Contacts of the helix formed by residues 298 - 303 (chain R) in PDB entry 1HI0
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 TYR 298 (chain R).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133R LEU* 3.4 42.0 + - + +
293R LYS* 4.7 4.4 - - + -
294R ILE* 3.0 34.2 + - + +
297R LYS* 1.3 111.5 + - + +
299R ALA* 1.3 63.6 + - - +
300R TYR 3.0 5.2 + - - +
301R THR 3.1 4.0 + - - -
302R PHE* 3.1 31.4 + - + +
437R ASP* 2.8 43.7 + - - -
440R TRP* 3.5 41.5 - + + -
441R GLN* 4.0 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 299 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294R ILE 3.3 0.8 + - - -
295R TYR 3.1 24.5 - - - +
296R SER* 2.9 11.6 + - - +
297R LYS 3.4 1.4 + - - -
298R TYR* 1.3 77.0 - - - +
300R TYR* 1.3 64.1 + - - +
303R HIS* 3.1 30.0 + - + +
313R LYS* 2.8 15.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 300 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298R TYR 3.0 1.8 + - - -
299R ALA* 1.3 76.1 - - - +
301R THR* 1.3 73.4 + - + +
313R LYS* 2.8 60.0 + - + +
316R GLU* 5.9 1.8 - - - -
317R TRP* 2.8 35.0 + + - -
440R TRP 3.7 1.1 - - - +
441R GLN* 3.5 25.3 - - - +
442R GLY* 3.4 22.2 - - - -
447R ARG* 3.2 33.0 + - + -
448R GLN 4.0 8.1 - - - -
449R ILE* 3.5 6.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 301 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298R TYR 3.1 2.6 + - - -
300R TYR* 1.3 90.1 - - + +
302R PHE* 1.3 74.9 + - - +
304R HIS* 3.0 7.8 + - - -
439R TYR* 4.1 4.5 - - + +
440R TRP* 3.0 46.5 + - - +
448R GLN* 2.7 44.0 - - + +
449R ILE* 4.0 0.7 - - - +
450R SER 2.7 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 302 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134R MET* 4.5 3.8 - - + -
294R ILE* 3.7 34.8 - - + +
295R TYR* 3.5 26.5 - - + -
298R TYR* 3.1 20.3 + - + +
301R THR* 1.3 94.7 - - - +
303R HIS* 1.3 60.7 + - - +
304R HIS* 3.4 18.5 + - - -
403R THR* 3.4 30.1 - - + -
407R SER* 3.7 7.6 - - - -
440R TRP* 3.6 54.5 - + - -
448R GLN* 4.1 0.2 - - - -
450R SER* 3.8 24.6 - - - +
451R LYS* 5.3 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 303 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295R TYR* 3.2 49.9 + + + +
299R ALA* 3.1 17.9 + - + +
302R PHE* 1.3 75.1 - - - +
304R HIS* 1.3 71.6 + - - +
305R THR* 3.4 24.7 - - + +
309R ASN* 3.4 8.4 + - - +
313R LYS* 3.4 14.6 + - - -
633R THR* 4.3 8.9 - - + +
635R ALA* 5.4 3.0 - - - +
636R ASP* 3.2 27.0 + - - -
----------------------------------------------------------
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