Contacts of the helix formed by residues 263 - 283 (chain A) in PDB entry 3OIO
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 VAL 263 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A GLU* 5.5 5.2 - - + +
256A PHE* 4.2 2.5 - - - -
257A LYS* 5.8 4.9 - - + -
262A THR* 1.3 85.7 + - - +
264A PRO* 1.3 78.2 - - + +
265A SER* 3.6 19.7 - - - +
266A LYS* 3.1 32.0 + - + +
267A TYR* 3.0 17.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 264 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A MSE 3.3 22.1 - - + +
238A THR* 4.0 29.6 - - + +
252A LEU* 4.2 7.0 - - + +
253A GLU* 3.9 28.5 - - + -
256A PHE* 3.6 41.0 - - + -
263A VAL* 1.3 88.3 - - + +
265A SER* 1.3 55.7 + - - +
267A TYR* 3.2 1.2 + - - +
268A TYR* 2.9 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 265 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A THR* 4.2 12.6 + - - -
263A VAL* 3.6 13.9 - - - +
264A PRO* 1.3 78.1 - - - +
266A LYS* 1.3 64.5 + - - +
268A TYR* 3.4 9.8 + - - +
269A LEU* 3.1 25.6 + - - +
272A ARG* 5.5 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 266 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A THR* 3.5 18.8 - - - +
263A VAL* 3.1 22.4 + - + +
265A SER* 1.3 80.6 + - - +
267A TYR* 1.3 64.2 + - - +
269A LEU* 3.3 13.7 + - + +
270A GLU* 3.0 28.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 267 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A VAL* 3.8 37.3 - - + +
228A MSE 4.2 7.9 - - - -
229A GLU* 4.9 2.4 + - - -
256A PHE* 3.7 28.7 - + + -
260A LEU* 3.8 26.5 - - + -
262A THR* 3.8 17.1 - - + +
263A VAL 3.0 6.8 + - - +
264A PRO 3.7 2.9 - - - +
266A LYS* 1.3 75.2 - - - +
268A TYR* 1.3 60.0 + - - +
270A GLU* 3.0 28.4 + - + +
271A LEU* 2.9 42.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 268 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A MSE 3.5 55.4 + - + -
231A ASN* 2.6 38.7 + - - +
235A PRO* 3.4 13.9 - - + -
236A LEU* 3.0 42.6 + - + +
238A THR* 5.9 0.9 - - - -
241A ILE* 3.8 7.0 - - + -
264A PRO 2.9 15.4 + - - +
265A SER* 3.5 10.1 - - - +
266A LYS 3.2 0.2 - - - -
267A TYR* 1.3 78.9 - - - +
269A LEU* 1.3 56.9 + - - +
271A LEU* 3.2 11.0 + - + +
272A ARG* 2.9 44.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 269 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A SER 3.1 13.8 + - - +
266A LYS* 3.4 15.7 - - + +
267A TYR 3.2 0.2 - - - -
268A TYR* 1.3 77.4 - - - +
270A GLU* 1.3 57.2 + - + +
272A ARG* 3.2 21.3 + - - +
273A LEU* 2.8 48.5 + - + +
296A PHE* 3.6 38.1 - - + -
301A HIS* 5.6 2.9 - - + +
305A THR* 4.7 15.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 270 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A THR* 4.2 13.5 + - - +
266A LYS* 3.0 18.2 + - - +
267A TYR* 3.0 36.6 + - + +
269A LEU* 1.3 76.2 - - - +
271A LEU* 1.3 57.6 + - - +
273A LEU* 3.3 7.4 + - - +
274A ASN* 2.9 38.4 + - - +
309A HIS* 3.7 30.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 271 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A VAL 4.4 0.7 - - - +
228A MSE 3.5 33.4 - - + +
229A GLU* 3.7 27.4 - - + +
232A ILE* 3.6 36.1 - - + -
267A TYR* 2.9 31.9 + - + +
268A TYR* 3.4 13.5 - - + +
270A GLU* 1.3 77.4 - - - +
272A ARG* 1.3 61.4 + - + +
274A ASN* 3.2 7.7 + - - +
275A ARG* 2.9 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 272 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A ILE* 3.8 22.9 - - + +
235A PRO* 3.9 30.5 - - - +
265A SER 5.5 1.0 + - - -
268A TYR* 2.9 29.8 + - + +
269A LEU* 3.7 26.6 - - - +
271A LEU* 1.3 78.3 - - + +
273A LEU* 1.3 56.4 + - - +
275A ARG* 3.3 4.0 + - - +
276A ALA* 2.9 27.0 + - - +
294A CYS* 2.8 33.4 + - + +
295A GLY* 3.4 27.1 + - - -
296A PHE* 3.5 29.0 - - + -
301A HIS* 5.3 2.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 273 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A LEU* 2.8 40.9 + - + +
270A GLU* 3.6 5.2 - - - +
272A ARG* 1.3 74.2 - - - +
274A ASN* 1.3 60.1 + - - +
276A ALA* 3.2 5.4 + - - +
277A ARG 2.9 23.2 + - - -
296A PHE* 3.4 27.8 - - + -
302A PHE* 4.2 3.6 - - + -
305A THR* 3.8 12.1 - - - +
306A TYR* 3.7 33.2 - - + +
309A HIS* 3.7 33.0 - - + +
310A PHE* 3.6 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 274 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A GLU* 2.9 33.5 + - - +
271A LEU* 3.7 6.5 - - - +
273A LEU* 1.3 72.3 - - - +
275A ARG* 1.3 66.5 + - - +
277A ARG* 3.2 12.7 + - - +
278A GLN* 3.0 30.3 + - - +
309A HIS* 4.2 10.1 + - - -
310A PHE* 3.6 26.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 275 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A GLU 5.1 2.6 + - - -
232A ILE* 3.5 48.2 - - + +
271A LEU* 2.9 13.8 + - + +
272A ARG 3.3 8.0 + - - +
274A ASN* 1.3 75.7 - - - +
276A ALA* 1.3 63.5 + - - +
278A GLN* 3.0 31.9 + - - +
279A LEU* 3.0 37.9 + - + +
293A ALA 5.7 0.2 - - - +
294A CYS* 3.8 14.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 276 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A ARG 2.9 14.6 + - - +
273A LEU* 3.3 10.5 - - - +
274A ASN 3.2 0.2 - - - -
275A ARG* 1.3 77.3 - - - +
277A ARG* 1.3 57.1 + - - +
279A LEU* 3.1 3.1 + - - +
280A LEU* 2.8 35.3 + - - +
290A ILE* 3.9 5.8 - - + +
294A CYS* 3.6 17.4 - - + -
302A PHE* 3.5 37.7 - - + -
306A TYR* 4.3 1.6 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
273A LEU 2.9 12.9 + - - +
274A ASN* 3.5 16.0 + - - +
275A ARG 3.2 0.2 - - - -
276A ALA* 1.3 77.8 - - - +
278A GLN* 1.3 65.8 + - + +
280A LEU* 3.2 3.9 + - - +
281A GLN* 3.0 57.4 + - - +
306A TYR* 3.2 22.8 - - + +
310A PHE* 3.8 27.5 - - + -
317A GLU* 3.6 25.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 278 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A ASN* 3.0 17.1 + - + +
275A ARG* 3.0 49.4 + - - +
277A ARG* 1.3 81.3 - - + +
279A LEU* 1.3 57.4 + - + +
281A GLN* 3.3 8.3 + - - +
282A GLN* 3.1 48.0 + - - +
----------------------------------------------------------
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 ARG* 3.0 26.7 + - + +
276A ALA 3.6 6.1 - - - +
278A GLN* 1.3 75.2 - - + +
280A LEU* 1.3 60.0 + - - +
282A GLN* 5.0 0.4 - - + -
283A THR* 2.8 56.8 + - + +
285A LYS* 4.0 15.3 - - - +
290A ILE* 3.8 23.8 - - + -
293A ALA* 4.3 16.2 - - + -
294A CYS* 3.7 29.8 - - - -
318A ARG* 3.0 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 280 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A ALA 2.8 24.0 + - - +
277A ARG 3.2 4.9 + - - +
279A LEU* 1.3 73.6 - - - +
281A GLN* 1.3 61.6 + - - +
283A THR 4.5 0.2 - - - +
287A ILE* 3.5 31.2 - - + -
290A ILE* 3.7 18.2 - - + -
302A PHE* 4.3 4.7 - - + -
306A TYR* 3.6 36.3 - - + +
314A PRO* 3.6 28.3 - - + +
317A GLU* 4.1 12.3 - - + -
318A ARG* 2.9 42.1 + - + +
321A ARG* 3.8 3.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 281 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A ARG* 3.0 57.9 + - - +
278A GLN* 3.3 9.6 + - - +
280A LEU* 1.3 80.3 - - - +
282A GLN* 1.3 67.0 + - + +
283A THR 4.0 0.2 - - - -
317A GLU* 3.4 22.9 + - + -
320A GLN 6.0 0.2 - - - -
321A ARG* 3.4 49.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 282 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A GLN* 3.1 33.3 + - - +
279A LEU* 3.3 0.6 + - + -
281A GLN* 1.3 90.5 + - + +
283A THR* 1.3 69.4 + - + +
321A ARG* 4.2 7.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 283 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A LEU* 2.8 42.4 + - + +
282A GLN* 1.3 88.2 - - + +
284A SER* 1.3 56.4 + - - +
285A LYS* 3.2 37.1 + - + +
290A ILE* 3.7 2.3 - - - +
318A ARG* 2.7 32.2 + - - -
321A ARG* 4.3 9.8 + - - +
----------------------------------------------------------
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