Contacts of the strand formed by residues 283 - 287 (chain A) in PDB entry 3RTC


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 283 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    262A  LEU*     3.8    31.0    -      -       +      -
    263A  VAL      3.2    13.7    +      -       -      +
    264A  LYS*     3.4    33.3    -      -       +      +
    265A  LEU*     2.7    30.1    +      -       -      +
    281A  GLU      4.8     2.9    -      -       -      +
    282A  LEU*     1.3    77.6    -      -       -      +
    284A  SER*     1.3    62.0    +      -       -      +
    285A  VAL*     4.1    17.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 284 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    265A  LEU*     3.7    15.1    -      -       -      +
    267A  VAL*     4.2     3.1    -      -       -      +
    272A  ASN*     2.8    55.5    +      -       -      +
    273A  LEU*     5.5     0.7    -      -       -      +
    275A  ALA*     3.7    19.1    -      -       -      +
    276A  THR*     4.0    14.8    -      -       -      +
    282A  LEU      4.0     1.8    +      -       -      -
    283A  ILE*     1.3    76.3    -      -       -      +
    285A  VAL*     1.3    58.4    +      -       -      +
    286A  PRO*     3.7     2.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 285 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    264A  LYS*     4.5    16.6    -      -       +      -
    265A  LEU      2.7    20.2    +      -       -      +
    266A  ALA*     3.8     2.7    -      -       -      -
    267A  VAL      3.3    23.2    +      -       -      +
    272A  ASN*     3.8     1.7    -      -       -      +
    283A  ILE*     4.1    20.2    -      -       +      -
    284A  SER*     1.3    70.3    -      -       -      +
    286A  PRO*     1.3    82.2    -      -       +      +
    287A  ILE*     4.2     6.7    -      -       +      -
    301A  GLU*     4.4     6.3    -      -       -      +
    305A  LEU*     4.1    31.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 286 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    267A  VAL      3.7     0.9    -      -       -      +
    269A  PHE*     3.9    19.7    -      -       +      -
    272A  ASN*     3.4    33.4    -      -       -      +
    284A  SER      3.8     1.6    -      -       -      +
    285A  VAL*     1.3    94.3    -      -       +      +
    287A  ILE*     1.3    62.2    +      -       -      +
    288A  ASP      4.1     0.9    +      -       -      -
    301A  GLU*     4.3     5.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 287 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    266A  ALA*     3.8    30.7    -      -       +      -
    267A  VAL      3.0    22.6    +      -       -      +
    268A  PRO*     3.3     6.0    -      -       +      +
    269A  PHE*     2.9    24.0    +      -       -      +
    285A  VAL*     4.0     8.1    -      -       +      +
    286A  PRO*     1.3    76.8    -      -       -      +
    288A  ASP*     1.3    61.5    +      -       -      +
    289A  THR*     3.5     6.4    +      -       +      -
    294A  PHE*     3.9    17.5    -      -       +      -
    298A  ASN*     3.1    39.9    -      -       +      +
    301A  GLU*     3.6    36.1    -      -       +      +
    302A  CYS*     4.8     3.8    -      -       -      -
    305A  LEU*     4.4     3.1    -      -       +      -
----------------------------------------------------------
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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