Contacts of the helix formed by residues 276 - 302 (chain D) in PDB entry 1FM9
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 GLU 276 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273D GLN* 5.9 1.4 - - - +
275D LYS* 1.3 84.9 - - + +
277D VAL* 1.3 78.1 + - + +
278D ALA* 3.4 20.9 + - + +
279D ILE* 3.5 3.7 - - + +
280D ARG* 3.1 21.0 + - - +
357D ARG* 3.2 47.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 277 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252D MET* 4.4 30.1 - - + -
255D LEU* 3.4 26.7 - - + -
276D GLU* 1.3 92.6 - - + +
278D ALA* 1.3 66.0 + - - +
279D ILE 3.4 0.4 - - - -
280D ARG* 3.6 14.5 - - + +
281D ILE* 3.6 18.9 + - - +
352D PHE* 4.5 12.8 - - + -
356D LEU* 4.3 14.0 - - + +
357D ARG 6.1 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 278 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200D 570 5.0 0.3 - - - -
276D GLU* 3.4 20.4 + - - +
277D VAL* 1.3 79.6 - - + +
279D ILE* 1.3 62.5 + - - +
280D ARG 3.1 1.8 - - - -
281D ILE* 3.2 5.5 + - - +
282D PHE* 2.9 29.1 + - - +
356D LEU* 4.6 10.5 - - + -
357D ARG* 4.7 2.0 - - + -
360D PHE* 3.7 45.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 279 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273D GLN 4.4 3.4 - - - +
275D LYS* 2.6 62.3 + - + +
276D GLU* 3.5 3.6 + - + +
278D ALA* 1.3 78.8 - - - +
280D ARG* 1.3 66.1 + - + +
282D PHE* 3.5 24.4 - - + +
283D GLN* 2.8 46.9 + - + +
360D PHE* 5.2 7.8 - - + -
462D ASP* 5.0 10.5 - - - +
463D MET 5.3 2.5 - - - +
464D SER* 5.9 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 280 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200D 570 3.7 11.6 - - + -
252D MET* 6.1 1.2 - - - +
255D LEU* 4.4 16.4 + - + +
256D MET* 4.2 33.7 - - - +
259D GLU* 2.6 39.1 + - - +
260D ASP* 4.6 7.5 + - - -
273D GLN* 3.0 57.4 - - - +
276D GLU 3.1 22.0 + - - +
277D VAL* 3.6 19.0 - - + +
278D ALA 3.1 0.2 - - - -
279D ILE* 1.3 77.7 - - - +
281D ILE* 1.3 62.3 + - - +
283D GLN* 3.0 26.2 - - - +
284D GLY* 3.1 7.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 281 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200D 570 3.8 50.0 - - + +
255D LEU* 4.2 12.6 - - + -
277D VAL 3.6 12.3 + - - +
278D ALA 3.2 7.0 + - - +
280D ARG* 1.3 74.4 - - - +
282D PHE* 1.3 67.1 + - - +
284D GLY* 3.2 0.9 + - - -
285D CYS* 3.0 26.4 + - - -
348D MET* 3.5 14.6 - - - -
352D PHE* 3.7 14.8 - - + -
353D LEU* 3.3 30.3 - - + -
356D LEU* 3.8 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 282 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200D 570 3.3 55.4 - + + -
278D ALA 2.9 17.2 + - - +
279D ILE* 3.5 24.7 - - + +
280D ARG 3.2 0.2 - - - -
281D ILE* 1.3 79.2 - - - +
283D GLN* 1.3 65.4 + - + +
286D GLN* 3.3 34.2 + - - +
360D PHE* 4.2 7.2 - + + -
453D LEU* 4.4 1.8 - - + -
456D ILE* 4.1 22.9 - - + -
463D MET* 4.0 26.0 - - - -
464D SER* 4.0 7.4 - - - -
465D LEU* 3.3 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 283 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259D GLU* 4.4 5.6 - - - +
270D LEU* 2.6 45.9 - - + +
271D GLN* 2.8 32.4 - - + +
272D GLU 4.5 1.0 - - - +
273D GLN 4.9 2.8 + - - -
279D ILE* 2.8 43.7 + - + +
280D ARG* 3.0 24.2 - - - +
282D PHE* 1.3 79.5 - - + +
284D GLY* 1.3 59.9 + - - +
286D GLN* 3.7 8.1 - - - +
287D PHE* 2.9 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 284 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200D 570 3.6 39.0 - - - -
270D LEU* 5.8 0.9 - - - -
280D ARG 3.1 10.5 + - - -
281D ILE 3.2 2.6 + - - -
283D GLN* 1.3 75.7 - - - +
285D CYS* 1.3 63.2 + - - +
287D PHE* 3.8 5.8 - - - +
288D ARG* 3.1 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 285 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200D 570 3.3 106.0 - - + +
281D ILE* 3.0 18.6 + - - +
282D PHE 4.3 0.2 - - - +
284D GLY* 1.3 72.2 - - - +
286D GLN* 1.3 56.6 + - - +
288D ARG* 3.2 4.7 + - - +
289D SER* 2.7 37.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 286 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200D 570 2.9 41.3 - - + -
270D LEU* 6.5 1.1 - - + -
282D PHE* 3.3 20.6 + - - +
283D GLN* 3.7 8.5 - - - +
285D CYS* 1.3 78.9 - - - +
287D PHE* 1.3 58.8 + - - +
289D SER* 3.3 2.4 + - - -
290D VAL* 3.0 30.8 + - + +
464D SER 3.6 14.3 + - - -
465D LEU* 3.0 17.4 - - - +
466D HIS* 3.2 38.7 + - + +
469D LEU* 3.8 4.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 287 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268D THR* 5.1 19.7 - - + -
269D PRO* 5.9 2.0 - - + -
270D LEU* 3.7 28.9 - - + -
283D GLN 2.9 18.1 + - - +
284D GLY* 3.8 7.0 - - - +
285D CYS 3.2 0.2 - - - -
286D GLN* 1.3 75.9 - - - +
288D ARG* 1.3 70.9 + - + +
290D VAL* 3.4 7.9 + - + +
291D GLU* 3.1 60.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 288 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200D 570 4.3 27.1 - - + +
226D PHE* 5.5 2.0 - - - -
227D PRO* 5.7 2.0 - - - +
284D GLY 3.1 18.1 + - - +
285D CYS* 3.2 6.0 + - - +
287D PHE* 1.3 84.6 - - + +
289D SER* 1.3 58.1 + - - +
291D GLU* 3.1 26.3 + - - +
292D ALA* 2.8 40.1 + - + +
295D GLU* 2.7 43.1 + - - -
329D MET* 6.4 0.2 - - - +
333D LEU* 6.2 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 289 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200D 570 2.9 47.1 + - - -
285D CYS 2.7 21.0 + - - -
286D GLN* 3.5 6.7 - - - -
288D ARG* 1.3 73.9 - - - +
290D VAL* 1.3 63.8 - - - +
292D ALA* 2.9 10.6 + - - +
293D VAL* 2.9 24.9 + - - +
326D ILE* 3.7 12.5 - - - +
469D LEU* 3.7 10.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 290 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286D GLN* 3.0 20.1 + - + +
287D PHE* 3.8 7.9 - - + +
288D ARG 3.3 0.2 - - - -
289D SER* 1.3 74.9 + - - +
291D GLU* 1.3 63.3 + - + +
293D VAL* 3.5 4.0 + - - +
294D GLN* 3.2 35.1 + - - +
466D HIS* 3.6 52.3 - - + +
468D LEU* 4.1 15.9 - - + +
469D LEU* 4.0 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 291 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287D PHE* 3.1 50.2 + - + +
288D ARG* 3.4 30.5 + - - +
290D VAL* 1.3 76.9 - - + +
292D ALA* 1.3 64.3 + - - +
294D GLN* 3.0 28.7 + - - +
295D GLU* 3.1 22.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 292 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288D ARG* 2.8 28.8 + - + +
289D SER* 2.9 10.3 + - - +
291D GLU* 1.3 77.6 - - - +
293D VAL* 1.3 57.9 + - - +
295D GLU* 3.0 13.5 + - - +
296D ILE* 2.8 38.7 + - + +
326D ILE* 3.7 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 293 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289D SER 2.9 18.6 + - - +
290D VAL 3.8 8.3 - - - +
291D GLU 3.3 0.2 - - - -
292D ALA* 1.3 74.7 - - - +
294D GLN* 1.3 54.0 + - - +
296D ILE* 3.8 7.6 - - - +
297D THR* 2.7 46.8 + - - +
322D VAL* 3.2 34.2 - - + +
326D ILE* 4.3 3.8 - - + -
468D LEU* 3.8 22.0 - - + -
469D LEU* 4.6 6.7 - - + -
472D ILE* 3.9 21.1 - - + -
690E LEU* 4.2 11.7 - - + -
693E LEU* 4.3 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 294 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290D VAL* 3.2 31.3 + - - +
291D GLU* 3.0 24.3 + - - +
293D VAL* 1.3 77.3 - - - +
295D GLU* 1.3 62.4 + - + +
297D THR* 3.5 6.3 + - - -
298D GLU* 3.2 29.8 + - - +
468D LEU* 4.9 3.8 - - + -
689E ILE* 6.1 1.6 - - + -
692E ARG* 5.4 2.1 + - - -
693E LEU* 4.3 25.9 - - + +
698E SER* 3.2 34.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 295 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225D SER* 3.4 28.5 - - - +
226D PHE* 3.8 19.8 - - + -
227D PRO* 3.9 18.7 - - + +
288D ARG* 2.7 45.3 + - - -
291D GLU* 3.1 17.6 + - - +
292D ALA* 3.0 6.5 + - - +
294D GLN* 1.3 75.0 - - + +
296D ILE* 1.3 65.4 + - - +
298D GLU* 3.3 6.8 + - - +
299D TYR* 3.0 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 296 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226D PHE* 4.2 17.9 - - + -
292D ALA* 2.8 27.5 + - + +
293D VAL* 3.8 3.6 - - - +
295D GLU* 1.3 71.6 - - - +
297D THR* 1.3 61.4 + - - +
299D TYR* 3.1 2.8 + - + +
300D ALA* 2.8 28.4 + - - +
318D LEU* 5.1 4.9 - - + -
322D VAL* 3.7 37.5 - - + +
325D ILE* 3.6 49.1 - - + -
326D ILE* 3.8 17.9 - - + -
329D MET* 5.2 1.8 - - - -
388D ILE* 5.6 0.4 - - + -
392D ILE* 4.4 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 297 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293D VAL* 2.7 34.3 + - - +
294D GLN* 3.7 8.3 - - - -
296D ILE* 1.3 78.3 - - - +
298D GLU* 1.3 62.8 + - - +
300D ALA* 3.3 7.7 + - - +
301D LYS* 3.3 22.5 + - + +
318D LEU* 4.1 18.6 - - + +
322D VAL* 5.2 0.5 - - - +
690E LEU* 4.7 2.8 - - + +
693E LEU* 3.9 41.6 - - + +
694E LEU* 4.1 19.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 298 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225D SER* 4.4 7.2 - - - +
294D GLN 3.2 15.9 + - - +
295D GLU* 3.7 8.7 - - - +
296D ILE 3.2 0.2 - - - -
297D THR* 1.3 81.0 - - - +
299D TYR* 1.3 64.1 + - - +
301D LYS* 2.9 40.5 + - - +
302D SER* 3.5 6.4 + - - -
693E LEU* 3.4 11.3 - - - +
696E GLU 4.6 1.0 - - - +
697E GLY* 3.3 29.1 - - - -
698E SER* 4.6 6.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 299 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218D LEU* 3.5 28.9 - - + +
221D SER* 3.1 28.3 - - - -
222D TYR* 3.7 24.0 - + + -
225D SER* 3.3 19.6 + - - +
226D PHE* 3.8 14.8 - + + -
295D GLU 3.0 14.9 + - - +
296D ILE* 3.1 4.7 + - - +
298D GLU* 1.3 77.2 - - - +
300D ALA* 1.3 62.3 + - - +
302D SER* 2.6 29.8 + - - -
303D ILE* 3.6 8.3 + - + +
385D ALA* 2.5 31.2 + - - -
388D ILE* 3.7 31.0 - - + -
389D ALA* 4.0 5.3 - - - +
392D ILE* 4.3 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 300 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296D ILE 2.8 12.7 + - - +
297D THR 3.5 9.9 - - - +
298D GLU 3.2 0.2 - - - -
299D TYR* 1.3 76.4 - - - +
301D LYS* 1.3 62.3 + - - +
303D ILE* 3.0 25.5 + - - +
306D PHE* 3.3 33.5 - - + +
318D LEU* 3.7 25.8 - - + -
392D ILE* 4.1 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 301 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297D THR* 3.4 20.0 - - + +
298D GLU* 2.9 34.1 + - - +
300D ALA* 1.3 75.1 - - - +
302D SER* 1.3 58.9 - - - +
303D ILE 3.3 4.7 + - - +
306D PHE* 3.9 2.5 - - + -
307D VAL* 3.7 38.9 - - + +
314D GLN* 5.0 0.2 - - - +
693E LEU 3.5 10.3 + - - -
694E LEU* 3.3 48.7 + - + +
695E GLN 4.9 1.2 + - - -
696E GLU 3.7 13.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 302 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217D HIS* 2.8 33.5 + - - -
218D LEU* 4.9 0.9 - - - +
221D SER* 2.9 38.1 + - - -
298D GLU 3.5 5.6 + - - -
299D TYR* 2.6 23.3 + - - -
301D LYS* 1.3 77.7 - - - +
303D ILE* 1.3 61.4 + - - +
304D PRO* 3.4 0.7 - - - +
----------------------------------------------------------
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