Contacts of the helix formed by residues 275 - 300 (chain A) in PDB entry 1XTG
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 ASP 275 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273A PHE 3.6 4.1 + - - +
274A ILE* 1.3 74.7 - - - +
276A SER* 1.3 65.4 + - - +
277A LEU* 3.1 38.1 + - - +
278A GLN* 3.1 31.1 + - - +
279A GLU* 2.9 27.0 + - - +
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Residues in contact with SER 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A ILE 3.8 0.8 + - - -
275A ASP* 1.3 76.8 + - - +
277A LEU* 1.3 67.8 + - - +
279A GLU* 3.2 11.5 + - - +
280A ASN* 2.9 36.9 + - - -
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Residues in contact with LEU 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A ASP* 3.1 19.3 + - - +
276A SER* 1.3 79.5 - - - +
278A GLN* 1.3 57.3 + - + +
280A ASN* 3.4 8.4 + - - +
281A GLU* 3.0 27.8 + - - +
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Residues in contact with GLN 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A ARG* 4.0 14.6 - - - +
260A PHE* 3.3 33.2 - - - -
273A PHE 4.8 1.0 - - - +
274A ILE* 4.1 3.3 - - + -
275A ASP* 3.1 39.4 + - + +
276A SER 3.2 0.2 - - - -
277A LEU* 1.3 74.7 - - + +
279A GLU* 1.3 64.8 + - - +
281A GLU* 3.1 14.3 + - - +
282A PHE* 3.0 43.5 + - + -
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Residues in contact with GLU 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A ILE* 4.3 14.4 - - + +
275A ASP 2.9 16.1 + - - +
276A SER* 3.2 12.4 + - - +
278A GLN* 1.3 77.0 - - - +
280A ASN* 1.3 65.6 + - - +
282A PHE* 3.2 12.0 + - - +
283A ARG* 3.1 24.6 + - + +
342A TYR* 4.9 7.0 + - + +
347A GLU* 3.6 23.6 - - - +
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Residues in contact with ASN 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A SER* 2.9 31.3 + - - +
277A LEU* 3.9 8.3 - - - +
279A GLU* 1.3 75.5 - - - +
281A GLU* 1.3 67.5 + - - +
283A ARG* 3.1 33.8 + - - +
284A LEU* 3.0 26.5 + - - +
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Residues in contact with GLU 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A ARG* 2.6 40.0 + - - -
277A LEU 3.0 14.7 + - - +
278A GLN* 3.1 17.8 + - - +
280A ASN* 1.3 77.7 - - - +
282A PHE* 1.3 67.3 + - - +
284A LEU* 3.9 4.8 - - - +
285A TYR* 3.0 31.6 + - + +
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Residues in contact with PHE 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A ILE* 3.8 45.3 - - + -
238A ASN* 5.6 1.1 - - + -
241A ARG* 3.2 34.8 - - + -
260A PHE* 3.8 21.1 - + - -
264A ARG* 4.9 0.4 - - - +
274A ILE* 4.4 5.2 - - + -
278A GLN* 3.0 34.0 + - + -
279A GLU* 3.6 8.5 - - - +
281A GLU* 1.3 86.0 - - - +
283A ARG* 1.3 65.9 + - - +
285A TYR* 3.0 8.9 + + + +
286A TYR* 3.0 42.6 + + + -
342A TYR* 3.6 14.6 - - - +
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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
----------------------------------------------------------
279A GLU* 3.1 16.4 + - + +
280A ASN* 3.1 29.9 + - - +
282A PHE* 1.3 79.5 - - - +
284A LEU* 1.3 62.3 + - - +
287A TYR* 3.0 24.9 + - + +
338A PHE* 3.5 9.1 - - + -
339A ASP* 3.4 37.7 + - - +
342A TYR* 3.8 37.8 + - + -
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Residues in contact with LEU 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A ASN 3.0 17.7 + - - +
281A GLU* 3.9 4.7 - - - +
283A ARG* 1.3 74.0 - - - +
285A TYR* 1.3 66.8 + - - +
287A TYR* 3.3 19.7 + - + +
288A ASN* 3.1 42.4 + - - +
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Residues in contact with TYR 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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177A ARG* 3.9 10.3 + - + +
281A GLU* 3.0 21.7 + - + +
282A PHE* 3.0 15.0 + + + +
284A LEU* 1.3 77.1 - - - +
286A TYR* 1.3 98.2 + + - +
288A ASN* 3.2 12.0 + - + +
289A LYS* 2.9 52.0 + - - +
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Residues in contact with TYR 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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177A ARG* 3.5 26.7 - - - +
234A GLY 3.6 5.6 - - - -
235A ILE* 3.5 50.9 - - + -
236A ALA 2.6 22.7 + - - -
237A ILE* 3.6 6.9 - - + -
238A ASN 4.2 3.1 + - - -
264A ARG* 4.2 8.5 - - - -
282A PHE* 3.0 41.6 + + + +
285A TYR* 1.3 94.0 - + - +
287A TYR* 1.3 65.5 + - - +
289A LYS* 3.1 8.7 + - + +
290A PHE* 3.0 29.7 + - + -
338A PHE* 3.7 11.7 - - + -
342A TYR* 3.9 14.8 - + + -
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Residues in contact with TYR 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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283A ARG* 3.0 20.5 + - + +
284A LEU* 3.4 23.6 - - + +
286A TYR* 1.3 75.6 - - - +
288A ASN* 1.3 73.8 + - - +
290A PHE* 3.3 4.5 + - - +
291A LYS* 3.1 56.5 + - + +
333A VAL* 3.6 36.3 + - + -
335A LYS* 3.3 48.5 - - + +
338A PHE* 3.4 28.9 - + + -
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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
----------------------------------------------------------
284A LEU* 3.1 34.0 + - - +
285A TYR* 3.3 11.5 - - + +
286A TYR 3.1 0.2 - - - -
287A TYR* 1.3 92.0 - - - +
289A LYS* 1.3 64.1 + - + +
291A LYS* 3.1 20.2 + - - +
292A ASP* 3.0 33.1 + - - +
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Residues in contact with LYS 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A ARG 3.9 8.1 - - - +
178A ASN* 3.6 50.1 - - + +
179A GLY* 4.3 4.7 - - - +
285A TYR* 2.9 51.0 + - + +
286A TYR* 3.1 17.6 + - + +
288A ASN* 1.3 78.1 - - - +
290A PHE* 1.3 62.5 + - + +
292A ASP* 3.2 19.0 + - + +
293A ILE* 3.1 26.0 + - - +
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Residues in contact with PHE 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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179A GLY* 4.3 7.4 - - - -
233A TYR* 3.8 30.7 - + + -
235A ILE* 3.9 19.1 - - + -
286A TYR* 3.0 16.8 + - + +
287A TYR 3.6 9.0 - - - +
288A ASN 3.2 0.2 - - - -
289A LYS* 1.3 77.9 - - + +
291A LYS* 1.3 60.2 + - - +
293A ILE* 3.3 8.2 + - + +
294A ALA* 3.0 23.0 + - - +
321A TYR* 3.6 47.7 - + + +
323A LEU* 4.5 3.2 - - + +
333A VAL* 3.5 20.6 - - + +
338A PHE* 3.4 32.3 - + + -
341A LEU* 4.2 19.1 - - + -
345A LEU* 5.8 2.0 - - + -
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Residues in contact with LYS 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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287A TYR* 3.1 48.1 + - + +
288A ASN* 3.1 22.0 + - - +
290A PHE* 1.3 74.1 - - - +
292A ASP* 1.3 62.8 + - - +
294A ALA* 3.3 4.7 + - - +
295A SER* 2.9 28.1 + - - -
333A VAL* 3.7 23.3 - - + +
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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
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180A TYR* 6.3 0.9 - - + -
288A ASN* 3.0 17.9 + - - +
289A LYS* 3.2 24.6 + - + +
291A LYS* 1.3 80.7 - - - +
293A ILE* 1.3 57.1 - - + +
295A SER* 3.2 9.0 + - - -
296A THR* 2.9 33.0 + - - +
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Residues in contact with ILE 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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117A PHE* 4.1 19.5 - - + -
178A ASN 4.5 0.2 - - - +
179A GLY* 3.4 40.6 - - - +
180A TYR* 4.0 24.5 - - + +
289A LYS 3.1 13.2 + - - +
290A PHE* 3.5 11.4 - - - +
291A LYS 3.2 0.2 - - - -
292A ASP* 1.3 75.0 - - + +
294A ALA* 1.3 62.2 + - - +
296A THR* 3.0 9.1 + - - -
297A LEU* 2.9 36.3 + - + +
321A TYR* 3.7 36.8 - - + +
323A LEU* 5.2 1.3 - - + -
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Residues in contact with ALA 294 (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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290A PHE 3.0 13.8 + - - +
291A LYS* 3.7 7.9 - - - +
293A ILE* 1.3 76.8 - - - +
295A SER* 1.3 57.0 + - - +
297A LEU* 3.3 5.7 + - - +
298A ASN* 3.0 35.3 + - - -
323A LEU* 3.9 32.1 - - + -
331A PHE* 4.1 19.1 - - + +
332A SER* 4.5 1.8 - - - -
333A VAL* 4.4 6.1 - - + -
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Residues in contact with SER 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A LYS 2.9 13.6 + - - -
292A ASP* 3.2 13.2 - - - -
294A ALA* 1.3 74.7 - - - +
296A THR* 1.3 64.3 + - - +
298A ASN* 3.2 19.2 + - - +
299A LYS* 3.2 42.7 + - - +
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Residues in contact with THR 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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117A PHE* 4.1 24.7 - - + -
119A GLY* 6.2 0.4 - - - -
124A ASP 4.5 14.2 - - - +
127A LEU* 4.8 8.5 - - + -
180A TYR* 4.7 9.6 + - - +
292A ASP* 2.9 17.4 + - - +
293A ILE* 3.0 11.7 + - - -
295A SER* 1.3 75.1 + - - +
297A LEU* 1.3 63.3 + - - +
299A LYS* 3.2 9.1 + - - +
300A ALA* 3.1 20.6 + - - +
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Residues in contact with LEU 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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117A PHE* 3.7 25.6 - - + -
127A LEU* 4.2 22.4 - - + -
293A ILE* 2.9 23.0 + - + +
294A ALA 3.6 7.2 - - - +
296A THR* 1.3 79.1 - - - +
298A ASN* 1.3 59.0 + - - +
300A ALA* 3.4 3.4 + - - -
314A LYS* 3.0 50.0 + - + +
317A PHE* 3.9 24.7 - - + -
323A LEU* 4.0 17.9 - - + -
331A PHE* 3.6 29.1 - - + -
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Residues in contact with ASN 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A ALA 3.0 23.1 + - - -
295A SER* 3.2 11.0 + - - +
297A LEU* 1.3 77.8 - - - +
299A LYS* 1.3 62.2 + - + +
300A ALA 3.4 0.7 + - - +
301A LYS* 4.0 9.5 + - - -
314A LYS* 4.5 5.6 + - - +
329A GLY 4.6 1.0 - - - +
330A LYS* 3.6 26.6 - - + +
331A PHE* 2.7 50.6 + - - +
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Residues in contact with LYS 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ASP* 4.8 15.0 - - - +
125A THR* 3.4 18.3 - - + +
295A SER* 3.2 34.7 + - - +
296A THR* 3.2 7.2 + - - +
297A LEU 3.2 0.2 - - - -
298A ASN* 1.3 80.0 - - + +
300A ALA* 1.3 60.8 + - - +
301A LYS* 3.0 33.1 + - - +
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Residues in contact with ALA 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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124A ASP 5.6 0.2 - - - +
125A THR* 3.4 11.7 - - - +
127A LEU* 3.8 30.3 - - + -
296A THR 3.1 12.1 + - - +
297A LEU* 3.6 4.7 - - - +
298A ASN 3.4 2.1 - - - +
299A LYS* 1.3 76.8 - - - +
301A LYS* 1.3 63.9 + - - +
302A SER 4.7 0.2 - - - +
310A LEU* 4.1 3.4 - - + +
314A LYS* 2.6 45.9 + - - -
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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) + - + + + + + -
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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