Contacts of the helix formed by residues 273 - 292 (chain A) in PDB entry 3IML
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 273 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A ARG* 4.1 11.1 - - - +
41A VAL 3.3 24.3 + - - +
42A ALA* 4.4 14.0 - - - +
122A ASP* 6.5 0.4 - - + -
269A LYS* 4.2 28.5 - - + +
270A ASP* 2.8 39.0 + - - +
271A PRO 3.6 2.1 - - - +
272A SER* 1.3 80.3 + - - +
274A VAL* 1.3 60.0 + - - +
275A ASP* 3.1 5.8 - - + +
276A ARG* 2.9 22.2 + - - +
277A SER* 3.2 10.0 + - - -
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Residues in contact with VAL 274 (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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120A ALA* 4.0 12.1 - - + -
121A GLY 5.0 1.3 - - - +
122A ASP* 3.8 29.8 - - + +
123A GLN 4.9 6.7 - - - +
126A MET* 3.8 8.7 - - - +
272A SER 3.4 5.3 + - - +
273A LYS* 1.3 68.3 - - - +
275A ASP* 1.3 71.0 + - - +
277A SER* 3.5 11.0 - - - +
278A ALA* 2.9 30.6 + - + +
304A TYR* 4.3 28.5 - - + -
341A PRO* 3.9 33.9 - - + -
344A ILE* 6.1 0.4 - - + -
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Residues in contact with ASP 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ASP* 5.3 6.1 - - - +
123A GLN 4.6 11.0 - - - +
124A GLY* 4.8 3.8 - - - -
125A LEU 5.3 1.2 - - - +
126A MET* 4.2 18.8 - - - +
264A GLY* 3.7 23.0 + - - +
265A ALA 4.1 5.2 - - - +
266A PHE* 3.3 20.5 - - - -
269A LYS* 2.9 35.0 + - + +
273A LYS* 3.1 3.7 + - + +
274A VAL* 1.3 82.9 - - - +
276A ARG* 1.3 58.6 + - - +
279A ALA* 3.5 7.8 - - - +
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Residues in contact with ARG 276 (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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26A ASP* 2.9 41.4 + - - -
29A LEU* 3.3 8.9 - - - +
265A ALA 5.2 0.2 - - - +
266A PHE* 3.1 35.6 + - + +
269A LYS* 2.8 44.3 + - + +
270A ASP 4.9 6.7 - - - +
271A PRO* 5.3 3.6 - - + -
273A LYS* 2.9 10.2 + - + +
275A ASP* 1.3 80.4 - - + +
277A SER* 1.3 64.2 + - - +
278A ALA 3.3 0.4 - - - -
279A ALA* 3.5 1.6 + - - +
280A TYR* 3.1 58.1 + - + -
350A LEU* 6.4 0.2 - - + -
355A TYR* 3.3 23.5 - - - -
358A THR* 3.0 20.4 + - - -
363A HIS* 3.8 4.6 - - - -
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Residues in contact with SER 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A PRO* 3.1 26.5 + - - -
272A SER 4.9 0.3 - - - -
273A LYS 3.2 7.3 + - - -
274A VAL* 3.5 12.0 - - - +
276A ARG* 1.3 80.6 - - - +
278A ALA* 1.3 59.3 + - - +
280A TYR* 3.4 3.0 + - - +
281A ALA 2.9 22.3 + - - -
341A PRO* 4.7 5.0 + - - +
344A ILE* 3.2 27.6 - - - +
345A ILE* 5.0 2.0 - - - -
350A LEU* 3.7 26.0 - - - -
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Residues in contact with ALA 278 (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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126A MET* 3.4 32.8 - - + +
127A PHE 5.8 0.2 - - - -
274A VAL* 2.9 20.7 + - + +
277A SER* 1.3 75.8 + - - +
279A ALA* 1.3 60.0 + - - +
281A ALA* 3.8 0.7 - - - +
282A GLY* 2.8 26.2 + - - -
302A VAL* 4.2 6.6 - - + +
304A TYR* 3.5 21.3 - - + +
344A ILE* 4.0 11.0 - - + -
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Residues in contact with ALA 279 (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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126A MET* 4.0 14.7 - - + +
127A PHE 4.4 13.0 - - - +
254A THR* 6.0 0.2 - - + -
266A PHE* 3.4 40.8 - - + -
274A VAL 3.9 2.6 + - - -
275A ASP 3.5 7.4 - - - +
276A ARG 3.5 2.8 + - - +
277A SER 3.4 0.2 - - - -
278A ALA* 1.3 78.7 - - - +
280A TYR* 1.3 57.0 + - - +
282A GLY* 3.3 1.7 + - - -
283A ARG* 3.0 24.1 + - - +
364A PHE* 3.6 12.2 - - + -
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Residues in contact with TYR 280 (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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266A PHE* 4.2 7.2 - + - -
276A ARG* 3.1 54.0 + - + +
277A SER* 3.6 6.3 - - - +
279A ALA* 1.3 74.3 - - + +
281A ALA* 1.3 60.8 + - - +
283A ARG* 3.4 1.9 + - - +
284A TYR 2.9 23.0 + - - -
348A LEU* 4.1 8.5 - - + -
350A LEU* 4.4 11.7 - - + -
355A TYR* 4.0 14.8 - + - -
358A THR* 3.7 5.2 + - - +
363A HIS* 2.7 33.4 + - + -
364A PHE* 3.5 27.6 - + - -
373A TRP* 3.2 62.7 - + + +
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Residues in contact with ALA 281 (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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277A SER 2.9 18.5 + - - +
278A ALA 3.8 3.1 - - - +
280A TYR* 1.3 75.4 - - - +
282A GLY* 1.3 58.0 + - - +
284A TYR* 3.1 10.0 - - - +
285A VAL* 2.8 35.1 + - - +
339A LEU* 4.8 10.3 - - + -
344A ILE* 3.7 32.1 - - + -
347A MET* 4.3 9.9 - - + -
348A LEU* 3.9 5.1 - - - +
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Residues in contact with GLY 282 (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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127A PHE 5.1 0.7 - - - -
128A GLY* 3.6 12.8 - - - -
278A ALA 2.8 18.4 + - - -
279A ALA 3.6 2.2 - - - -
281A ALA* 1.3 77.1 - - - +
283A ARG* 1.3 56.3 + - - +
285A VAL* 3.3 3.6 + - - -
286A ALA* 2.9 31.0 + - - +
300A ILE* 3.4 20.0 - - - +
302A VAL* 5.7 5.4 - - - -
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Residues in contact with ARG 283 (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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128A GLY* 3.8 3.5 - - - -
129A TYR 3.1 24.6 + - - +
130A ALA* 3.6 8.1 - - - +
136A GLU 2.8 27.9 + - - -
137A LEU 2.8 22.2 + - - -
138A MET* 3.5 25.1 - - - +
255A TYR* 3.4 18.2 - - - +
279A ALA 3.0 7.2 + - - +
280A TYR 3.6 7.4 - - - +
282A GLY* 1.3 71.3 - - - +
284A TYR* 1.3 56.5 + - - +
286A ALA 3.2 1.2 + - - -
287A LYS* 2.7 47.5 + - - +
364A PHE* 3.5 33.9 - - + +
365A GLY* 3.8 0.4 - - - -
373A TRP* 4.1 9.4 - - + +
374A GLU* 2.8 34.5 + - - +
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Residues in contact with TYR 284 (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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280A TYR 2.9 14.3 + - - +
281A ALA* 3.1 11.0 - - - +
283A ARG* 1.3 76.8 - - - +
285A VAL* 1.3 61.6 + - - +
287A LYS* 3.8 0.9 - - - +
288A ASN* 2.8 42.8 + - - -
337A PHE* 3.5 35.9 - + - -
347A MET* 3.8 32.2 + - + +
348A LEU* 3.8 15.0 - - + -
372A SER 3.7 11.0 - - - -
373A TRP* 3.3 32.5 - - - +
375A ALA 3.4 18.4 - - - -
377A ASP* 2.6 27.8 + - - -
378A LYS* 3.6 14.6 - - + -
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Residues in contact with VAL 285 (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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281A ALA* 2.8 25.4 + - + +
282A GLY 3.7 3.4 - - - +
284A TYR* 1.3 68.0 - - + +
286A ALA* 1.3 68.2 + - - +
288A ASN* 3.1 4.3 + - - +
289A ILE* 3.0 29.8 + - + +
300A ILE* 3.6 28.3 - - + -
333A VAL* 3.6 30.7 - - + -
337A PHE* 3.8 41.9 - - + -
339A LEU* 4.4 8.7 - - + -
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Residues in contact with ALA 286 (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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128A GLY 3.8 4.7 - - - +
129A TYR* 3.6 36.3 - - - +
130A ALA* 3.3 11.0 - - - +
282A GLY 2.9 20.6 + - - +
283A ARG 3.7 2.0 - - - +
285A VAL* 1.3 74.7 - - - +
287A LYS* 1.3 62.2 + - - +
289A ILE* 3.3 13.3 + - - +
290A VAL* 3.3 18.2 + - - +
298A ALA* 3.8 10.4 - - - +
300A ILE* 4.2 5.1 - - + +
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Residues in contact with LYS 287 (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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130A ALA* 3.6 8.5 - - - +
136A GLU 3.4 17.9 + - - -
137A LEU* 3.8 23.1 - - + +
283A ARG* 2.7 34.2 + - - +
284A TYR* 3.8 4.7 - - - +
286A ALA* 1.3 75.6 - - - +
288A ASN* 1.3 59.2 + - - +
290A VAL 3.3 0.9 + - - -
291A ALA* 2.9 32.7 + - + +
367A GLU* 3.2 24.0 + - - +
373A TRP 4.7 0.2 - - - +
374A GLU* 2.6 65.9 + - - +
375A ALA 5.3 2.5 - - - -
376A ALA* 5.4 7.9 - - + +
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Residues in contact with ASN 288 (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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284A TYR* 2.8 43.0 + - - +
285A VAL 3.1 3.8 + - - +
287A LYS* 1.3 74.7 - - - +
289A ILE* 1.3 60.4 + - - +
291A ALA* 4.2 4.9 - - - -
292A ALA* 2.9 31.4 + - - +
337A PHE* 4.1 7.4 - - + -
375A ALA 3.2 20.0 + - - -
376A ALA* 3.1 13.1 - - - +
378A LYS* 2.9 33.1 + - - -
379A ALA* 3.1 10.0 + - - +
382A LEU* 3.8 17.1 - - + +
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Residues in contact with ILE 289 (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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285A VAL* 3.0 39.4 + - + +
286A ALA* 3.5 8.1 - - - +
287A LYS 3.2 0.2 - - - -
288A ASN* 1.3 78.2 - - - +
290A VAL* 1.3 62.6 + - - +
292A ALA* 3.5 1.1 + - - +
293A GLY 3.5 1.7 + - - -
294A LEU* 3.2 42.7 + - + +
295A ALA* 4.2 11.4 - - + -
298A ALA* 3.7 21.1 - - + -
300A ILE* 5.5 1.6 - - + -
316A VAL* 3.8 15.9 - - + -
318A THR* 5.0 0.2 - - + -
329A ILE* 3.7 32.5 - - + -
333A VAL* 4.1 6.5 - - + -
382A LEU* 4.3 14.1 - - + -
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Residues in contact with VAL 290 (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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130A ALA* 3.6 26.9 - - + +
131A CYS 4.3 1.6 - - - -
132A ASP* 4.3 16.2 - - + +
137A LEU* 4.3 19.5 - - + -
286A ALA 3.3 13.9 + - - +
287A LYS 3.3 5.9 + - - +
289A ILE* 1.3 75.9 - - + +
291A ALA* 1.3 60.5 + - - +
293A GLY* 2.9 21.3 + - - -
295A ALA 3.5 18.4 - - - +
296A SER* 3.9 11.9 - - - +
297A ARG* 3.9 15.0 - - - -
298A ALA* 4.0 6.3 - - + +
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Residues in contact with ALA 291 (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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137A LEU* 3.8 16.9 - - + +
287A LYS 2.9 19.8 + - - +
288A ASN* 4.1 1.3 - - - +
290A VAL* 1.3 76.3 - - - +
292A ALA* 1.3 60.8 + - - +
293A GLY* 3.3 1.0 + - - -
376A ALA* 3.8 28.3 - - + -
379A ALA* 3.8 11.9 - - + +
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Residues in contact with ALA 292 (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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288A ASN 2.9 20.4 + - - +
289A ILE 3.7 6.3 - - - +
290A VAL 3.1 0.2 - - - -
291A ALA* 1.3 76.2 - - - +
293A GLY* 1.3 59.4 + - - +
294A LEU* 3.7 6.9 + - + -
379A ALA* 3.2 30.2 - - - +
382A LEU* 3.8 15.9 - - + -
383A ALA* 3.4 22.4 - - - +
388A VAL* 3.7 9.4 - - - +
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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