Contacts of the helix formed by residues 290 - 309 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A LYS* 5.1 6.3 - - - +
55A VAL 3.8 15.8 + - - +
56A ALA* 4.4 14.2 - - - +
135A ASP* 5.6 6.1 - - - +
286A LYS* 4.0 29.8 - - + -
287A ASP* 3.3 35.4 + - - +
289A THR* 1.3 83.7 + - - +
291A VAL* 1.3 63.2 + - - +
292A ASP* 3.0 13.5 - - + +
293A ARG* 2.9 18.4 + - + +
294A SER* 3.4 11.9 + - - -
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Residues in contact with VAL 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A ALA* 4.1 16.2 - - + -
134A GLY 3.3 25.4 - - - +
135A ASP* 4.1 14.7 + - + +
137A GLY* 5.4 3.8 - - - -
139A MET* 3.6 19.2 - - + +
289A THR 3.6 5.7 + - - +
290A LYS* 1.3 70.6 - - - +
292A ASP* 1.3 65.9 + - - +
293A ARG 3.1 0.2 - - - -
294A SER* 4.7 2.9 - - - -
295A ALA* 3.1 41.9 + - + +
296A ALA 3.7 0.5 + - - -
321A TYR* 4.6 8.1 - - + -
358A PRO* 4.0 28.9 - - + -
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Residues in contact with ASP 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A ASP* 5.7 1.7 - - - +
139A MET* 3.1 23.6 - - - +
281A GLY* 3.9 22.6 + - - +
282A ALA 4.2 12.6 - - - +
283A PHE* 3.1 21.6 - - - -
286A LYS* 3.8 20.1 + - + +
290A LYS* 4.5 9.3 - - + +
291A VAL* 1.3 81.8 - - - +
293A ARG* 1.3 58.4 + - - +
296A ALA* 3.3 10.2 - - - +
403A SO4 4.2 1.9 + - - -
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Residues in contact with ARG 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A ASP* 2.8 43.0 + - - -
43A LEU* 3.7 5.9 - - - +
283A PHE* 3.0 39.7 + - + +
284A SER* 3.7 1.4 - - - +
285A GLY 3.8 0.4 - - - +
286A LYS* 3.0 26.5 + - + +
287A ASP 4.5 10.8 - - - +
288A TYR* 5.4 1.1 - - - +
290A LYS* 2.9 12.0 + - + +
292A ASP* 1.3 78.4 - - + +
294A SER* 1.3 66.7 + - - +
296A ALA* 3.0 15.4 + - - +
297A TYR* 3.0 42.2 + - + +
372A TYR* 3.4 23.7 - - - -
375A THR* 3.0 25.1 - - - +
380A HIS* 3.7 4.0 + - - -
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Residues in contact with SER 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A TYR* 2.7 33.6 + - - -
289A THR 5.8 0.2 - - - -
290A LYS 3.4 7.2 + - - -
291A VAL* 4.7 4.7 - - - -
293A ARG* 1.3 77.4 - - - +
295A ALA* 1.3 58.4 + - - +
297A TYR* 3.1 8.9 + - - +
298A ALA 2.9 22.7 + - - -
358A PRO* 5.3 4.5 - - - -
361A ILE* 3.7 18.8 - - - +
362A VAL* 4.6 3.8 - - - +
367A LEU* 3.6 25.3 - - - +
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Residues in contact with ALA 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A MET* 3.8 11.3 - - + +
291A VAL* 3.1 25.5 + - + +
294A SER* 1.3 76.5 - - - +
296A ALA* 1.3 59.0 + - - +
297A TYR 3.2 0.2 - - - -
298A ALA* 3.6 9.3 - - - +
299A ALA* 3.0 28.9 + - - +
319A VAL* 4.3 2.4 - - - +
321A TYR* 3.5 38.1 + - + +
361A ILE* 4.2 3.6 - - + -
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Residues in contact with ALA 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A MET* 3.7 16.5 - - + +
140A PHE 4.1 8.6 - - - +
283A PHE* 3.7 20.2 - - + -
291A VAL 3.7 0.8 + - - -
292A ASP 3.3 17.0 - - - +
293A ARG 3.0 10.2 + - - +
295A ALA* 1.3 77.9 - - - +
297A TYR* 1.3 62.9 + - - +
299A ALA* 3.5 5.3 + - - +
300A ARG* 3.1 22.2 + - - +
381A PHE* 4.1 6.5 - - + -
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Residues in contact with TYR 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283A PHE* 4.2 9.4 - + - -
293A ARG* 3.0 53.4 + - + -
294A SER* 3.2 10.3 - - - +
296A ALA* 1.3 76.2 - - + +
298A ALA* 1.3 64.9 + - - +
300A ARG* 3.2 2.1 + - - +
301A TRP* 3.0 18.9 + - - +
365A LEU* 4.5 4.3 - - + -
367A LEU* 4.3 8.5 - - + -
372A TYR* 4.2 9.3 - + - -
375A THR* 3.7 4.3 + - - +
380A HIS* 2.7 39.3 + + + -
381A PHE* 3.6 24.7 - + - -
388A TRP* 3.4 66.8 - + + +
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Residues in contact with ALA 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294A SER 2.9 8.7 + - - +
295A ALA 3.6 7.4 - - - +
297A TYR* 1.3 76.0 - - - +
299A ALA* 1.3 56.5 + - - +
301A TRP* 3.1 12.5 - - + +
302A VAL* 3.1 32.4 + - - +
319A VAL* 6.1 0.9 - - + -
321A TYR* 5.2 0.2 - - - +
356A LEU* 3.9 12.8 - - + -
361A ILE* 3.3 41.3 - - + -
365A LEU* 4.1 8.0 - - + +
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Residues in contact with ALA 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A PHE* 3.6 24.2 - - - +
141A GLY* 3.4 15.6 - - - +
295A ALA 3.0 17.9 + - - +
296A ALA* 3.7 1.3 - - - +
297A TYR 3.3 0.2 - - - -
298A ALA* 1.3 72.9 - - - +
300A ARG* 1.3 63.4 + - - +
302A VAL* 3.8 4.9 + - - -
303A ALA* 3.2 16.8 + - - +
317A VAL* 3.5 11.7 - - + +
319A VAL* 3.7 23.9 - - + +
356A LEU* 5.9 0.9 - - - -
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Residues in contact with ARG 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A GLY* 4.0 2.6 - - - -
142A TYR 2.7 34.1 + - - -
143A ALA* 3.5 10.1 - - - +
149A GLU 2.7 29.9 + - - -
150A CYS* 3.0 21.6 + - - +
151A MET* 3.4 16.9 - - - +
272A TYR* 3.6 20.6 - - - +
296A ALA 3.1 12.2 + - - +
297A TYR 3.2 8.0 + - - +
299A ALA* 1.3 72.4 - - - +
301A TRP* 1.3 57.7 + - - +
303A ALA* 3.1 3.1 + - - +
304A LYS* 2.7 43.9 + - - +
381A PHE* 3.5 21.2 - - + +
388A TRP* 4.1 7.6 - - + +
389A GLU* 2.8 38.6 + - - +
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Residues in contact with TRP 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297A TYR 3.0 12.9 + - - +
298A ALA* 3.1 18.2 - - + +
300A ARG* 1.3 77.7 - - - +
302A VAL* 1.3 61.9 + - - +
304A LYS* 3.2 2.3 + - - +
305A SER* 2.9 29.3 + - - -
354A PHE* 4.0 26.0 - + - -
355A ASP 6.2 0.7 - - - -
356A LEU* 5.0 7.0 - - + -
361A ILE* 6.0 3.6 - - + -
364A ASP* 4.2 25.8 - - + -
365A LEU* 3.7 34.5 - - + -
387A PRO 4.1 2.8 + - - -
388A TRP* 3.3 26.7 - - + +
390A VAL 2.7 29.6 + - - -
391A PRO* 4.6 0.7 - - + -
392A LYS* 3.9 35.5 - - + +
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Residues in contact with VAL 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298A ALA 3.1 17.2 + - - +
299A ALA* 4.3 2.2 - - - +
301A TRP* 1.3 74.0 - - - +
303A ALA* 1.3 65.2 - - - +
305A SER* 3.5 0.9 - - - -
306A LEU* 2.9 37.3 + - + +
317A VAL* 3.7 30.3 - - + -
331A ILE* 5.3 0.2 - - + -
350A VAL* 4.5 12.8 - - + -
354A PHE* 3.6 45.3 - - + -
356A LEU* 4.1 20.9 - - + -
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Residues in contact with ALA 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A TYR* 3.7 31.6 - - - +
143A ALA* 3.5 10.3 - - + +
299A ALA 3.2 6.5 + - - +
300A ARG 3.1 7.5 + - - +
302A VAL* 1.3 82.4 - - - +
304A LYS* 1.3 63.4 + - - +
306A LEU* 3.2 10.3 + - - +
307A VAL* 3.3 12.3 + - - +
315A VAL* 3.8 9.1 - - + +
317A VAL* 3.4 24.7 - - + -
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Residues in contact with LYS 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A ALA* 3.6 10.2 - - - +
148A GLU 5.2 0.9 - - - -
149A GLU* 3.7 20.9 + - - +
150A CYS* 4.0 18.2 - - + -
300A ARG* 2.7 28.5 + - - +
301A TRP* 3.7 5.4 - - + +
303A ALA* 1.3 73.1 - - - +
305A SER* 1.3 61.5 + - - +
307A VAL* 3.5 2.1 + - - +
308A LYS* 3.0 31.7 + - + +
382A GLY 4.2 6.1 + - - -
384A SER* 4.7 6.1 - - - +
388A TRP 4.6 0.4 - - - +
389A GLU* 2.6 69.2 + - - +
391A PRO* 4.6 17.3 - - + -
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Residues in contact with SER 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301A TRP* 2.9 19.6 + - - -
302A VAL 3.5 3.8 - - - -
304A LYS* 1.3 74.6 - - - +
306A LEU* 1.3 58.9 + - - +
308A LYS* 3.3 1.7 + - - +
309A ALA* 2.8 33.2 + - - +
354A PHE* 3.5 23.9 - - - -
391A PRO* 3.7 13.4 - - - +
392A LYS* 2.9 28.9 + - - +
394A LEU* 4.0 11.0 - - - +
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Residues in contact with LEU 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302A VAL* 2.9 28.0 + - + +
303A ALA* 3.2 5.1 + - - +
305A SER* 1.3 73.3 - - - +
307A VAL* 1.3 66.6 + - - +
309A ALA 3.2 9.0 + - - -
311A LEU* 3.3 28.4 + - + +
312A CYS* 3.9 13.9 - - - -
315A VAL* 4.1 22.4 - - + -
317A VAL* 5.1 0.4 - - + -
333A ILE* 4.3 13.2 - - + -
346A LEU* 4.8 11.7 - - + -
349A VAL* 5.2 2.5 - - + -
350A VAL* 3.9 31.0 - - + -
354A PHE* 4.7 6.5 - - + -
394A LEU* 3.7 25.1 - - + -
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Residues in contact with VAL 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A ALA* 3.6 20.0 - - + +
144A THR 4.6 0.2 - - - -
145A ASP* 4.5 16.9 - - + +
150A CYS* 3.3 32.8 - - + -
303A ALA 3.3 7.9 + - - +
304A LYS 4.0 2.0 - - - +
306A LEU* 1.3 75.3 - - - +
308A LYS* 1.3 67.0 + - + +
310A GLY* 3.0 15.4 + - - -
312A CYS* 3.3 23.3 - - - +
313A ARG* 4.4 4.0 - - - -
314A ARG 4.4 4.5 - - - +
315A VAL* 3.4 27.4 - - + -
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Residues in contact with LYS 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A GLU* 3.9 15.2 + - - +
150A CYS* 3.5 32.1 - - - -
304A LYS* 3.0 23.1 + - + +
305A SER 3.6 4.0 - - - +
306A LEU 3.2 0.2 - - - -
307A VAL* 1.3 78.7 - - + +
309A ALA* 1.3 56.1 + - - +
310A GLY* 3.1 5.2 + - - -
391A PRO* 3.7 32.9 - - + +
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Residues in contact with ALA 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A SER 2.8 16.7 + - - +
306A LEU 3.2 4.8 + - - +
308A LYS* 1.3 73.1 - - - +
310A GLY* 1.3 53.9 + - - +
311A LEU* 3.0 11.0 + - + -
392A LYS 5.6 0.4 - - - +
393A LYS 4.5 4.7 - - - +
394A LEU* 4.0 19.7 - - + -
396A PHE* 3.2 40.1 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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