Contacts of the strand formed by residues 325 - 327 (chain L) in PDB entry 1RBO
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.
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 HIS 325 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158L GLU* 2.7 37.3 + - - -
199L PHE* 4.3 5.6 - + - -
239L TYR* 3.8 15.8 + + - -
264L ILE* 3.7 23.5 - - + +
291L LEU 3.3 2.4 + - - -
292L HIS* 3.1 35.5 + - - +
293L ILE* 2.9 29.0 + - - +
323L GLY* 4.3 0.7 - - - -
324L ASP* 1.3 86.1 + - + +
326L ILE* 1.3 62.8 + - - +
374L VAL* 3.7 4.4 - - - +
375L LEU* 3.1 19.2 - - + +
377L VAL* 3.5 14.4 - - + +
399L VAL* 4.1 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 326 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269L TYR* 3.7 27.8 - - + +
293L ILE* 3.4 17.3 - - + +
295L ARG* 4.9 3.1 - - + -
311L PHE* 3.8 19.1 - - + -
315L ALA* 4.5 5.8 - - - -
318L LEU* 3.8 26.0 - - + -
325L HIS* 1.3 78.0 - - - +
327L HIS* 1.3 71.9 + - - +
328L SER 3.4 0.3 + - - -
349L LEU* 3.6 31.0 - - + -
374L VAL* 3.8 13.7 - - + -
375L LEU 3.0 6.5 + - - +
376L PRO* 3.5 2.7 - - + +
377L VAL* 2.9 23.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 327 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292L HIS* 3.0 39.5 + + - -
293L ILE 3.3 9.2 + - - +
294L HIS* 3.4 20.6 - + - -
295L ARG* 3.2 25.4 - - + -
311L PHE* 3.6 4.7 - - - -
326L ILE* 1.3 83.6 - - - +
328L SER* 1.3 60.0 + - - +
377L VAL* 3.4 10.3 - - + +
379L SER* 3.6 8.0 - - - -
401L GLN* 3.5 17.7 + - - -
476L CAP 2.7 64.3 + - - +
----------------------------------------------------------
Back to top of page
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