Contacts of the helix formed by residues 287 - 302 (chain F) in PDB entry 5MGX
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 287 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282F GLN* 2.9 26.8 + - + +
285F LEU* 3.1 10.0 - - + +
286F ASP* 1.3 72.7 - - - +
288F TYR* 1.3 53.7 + - - +
289F ARG* 4.4 8.0 + - + +
290F ALA* 3.3 30.0 + - + +
291F ALA* 2.9 34.1 + - - +
293F ARG* 5.0 5.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 288 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283F LEU* 4.2 10.8 - - + -
286F ASP* 3.0 50.0 + - + -
287F HIS* 1.3 71.2 + - - +
289F ARG* 1.3 60.1 + - - +
291F ALA* 3.4 2.1 + - - +
292F LEU* 3.0 31.5 + - - +
315F VAL* 3.6 28.3 - - + +
318F GLN* 3.0 49.7 + - + +
319F GLN* 3.6 33.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 289 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287F HIS* 3.4 8.5 + - + +
288F TYR* 1.3 77.0 - - - +
290F ALA* 1.3 59.8 - - - +
292F LEU* 3.6 10.8 - - + +
293F ARG* 3.3 49.6 + - - +
319F GLN* 4.7 11.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 290 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282F GLN* 3.2 23.0 + - - +
287F HIS* 3.3 37.5 + - + +
289F ARG* 1.3 76.4 - - - +
291F ALA* 1.4 62.0 + - - +
293F ARG* 3.2 22.6 + - - +
294F SER* 3.0 26.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 291 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279F ALA* 3.8 8.8 - - + +
282F GLN* 3.4 23.5 + - + -
283F LEU* 3.9 12.6 - - - +
287F HIS 2.9 18.6 + - - +
288F TYR 3.8 4.5 - - - +
290F ALA* 1.4 74.6 - - - +
292F LEU* 1.4 56.3 + - - +
294F SER* 3.5 2.4 + - - -
295F CYS* 2.9 36.0 + - - +
315F VAL* 4.0 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 292 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288F TYR 3.0 17.5 + - - +
289F ARG* 3.6 11.2 - - + +
291F ALA* 1.4 74.1 - - - +
293F ARG* 1.4 55.2 + - - +
295F CYS* 3.4 5.1 + - - +
296F SER* 2.9 40.5 + - - +
312F LYS* 3.8 37.2 - - + -
315F VAL* 3.7 10.7 - - + +
316F LEU* 4.2 17.0 - - + -
319F GLN* 3.3 38.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 293 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287F HIS* 5.0 5.3 + - - -
289F ARG* 3.3 37.7 + - - +
290F ALA* 3.2 31.4 + - - +
292F LEU* 1.4 73.6 - - - +
294F SER* 1.3 60.0 + - - +
296F SER* 3.4 6.1 + - - -
297F LEU* 2.9 41.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 294 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275F LEU* 3.5 34.7 - - - +
278F LEU* 4.0 9.3 - - - +
279F ALA* 3.8 4.3 - - - -
282F GLN* 2.7 31.3 + - - -
290F ALA 3.0 5.0 + - - -
291F ALA 3.7 4.5 - - - -
293F ARG* 1.3 77.3 - - - +
295F CYS* 1.4 59.7 + - - +
297F LEU* 3.3 5.9 + - - +
298F VAL* 3.1 29.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 295 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276F ASN* 5.4 0.4 - - - -
279F ALA* 3.8 13.2 - - - -
291F ALA* 2.9 26.4 + - - +
292F LEU* 3.6 7.2 - - - +
293F ARG 3.3 0.2 - - - -
294F SER* 1.4 73.2 - - - +
296F SER* 1.3 56.7 + - - +
298F VAL* 3.3 8.1 + - - +
299F LEU* 3.1 34.1 + - - +
308F ALA* 3.7 10.9 - - - +
311F ARG* 3.7 19.3 - - - -
312F LYS* 3.6 41.7 - - + -
315F VAL* 5.4 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 296 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292F LEU* 2.9 22.7 + - - +
293F ARG* 3.8 6.3 - - - -
295F CYS* 1.3 71.9 - - - +
297F LEU* 1.4 59.5 + - - +
299F LEU* 3.5 6.7 + - - +
300F GLU* 3.1 34.0 + - - +
312F LYS* 3.1 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 297 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271F LYS* 6.4 0.4 - - - +
275F LEU* 4.1 29.8 - - + -
293F ARG* 2.9 29.7 + - + +
294F SER* 3.3 5.4 + - - +
296F SER* 1.4 72.8 - - - +
298F VAL* 1.4 65.5 + - - +
300F GLU* 3.3 13.7 + - + +
301F HIS* 3.1 32.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 298 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272F VAL* 3.5 28.4 - - + +
275F LEU* 3.6 12.8 - - + -
276F ASN* 3.5 35.7 - - - +
294F SER 3.1 15.9 + - - +
295F CYS* 3.3 7.4 + - - +
297F LEU* 1.4 75.6 - - - +
299F LEU* 1.3 49.9 + - - +
301F HIS* 3.1 7.6 + - - +
302F GLN* 2.8 31.2 + - - +
305F ASN* 3.8 16.8 - - + +
308F ALA* 3.6 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 299 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295F CYS 3.1 20.6 + - - +
296F SER* 3.5 6.3 + - - +
297F LEU 3.3 0.2 - - - -
298F VAL* 1.3 72.7 - - - +
300F GLU* 1.3 62.3 + - - +
301F HIS 3.3 0.2 - - - -
302F GLN 3.5 16.6 - - - +
303F PRO* 3.2 33.1 - - + +
305F ASN 3.9 3.1 - - - +
308F ALA* 3.8 28.0 - - + +
309F LEU* 3.7 37.7 - - + -
312F LYS* 3.9 28.9 - - + +
328F ILE* 6.4 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 300 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296F SER* 3.1 19.8 + - - +
297F LEU* 3.5 16.6 - - + +
298F VAL 3.2 0.6 - - - -
299F LEU* 1.3 76.7 - - - +
301F HIS* 1.4 63.8 + - + +
303F PRO* 4.9 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 301 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268F LEU* 3.6 34.7 - - + +
271F LYS* 4.5 15.2 + - - -
272F VAL* 3.7 26.0 - - + +
275F LEU* 5.6 3.8 - - + +
297F LEU* 3.1 32.7 - - + +
298F VAL 3.1 6.3 + - - +
300F GLU* 1.4 83.6 - - + +
302F GLN* 1.3 64.3 + - + +
303F PRO* 3.8 6.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 302 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269F GLN* 3.7 33.5 + - - +
272F VAL* 3.7 25.2 - - + +
298F VAL 2.8 13.2 + - - +
299F LEU* 3.5 13.0 - - - +
301F HIS* 1.3 78.6 - - + +
303F PRO* 1.4 65.5 - - - +
304F ASP* 3.2 7.4 + - - +
305F ASN* 3.1 44.7 + - + +
----------------------------------------------------------
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