Contacts of the helix formed by residues 329 - 355 (chain F) in PDB entry 1SMK
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 ASN 329 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229F LEU* 6.1 0.2 - - - +
230F SER* 3.3 22.8 + - - +
243F ILE* 5.7 7.3 - - - +
328F LEU* 1.3 73.0 - - - +
330F GLU* 1.3 58.9 + - - +
331F TYR* 3.2 11.7 + - - +
332F GLU* 2.8 55.3 + - - +
333F ARG* 2.8 32.5 + - - +
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Residues in contact with GLU 330 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329F ASN* 1.3 71.6 - - - +
331F TYR* 1.3 68.7 + - - +
333F ARG* 2.9 24.1 + - - +
334F ILE* 2.9 37.0 + - - +
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Residues in contact with TYR 331 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229F LEU* 5.5 0.2 - - + -
243F ILE* 3.3 36.6 - - + -
244F SER* 3.8 17.2 + - - -
247F THR* 3.4 35.7 - - + +
248F ASP* 5.2 2.4 + - - -
329F ASN* 3.2 9.8 + - - +
330F GLU* 1.3 78.8 + - - +
332F GLU* 1.3 69.5 + - + +
334F ILE* 3.3 8.7 + - + +
335F GLY* 2.9 23.4 + - - -
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Residues in contact with GLU 332 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226F LEU* 4.1 9.7 - - + +
227F PRO 4.6 7.6 - - - +
228F LEU* 3.3 18.1 - - + -
229F LEU* 2.9 16.5 + - + +
230F SER* 2.7 43.7 + - - -
328F LEU* 3.6 15.3 - - + +
329F ASN* 2.8 41.6 + - - +
331F TYR* 1.3 84.3 - - + +
333F ARG* 1.3 61.7 + - - +
335F GLY* 3.1 3.2 + - - +
336F LEU* 2.8 31.1 + - - +
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Residues in contact with ARG 333 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326F GLY 4.4 6.3 + - - -
327F PRO* 4.4 3.2 - - - +
328F LEU* 3.3 49.1 + - + +
329F ASN 2.8 31.3 + - - +
330F GLU* 2.9 17.5 + - - +
332F GLU* 1.3 72.9 - - - +
334F ILE* 1.3 65.6 + - + +
336F LEU* 3.4 15.0 + - - +
337F GLU* 3.2 19.8 + - - +
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Residues in contact with ILE 334 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330F GLU* 2.9 34.6 + - - +
331F TYR* 3.6 9.6 - - + +
333F ARG* 1.3 78.3 - - + +
335F GLY* 1.3 65.1 + - - +
337F GLU* 3.1 13.0 + - + +
338F LYS* 3.1 34.7 + - + +
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Residues in contact with GLY 335 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223F VAL 4.4 2.6 - - - +
226F LEU* 3.9 17.5 - - - +
331F TYR* 2.9 15.1 + - - -
332F GLU 3.1 4.0 + - - -
334F ILE* 1.3 79.7 - - - +
336F LEU* 1.3 55.8 + - - +
338F LYS* 3.2 16.4 + - - +
339F ALA* 2.8 28.8 + - - +
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Residues in contact with LEU 336 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226F LEU* 3.6 16.5 - - + +
303F THR* 4.7 1.6 - - + -
308F PHE* 3.7 26.5 - - + -
325F LEU* 3.7 22.9 - - + -
328F LEU* 3.9 14.1 - - + -
332F GLU 2.8 17.2 + - - +
333F ARG* 3.6 14.6 - - - +
334F ILE 3.2 0.2 - - - -
335F GLY* 1.3 76.5 - - - +
337F GLU* 1.3 58.6 + - - +
339F ALA* 4.1 1.8 - - + -
340F LYS* 2.8 65.2 + - + +
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Residues in contact with GLU 337 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333F ARG 3.2 10.2 + - - +
334F ILE* 3.1 19.4 + - + +
336F LEU* 1.3 81.7 - - - +
338F LYS* 1.3 61.5 + - + +
340F LYS* 3.6 19.7 + - - +
341F LYS* 3.3 26.9 + - + +
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Residues in contact with LYS 338 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223F VAL* 4.2 35.6 - - + +
251F GLN* 5.4 4.8 + - - +
334F ILE* 3.1 30.2 + - + +
335F GLY* 3.2 12.7 + - - +
337F GLU* 1.3 77.2 - - + +
339F ALA* 1.3 62.8 + - - +
341F LYS* 3.4 10.4 + - - +
342F GLU* 3.2 22.9 + - - +
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Residues in contact with ALA 339 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218F GLY* 5.0 7.2 - - - -
223F VAL 3.7 19.9 + - - +
224F THR* 3.8 22.2 - - - +
226F LEU* 4.8 7.6 - - + -
308F PHE* 5.4 1.1 - - + -
335F GLY 2.8 17.0 + - - +
336F LEU* 3.1 11.9 + - + +
338F LYS* 1.3 78.5 - - - +
340F LYS* 1.3 57.3 + - - +
342F GLU 3.4 0.2 + - - -
343F LEU* 2.8 35.1 + - - +
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Residues in contact with LYS 340 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303F THR* 4.2 11.2 - - - +
304F GLU* 3.4 38.7 + - - +
305F LEU* 3.6 25.0 - - + +
308F PHE* 4.6 5.4 - - + -
336F LEU* 2.8 56.1 + - + +
337F GLU* 3.9 22.5 + - - +
339F ALA* 1.3 72.2 - - - +
341F LYS* 1.3 64.7 + - - +
344F ALA* 2.9 26.5 + - - +
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Residues in contact with LYS 341 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337F GLU* 3.3 14.4 + - + +
338F LYS* 3.4 12.3 - - + +
340F LYS* 1.3 81.7 - - - +
342F GLU* 1.3 62.4 + - + +
344F ALA* 3.5 15.0 - - - +
345F GLY 3.9 2.8 + - - -
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Residues in contact with GLU 342 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221F ALA* 4.3 9.4 - - - +
222F GLY* 5.0 1.7 - - - -
223F VAL* 3.6 23.7 + - + +
224F THR* 3.8 20.8 - - + +
338F LYS 3.2 11.1 + - - +
341F LYS* 1.3 77.2 - - + +
343F LEU* 1.3 67.2 + - - +
344F ALA 3.1 2.0 - - - -
345F GLY* 3.1 13.2 + - - -
346F SER* 3.3 16.4 + - - +
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Residues in contact with LEU 343 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165F ASN* 3.6 40.4 - - + +
218F GLY* 3.7 20.2 - - - +
219F GLY* 4.2 1.8 - - - +
224F THR* 3.9 8.2 - - + +
297F PHE* 4.0 10.8 - - + -
305F LEU* 3.7 15.0 - - + -
307F PHE 3.9 7.2 - - - +
308F PHE* 3.7 32.8 - - + -
339F ALA 2.8 18.3 + - - +
342F GLU* 1.3 77.8 - - - +
344F ALA* 1.3 62.4 - - - +
346F SER* 3.4 3.2 + - - -
347F ILE* 3.1 35.4 + - + +
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Residues in contact with ALA 344 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305F LEU* 4.1 18.6 - - + +
340F LYS 2.9 18.5 + - - +
341F LYS* 3.5 9.6 - - - +
342F GLU 3.1 0.2 - - - -
343F LEU* 1.3 77.0 - - - +
345F GLY* 1.3 63.0 + - - +
347F ILE* 3.4 5.5 + - - +
348F GLU* 3.1 22.5 + - - +
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Residues in contact with GLY 345 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341F LYS 3.9 2.8 + - - -
342F GLU 3.1 8.5 + - - -
344F ALA* 1.3 80.4 - - - +
346F SER* 1.3 52.1 + - - +
348F GLU* 3.2 6.4 + - - +
349F LYS* 2.7 36.5 + - - +
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Residues in contact with SER 346 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165F ASN* 3.8 26.7 + - - +
166F SER* 2.6 32.9 + - - -
224F THR* 5.5 0.7 - - - +
342F GLU* 3.3 19.5 + - - +
343F LEU* 3.7 9.8 - - - -
344F ALA 3.3 0.2 - - - -
345F GLY* 1.3 75.2 - - - +
347F ILE* 1.3 62.7 + - - +
349F LYS* 3.7 6.2 - - - +
350F GLY 3.2 10.2 + - - -
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Residues in contact with ILE 347 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165F ASN 4.0 15.5 - - - +
169F PRO* 4.0 17.1 - - + +
297F PHE* 4.8 0.2 - - + -
305F LEU* 3.9 23.8 - - + -
306F PRO* 4.0 24.9 - - + -
307F PHE* 3.7 30.7 - - + +
343F LEU* 3.1 27.8 + - + +
344F ALA* 3.7 4.7 - - - +
346F SER* 1.3 72.3 - - - +
348F GLU* 1.3 63.8 + - - +
350F GLY* 3.1 2.8 + - - -
351F VAL* 2.8 37.0 + - + +
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Residues in contact with GLU 348 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344F ALA 3.1 11.7 + - - +
345F GLY* 3.6 9.0 - - - +
347F ILE* 1.3 79.6 - - - +
349F LYS* 1.3 66.0 + - - +
351F VAL* 4.4 12.4 - - - +
352F SER* 2.8 46.2 + - - -
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Residues in contact with LYS 349 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131F ASP* 5.8 2.6 + - - -
134F PHE* 3.8 50.3 - - + +
166F SER* 4.4 4.7 - - - +
345F GLY 2.7 22.2 + - - +
346F SER* 3.7 9.0 - - - +
348F GLU* 1.3 71.4 - - - +
350F GLY* 1.3 61.4 + - - +
352F SER* 3.7 6.2 - - - -
353F PHE* 3.3 20.4 + - - +
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Residues in contact with GLY 350 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134F PHE* 4.7 0.4 - - - -
166F SER* 3.7 27.1 - - - -
170F ILE* 3.2 29.6 - - - +
346F SER 3.2 6.4 + - - -
347F ILE 3.1 6.3 + - - -
348F GLU 3.0 0.4 - - - -
349F LYS* 1.3 79.2 - - - +
351F VAL* 1.3 65.9 + - - +
353F PHE* 3.1 11.3 + - - +
354F ILE 3.6 2.1 + - - -
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Residues in contact with VAL 351 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169F PRO* 3.9 17.2 - - + +
173F GLU* 3.5 38.3 - - + +
306F PRO* 6.2 0.7 - - + -
307F PHE* 5.2 4.5 - - + -
347F ILE* 2.8 32.1 + - + +
348F GLU* 4.0 16.8 - - - +
350F GLY* 1.3 71.4 - - - +
352F SER* 1.3 64.4 + - - +
354F ILE* 3.2 5.5 + - - +
355F ARG* 3.0 32.7 + - + +
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Residues in contact with SER 352 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348F GLU* 2.8 31.3 + - - -
349F LYS* 3.7 7.0 - - - -
351F VAL* 1.3 77.5 - - - +
353F PHE* 1.3 63.3 + - - +
354F ILE 3.1 1.0 + - - -
355F ARG* 3.2 25.9 + - - +
356F SER* 3.7 6.1 + - - -
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Residues in contact with PHE 353 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134F PHE* 4.4 11.7 - + + -
135F LYS* 4.3 17.0 - - + -
138F ALA* 3.5 39.5 - - + -
139F GLY* 3.6 14.8 - - - -
142F LYS* 4.2 13.1 + - + -
170F ILE* 3.7 16.8 - - + -
349F LYS 3.3 11.5 + - - +
350F GLY* 3.1 12.4 + - - +
352F SER* 1.3 80.3 - - - +
354F ILE* 1.3 81.5 + - + +
356F SER* 4.6 7.3 - - - -
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Residues in contact with ILE 354 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142F LYS* 3.6 34.5 + - + +
170F ILE* 3.4 42.0 - - + +
173F GLU* 3.5 34.3 - - + +
174F VAL* 3.6 21.1 - - + +
177F LYS* 5.1 14.4 - - + +
350F GLY 3.6 0.2 + - - -
351F VAL 3.2 3.8 + - - +
352F SER 3.2 0.6 - - - -
353F PHE* 1.3 83.5 - - + +
355F ARG* 1.3 60.1 + - - +
356F SER* 2.7 22.8 + - - +
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Residues in contact with ARG 355 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173F GLU* 2.8 26.6 + - - +
176F LYS* 4.4 20.3 - - - +
177F LYS* 6.0 5.5 - - - +
351F VAL* 3.0 34.3 + - + +
352F SER* 3.2 10.4 + - - +
354F ILE* 1.3 74.5 - - - +
356F SER* 1.3 68.6 + - - +
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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
------------------------------------------------------------
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