Contacts of the helix formed by residues 290 - 309 (chain B) in PDB entry 1QM4
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 LYS 290 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B LYS* 5.1 6.5 - - - +
55B VAL 3.8 15.8 + - - +
56B ALA* 4.4 14.2 - - - +
135B ASP* 5.8 4.7 - - - +
286B LYS* 4.1 23.3 - - + -
287B ASP* 3.3 40.0 + - - +
289B THR* 1.3 81.6 + - - +
291B VAL* 1.3 64.8 + - - +
292B ASP* 4.3 9.6 - - + +
293B ARG* 2.9 15.6 + - - +
294B SER* 3.4 12.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 291 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B ALA* 4.2 14.8 - - + -
134B GLY 3.3 25.8 - - - +
135B ASP* 4.2 14.3 + - + +
137B GLY* 5.4 2.9 - - - -
139B MET* 3.7 18.7 - - + +
289B THR 3.6 5.8 + - - +
290B LYS* 1.3 69.1 - - - +
292B ASP* 1.3 64.8 + - - +
293B ARG 3.1 0.4 - - - -
294B SER* 4.7 3.8 - - - -
295B ALA* 3.0 44.7 + - + +
321B TYR* 4.5 9.2 - - + -
358B PRO* 4.1 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 292 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B ASP* 5.8 1.3 - - - +
139B MET* 3.1 24.3 - - - +
281B GLY* 4.0 22.0 + - - +
282B ALA 4.2 13.0 - - - +
283B PHE* 3.2 21.5 - - - -
286B LYS* 3.8 19.4 + - + +
290B LYS* 3.0 9.1 - - + +
291B VAL* 1.3 82.5 - - - +
293B ARG* 1.3 57.7 + - - +
296B ALA* 3.4 9.9 - - - +
401B SO4 4.6 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 293 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B ASP* 2.8 44.0 + - - -
43B LEU* 3.6 7.3 - - - +
283B PHE* 3.1 35.2 + - + +
284B SER* 4.2 1.4 - - - +
285B GLY 3.8 0.8 - - - +
286B LYS* 2.9 29.2 + - + +
287B ASP 4.4 9.9 - - - +
288B TYR* 5.4 1.3 - - - +
290B LYS* 2.9 10.9 + - + +
292B ASP* 1.3 79.2 - - + +
294B SER* 1.3 67.0 + - - +
296B ALA* 3.1 15.1 + - - +
297B TYR* 3.0 42.3 + - + +
372B TYR* 3.5 23.8 - - - +
375B THR* 3.0 25.1 - - - +
380B HIS* 3.7 3.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 294 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B TYR* 2.6 32.9 + - - -
289B THR 5.7 0.2 - - - -
290B LYS 3.4 7.6 + - - -
291B VAL* 4.7 5.2 - - - -
293B ARG* 1.3 77.2 - - - +
295B ALA* 1.3 52.4 + - - +
297B TYR* 3.1 9.6 - - - +
298B ALA 2.8 28.6 + - - -
358B PRO* 5.4 4.3 - - - -
361B ILE* 3.7 18.9 - - - +
362B VAL* 4.7 3.6 - - - +
367B LEU* 3.7 25.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 295 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B MET* 3.7 11.8 - - + +
291B VAL* 3.0 24.4 + - + +
294B SER* 1.3 75.6 - - - +
296B ALA* 1.3 59.1 + - - +
297B TYR 3.2 0.2 - - - -
298B ALA* 3.6 9.5 - - - +
299B ALA* 2.9 29.5 + - - +
319B VAL* 4.3 2.4 - - - +
321B TYR* 3.5 36.3 - - + +
361B ILE* 4.3 4.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 296 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B MET* 3.7 17.4 - - + +
140B PHE 4.1 9.7 - - - +
283B PHE* 3.8 20.9 - - + -
291B VAL 3.7 0.8 + - - -
292B ASP 3.4 15.9 - - - +
293B ARG 3.1 11.1 + - - +
295B ALA* 1.3 77.2 - - - +
297B TYR* 1.3 58.9 + - + +
299B ALA* 3.5 3.1 + - - +
300B ARG* 3.1 25.5 + - - +
381B PHE* 4.0 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 297 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B PHE* 4.3 8.3 - + - -
293B ARG* 3.0 50.9 + - + -
294B SER* 3.1 12.5 + - - +
296B ALA* 1.3 77.9 - - + +
298B ALA* 1.3 56.3 + - - +
300B ARG* 3.1 2.3 + - - +
301B TRP 2.9 24.4 + - - -
365B LEU* 4.5 4.5 - - + -
367B LEU* 4.3 9.2 - - + -
372B TYR* 4.2 9.3 - + - -
375B THR* 3.7 4.5 + - - +
380B HIS* 2.7 39.9 + + + -
381B PHE* 3.6 26.2 - + - -
388B TRP* 3.4 62.6 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 298 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B SER 2.8 8.6 + - - +
295B ALA 3.6 6.7 - - - +
297B TYR* 1.3 76.2 - - - +
299B ALA* 1.3 56.8 + - - +
301B TRP* 3.1 12.8 - - + +
302B VAL* 3.1 32.2 + - - +
321B TYR* 5.2 0.4 - - - +
356B LEU* 3.8 13.0 - - + -
361B ILE* 3.3 41.3 - - + -
365B LEU* 4.1 8.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 299 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B PHE* 3.6 25.6 - - - +
141B GLY* 3.5 11.1 - - - +
295B ALA 2.9 17.5 + - - +
296B ALA* 3.7 1.8 - - - +
297B TYR 3.3 0.2 - - - -
298B ALA* 1.3 72.3 - - - +
300B ARG* 1.3 65.3 + - - +
302B VAL* 4.2 5.8 - - - -
303B ALA* 3.1 22.5 + - - +
317B VAL* 3.5 10.8 - - + +
319B VAL* 3.7 21.9 - - + +
356B LEU* 5.9 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 300 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B GLY* 4.0 2.6 - - - -
142B TYR 2.7 33.5 + - - -
143B ALA* 3.5 10.3 - - - +
149B GLU 2.8 28.9 + - - -
150B CYS* 3.1 18.2 + - - +
151B MET* 3.4 21.3 - - - +
272B TYR* 3.6 20.2 - - - +
296B ALA 3.1 13.3 + - - +
297B TYR 3.1 7.8 + - - +
299B ALA* 1.3 73.2 - - - +
301B TRP* 1.3 57.6 + - - +
303B ALA* 3.1 3.4 + - - +
304B LYS* 2.8 43.7 + - - +
381B PHE* 3.6 19.3 - - + +
388B TRP* 4.1 8.5 - - + +
389B GLU* 2.8 39.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 301 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B TYR 2.9 12.6 + - - +
298B ALA* 3.1 19.7 - - + +
300B ARG* 1.3 77.6 - - - +
302B VAL* 1.3 57.3 + - - +
304B LYS* 3.1 2.8 + - + +
305B SER* 2.9 35.1 + - - -
354B PHE* 3.9 25.4 - + - -
355B ASP 6.2 0.9 - - - -
356B LEU* 5.0 5.6 - - + -
361B ILE* 6.0 3.6 - - + -
364B ASP* 4.2 26.5 - - + -
365B LEU* 3.7 34.1 - - + -
387B PRO 4.2 2.6 + - - -
388B TRP* 3.3 27.4 - - + +
390B VAL 2.7 30.2 + - - -
391B PRO* 4.6 0.4 - - + -
392B LYS* 3.9 36.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 302 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B ALA 3.1 16.2 + - - +
299B ALA* 4.5 2.0 - - - -
301B TRP* 1.3 74.7 - - + +
303B ALA* 1.3 67.7 + - - +
305B SER* 3.5 0.9 - - - -
306B LEU* 2.9 36.8 + - + +
317B VAL* 3.7 29.8 - - + -
333B ILE* 5.0 0.2 - - + -
350B VAL* 4.6 12.6 - - + -
354B PHE* 3.7 44.0 - - + -
356B LEU* 4.1 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 303 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B TYR* 3.6 31.4 - - - +
143B ALA* 3.5 11.6 - - + +
299B ALA 3.1 12.8 + - - +
300B ARG 3.1 4.6 + - - +
302B VAL* 1.3 80.3 - - - +
304B LYS* 1.3 62.5 + - - +
306B LEU* 3.3 9.7 + - - +
307B VAL* 3.3 12.3 + - - +
315B VAL* 3.7 9.1 - - + +
317B VAL* 3.4 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 304 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B ALA* 3.7 8.7 - - - +
148B GLU 5.2 0.9 - - - -
149B GLU* 3.7 19.0 + - - +
150B CYS* 3.9 19.5 - - + -
300B ARG* 2.8 27.5 + - - +
301B TRP* 3.6 4.9 - - - +
303B ALA* 1.3 72.8 - - - +
305B SER* 1.3 62.8 + - - +
307B VAL* 3.6 1.2 + - - +
308B LYS* 3.0 33.3 + - + +
382B GLY 4.1 6.5 + - - -
384B SER* 4.6 6.3 - - - +
388B TRP 4.6 0.4 - - - +
389B GLU* 2.6 71.2 + - - +
391B PRO* 4.6 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 305 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B TRP* 2.9 20.7 + - - -
302B VAL 3.5 4.5 - - - -
304B LYS* 1.3 78.1 - - - +
306B LEU* 1.3 57.7 + - - +
308B LYS* 3.4 1.9 + - - +
309B ALA* 2.8 32.7 + - - +
354B PHE* 3.5 23.4 - - - -
391B PRO* 3.7 12.6 - - - +
392B LYS* 3.0 28.7 + - - +
394B LEU* 4.0 11.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 306 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B VAL* 2.9 28.7 + - + +
303B ALA* 3.6 4.7 - - - +
305B SER* 1.3 73.1 - - - +
307B VAL* 1.3 66.9 + - - +
309B ALA* 3.2 8.8 + - - -
311B LEU* 3.2 29.9 + - + +
312B CYS* 4.0 13.9 - - - -
315B VAL* 4.2 22.7 - - + -
317B VAL* 5.1 0.2 - - + -
333B ILE* 4.2 13.7 - - + -
346B LEU* 4.8 11.2 - - + +
349B VAL* 5.2 1.8 - - + -
350B VAL* 3.8 31.2 - - + -
354B PHE* 4.7 6.7 - - + -
394B LEU* 3.7 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 307 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B ALA* 3.6 19.3 - - + +
144B THR 4.4 0.2 - - - +
145B ASP* 4.4 17.5 - - + +
150B CYS* 3.2 32.1 - - + -
303B ALA 3.3 7.9 + - - +
304B LYS 4.1 1.3 - - - +
306B LEU* 1.3 74.2 - - - +
308B LYS* 1.3 68.0 + - + +
310B GLY* 2.8 17.0 + - - -
312B CYS* 3.2 23.5 - - - +
313B ARG* 4.5 4.0 - - - -
314B ARG 4.4 4.0 - - - +
315B VAL* 3.4 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 308 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B GLU* 3.9 22.1 + - - +
150B CYS* 3.6 24.5 - - - -
304B LYS* 3.0 23.6 + - + +
305B SER 3.6 4.5 - - - +
306B LEU 3.2 0.2 - - - -
307B VAL* 1.3 80.1 - - + +
309B ALA* 1.3 57.2 + - - +
310B GLY* 3.1 4.9 + - - -
391B PRO* 3.7 32.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 309 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B SER 2.8 17.9 + - - +
306B LEU 3.2 4.8 + - - +
308B LYS* 1.3 74.4 - - - +
310B GLY* 1.3 55.1 + - - +
311B LEU* 3.1 11.1 + - + -
392B LYS 5.5 0.4 - - - +
393B LYS 4.5 4.9 - - - +
394B LEU* 3.9 20.4 - - + -
396B PHE* 3.2 39.7 - - + -
----------------------------------------------------------
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