Contacts of the helix formed by residues 273 - 293 (chain A) in PDB entry 5I2S
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 GLN 273 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A LEU 3.8 7.2 + - - +
272A ILE* 1.3 78.8 - - - +
274A ASP* 1.3 66.0 + - - +
275A VAL* 3.7 20.4 - - + +
276A GLU* 3.4 33.1 + - - +
277A ARG* 2.9 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 274 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A ILE 3.5 3.9 + - - +
273A GLN* 1.3 73.4 + - - +
275A VAL* 1.3 58.4 + - - +
277A ARG* 2.6 33.3 + - - +
278A ILE* 2.9 42.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 275 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A GLN* 3.7 21.5 - - + +
274A ASP* 1.3 77.1 - - - +
276A GLU* 1.3 66.0 + - + +
278A ILE* 3.4 2.9 + - - +
279A LEU* 2.9 35.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 276 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A SER* 3.7 17.4 - - - +
28A SER 4.9 2.8 - - - +
32A TRP* 4.7 11.1 + - - -
271A LEU 5.3 0.2 - - - +
272A ILE* 4.4 3.9 - - + +
273A GLN* 3.3 38.5 + - + +
275A VAL* 1.3 83.3 - - + +
277A ARG* 1.3 62.9 + - - +
279A LEU* 4.0 4.2 - - - +
280A ASP* 2.9 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 277 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A SER* 3.6 11.3 + - - +
269A VAL* 4.6 20.6 - - - -
272A ILE* 3.7 15.8 + - + +
273A GLN 2.9 17.4 + - - +
274A ASP* 2.6 40.4 + - - +
276A GLU* 1.3 77.2 - - - +
278A ILE* 1.3 78.9 + - - +
280A ASP* 3.8 1.6 - - - +
281A TYR* 2.9 32.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 278 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A ASP* 2.9 26.6 + - + +
275A VAL* 4.2 3.4 - - - +
277A ARG* 1.3 97.5 - - - +
279A LEU* 1.3 62.4 + - - +
281A TYR* 3.8 9.2 - - + +
282A SER* 2.8 34.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 279 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A VAL* 2.9 24.3 + - + +
276A GLU* 4.0 3.8 - - - +
278A ILE* 1.3 77.2 - - - +
280A ASP* 1.3 66.2 + - - +
282A SER* 3.2 9.0 + - - +
283A LEU* 3.0 48.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 280 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A PRO* 4.9 16.0 - - + +
27A SER* 2.9 36.5 + - - +
28A SER 4.6 0.2 + - - -
276A GLU* 2.9 19.5 + - - +
277A ARG 3.8 2.7 - - - +
279A LEU* 1.3 82.5 - - - +
281A TYR* 1.3 61.3 + - - +
283A LEU* 3.5 10.8 + - - +
284A CYS* 3.0 24.1 + - - +
304A TYR 4.7 2.4 - - - +
308A LYS* 3.4 32.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 281 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A HIS* 3.9 17.9 + + - -
24A CYS* 4.2 18.2 - - + -
25A PRO 5.6 1.5 + - - -
277A ARG* 2.9 20.9 + - + +
278A ILE* 3.9 9.4 - - + +
280A ASP* 1.3 72.8 - - - +
282A SER* 1.3 73.1 + - - +
284A CYS* 3.1 4.4 + - - -
285A GLN* 2.8 58.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 282 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A ILE* 2.8 26.7 + - - -
279A LEU* 3.4 12.5 - - - +
281A TYR* 1.3 76.8 - - - +
283A LEU* 1.3 60.0 + - - +
285A GLN* 3.3 12.6 + - - +
286A GLU* 2.9 45.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 283 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A LEU* 3.0 46.1 + - + +
280A ASP* 4.0 10.1 - - - +
282A SER* 1.3 73.3 - - - +
284A CYS* 1.3 66.8 + - - +
286A GLU* 3.1 16.3 + - - +
287A THR* 3.0 28.4 + - - +
304A TYR* 3.5 54.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 284 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A TYR 3.5 8.3 - - - -
24A CYS* 2.0 58.3 - - + -
25A PRO* 3.7 6.7 - - + -
280A ASP 3.0 18.6 + - - +
281A TYR 3.1 1.5 + - - +
283A LEU* 1.3 78.7 - - - +
285A GLN* 1.3 55.0 + - - +
287A THR* 3.3 4.2 + - - -
288A TRP* 3.0 37.4 + - - -
304A TYR* 3.5 20.3 - - - +
305A LEU* 3.6 8.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 285 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A HIS* 3.5 33.9 - - + +
281A TYR* 2.8 44.3 + - + +
282A SER* 3.3 12.8 + - - +
284A CYS* 1.3 71.4 - - - +
286A GLU* 1.3 82.6 + - - +
288A TRP* 3.7 2.0 - - - +
289A SER* 2.9 30.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 286 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A SER* 2.9 29.6 + - - +
283A LEU* 3.1 19.5 + - - +
285A GLN* 1.3 92.4 + - - +
287A THR* 1.3 60.4 + - + +
289A SER* 3.1 8.2 + - - -
290A LYS* 2.9 37.2 + - - +
504A YB 2.4 30.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 287 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A LEU 3.0 15.0 + - - +
284A CYS 3.6 0.3 + - - -
286A GLU* 1.3 76.0 - - + +
288A TRP* 1.3 61.7 + - - +
290A LYS* 3.3 10.5 + - - +
291A ILE* 2.9 34.1 + - - +
297A ILE* 5.1 2.2 - - - -
301A ASP* 3.0 53.1 + - - +
304A TYR* 3.4 18.8 - - + -
305A LEU* 3.3 22.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 288 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A VAL* 4.5 3.1 - - + -
21A TYR* 3.4 53.6 - + - -
22A HIS* 3.5 37.2 - + + +
23A TYR 2.9 29.6 + - - +
24A CYS* 3.9 1.8 - - - -
284A CYS* 3.0 34.4 + - - +
285A GLN 3.7 0.2 - - - +
287A THR* 1.3 77.8 + - - +
289A SER* 1.3 57.8 + - - +
291A ILE* 3.2 21.4 + - + +
292A ARG* 2.9 47.6 + - + +
305A LEU* 3.3 16.7 - - + +
316A PHE* 4.2 14.6 - + - -
323A LEU* 3.6 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 289 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A HIS* 5.4 0.2 - - - -
285A GLN* 2.9 26.9 + - - -
286A GLU* 3.1 10.5 + - - -
288A TRP* 1.3 73.6 - - - +
290A LYS* 1.3 66.0 + - - +
292A ARG* 3.2 6.2 + - - +
293A ALA* 3.0 24.3 + - - +
295A LEU* 5.5 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 290 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A GLU* 2.9 24.7 + - - +
287A THR* 3.5 10.5 - - - +
289A SER* 1.3 75.7 - - - +
291A ILE* 1.3 51.9 + - - +
293A ALA* 2.7 32.6 + - - +
295A LEU* 3.4 37.3 + - + +
296A PRO 4.1 12.6 - - - +
297A ILE* 3.7 10.1 - - + -
301A ASP* 3.3 38.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 291 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A THR* 2.9 23.2 + - - +
288A TRP* 3.5 24.5 - - + +
290A LYS* 1.3 76.6 - - - +
292A ARG* 1.3 59.8 + - - +
293A ALA 2.7 14.6 - - - +
295A LEU 4.8 2.0 - - - -
297A ILE* 3.8 32.1 - - + -
305A LEU* 4.2 14.8 - - + -
323A LEU* 3.5 23.6 - - + -
402A ALA 3.8 15.1 - - - +
403A GLN* 5.2 2.1 - - - -
404A VAL* 3.6 38.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 292 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A VAL* 4.6 0.4 - - - +
18A PRO 2.9 22.2 + - - -
19A SER* 3.4 28.1 + - - +
20A ASN* 4.0 5.2 - - - +
21A TYR* 3.3 27.8 + - - +
22A HIS* 6.1 1.6 - - - +
288A TRP* 2.9 35.5 + - + +
289A SER* 3.8 5.6 - - - +
290A LYS 3.2 0.2 - - - -
291A ILE* 1.3 73.4 - - - +
293A ALA* 1.3 64.0 + - - +
404A VAL* 3.3 33.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 293 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A SER 3.0 16.1 + - - +
290A LYS 2.7 15.0 - - - +
291A ILE* 2.7 14.6 - - - +
292A ARG* 1.3 77.2 - - - +
294A GLY* 1.3 63.0 + - - +
295A LEU* 3.1 23.6 - - + -
----------------------------------------------------------
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