    22.2    -      -       +      +
    333A  ALA*     3.7    30.7    -      -       -      +
    336A  ALA*     4.3    12.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 294 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    287A  VAL*     3.3     2.1    -      -       -      -
    288A  THR*     2.8    40.8    +      -       -      +
    293A  PRO*     1.3    73.2    -      -       -      +
    295A  ILE*     1.3    68.9    +      -       -      +
    296A  TRP*     3.2    55.5    -      -       +      +
    321A  ASP*     4.8    13.7    -      -       -      +
    322A  HIS*     3.5    14.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 295 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    286A  LEU      3.7     3.4    -      -       -      +
    287A  VAL*     3.8    17.3    -      -       +      -
    293A  PRO*     4.5     7.2    -      -       +      +
    294A  LYS*     1.3    80.6    +      -       -      +
    296A  TRP*     1.3    59.9    +      -       -      +
    297A  VAL      3.5    23.6    -      -       -      +
    298A  LYS*     3.7    32.3    -      -       +      -
    336A  ALA*     3.5    31.9    -      -       +      +
    340A  MET*     3.8    10.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 296 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    286A  LEU*     2.7    28.0    +      -       +      +
    287A  VAL*     4.3     0.7    -      -       -      -
    288A  THR*     2.9    35.2    +      -       +      +
    294A  LYS*     3.2    53.8    +      -       +      +
    295A  ILE*     1.3    75.0    -      -       -      +
    297A  VAL*     1.3    68.1    +      -       +      +
    301A  GLU*     4.4     3.5    -      -       -      +
    309A  TRP*     4.7     2.4    -      -       -      -
    313A  GLN*     4.6    19.7    +      -       +      +
    316A  GLU*     5.0     4.3    -      -       +      -
    317A  ILE*     3.6    39.0    -      -       +      -
    321A  ASP*     3.4    39.0    -      -       +      -
    322A  HIS*     5.3     0.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 297 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    284A  TYR*     3.1    23.8    -      -       +      +
    285A  GLY*     3.3     4.9    -      -       -      -
    286A  LEU*     3.0    42.4    +      -       +      +
    295A  ILE*     3.5    11.1    -      -       -      +
    296A  TRP*     1.3    86.4    -      -       -      +
    298A  LYS*     1.3    64.4    +      -       -      +
    301A  GLU*     3.4    11.2    -      -       -      +
    304A  SER*     3.8    15.9    -      -       -      -
    309A  TRP*     3.8    22.2    -      -       +      -
    310A  VAL*     4.6    10.1    -      -       +      -
    313A  GLN*     4.1    17.7    -      -       +      -
    340A  MET*     3.8     1.9    -      -       -      +
----------------------------------------------------------
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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