Contacts of the strand formed by residues 552 - 556 (chain B) in PDB entry 1RL3


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 PHE 552 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    514B  LYS*     5.9     8.1    -      -       +      -
    516B  ILE*     3.2    26.9    -      -       +      -
    518B  LYS*     4.5     0.2    -      -       -      +
    550B  ALA      4.0     5.4    -      -       -      -
    551B  MET*     1.3    82.7    -      -       -      +
    553B  PRO*     1.3    71.7    -      -       -      +
    554B  VAL*     3.1    31.9    -      -       +      -
    571B  ASN*     3.6    26.2    -      -       -      -
    573B  TYR*     4.4     2.9    -      +       -      -
    622B  TRP*     4.0     4.9    -      -       -      -
    623B  GLY*     3.1    40.4    +      -       -      +
    624B  ILE*     3.2    28.9    -      -       -      -
    625B  ASP*     4.3     1.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 553 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    516B  ILE*     5.0     3.6    -      -       +      -
    518B  LYS*     3.8    23.1    -      -       +      -
    522B  THR*     4.9    13.5    -      -       +      -
    552B  PHE*     1.3    89.8    -      -       +      +
    554B  VAL*     1.3    67.3    +      -       -      +
    620B  LYS*     4.5    10.8    -      -       +      +
    621B  LEU      3.6     8.3    -      -       -      +
    622B  TRP*     3.7    29.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 554 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    552B  PHE*     3.1    31.2    -      -       +      -
    553B  PRO*     1.3    83.3    -      -       -      +
    555B  SER*     1.3    59.2    +      -       -      +
    556B  PHE*     4.0    22.4    -      -       +      -
    573B  TYR*     4.2    13.5    -      -       +      -
    619B  VAL      4.3     0.2    -      -       -      +
    620B  LYS*     3.5     5.9    -      -       -      +
    621B  LEU*     2.6    62.5    +      -       +      +
    622B  TRP      4.4     0.2    -      -       -      +
    623B  GLY      4.5     2.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 555 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    554B  VAL*     1.3    74.3    -      -       -      +
    556B  PHE*     1.3    82.2    +      -       -      +
    557B  ILE*     6.0     0.5    -      -       -      +
    560B  GLU*     5.5     0.3    -      -       -      +
    619B  VAL      3.5    11.8    +      -       -      -
    620B  LYS*     4.7    10.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 556 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    554B  VAL*     4.0    26.0    -      -       +      -
    555B  SER*     1.3    94.6    +      -       -      +
    557B  ILE*     1.3    65.3    +      -       -      +
    560B  GLU*     3.8    33.9    -      -       +      -
    561B  THR      4.1    15.5    -      -       -      -
    562B  VAL*     3.6    43.1    -      -       +      -
    573B  TYR*     5.0     2.9    -      +       -      -
    615B  ALA*     4.7     3.1    -      -       +      -
    617B  THR      4.4     0.3    -      -       -      +
    618B  ASN*     3.5     2.4    -      -       -      +
    619B  VAL*     3.0    43.6    +      -       +      +
    621B  LEU*     4.4    11.0    -      -       +      -
----------------------------------------------------------
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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