Contacts of the helix formed by residues 262 - 288 (chain L) in PDB entry 6PSU
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 VAL 262 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160L ASP 3.8 14.8 - - - +
161L LEU 3.7 17.3 - - - +
162L ILE* 3.6 1.5 - - - +
163L THR* 3.1 23.3 - - - +
261L LEU* 1.3 76.3 - - - +
263L PRO* 1.3 74.7 - - + +
264L LYS* 4.3 22.0 - - + +
265L GLN* 3.2 19.9 + - + +
266L PHE 2.9 21.3 + - - -
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Residues in contact with PRO 263 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163L THR* 4.2 4.5 - - - +
261L LEU 4.1 3.6 - - - +
262L VAL* 1.3 95.2 - - + +
264L LYS* 1.3 49.7 + - + +
266L PHE* 2.8 16.5 + - + +
267L ASP* 2.5 47.1 + - - +
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Residues in contact with LYS 264 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262L VAL* 3.3 21.4 - - + +
263L PRO* 1.3 76.9 - - + +
265L GLN* 1.3 61.7 + - + +
267L ASP* 2.6 29.3 - - - +
268L TYR* 2.9 17.0 + - - +
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Residues in contact with GLN 265 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143L TYR* 4.0 7.0 - - - -
144L LEU* 5.9 0.9 - - - -
147L GLN* 2.9 56.4 + - + +
161L LEU* 3.9 23.6 - - + +
261L LEU* 3.8 11.3 - - + +
262L VAL* 3.2 18.0 + - + +
264L LYS* 1.3 81.6 - - + +
266L PHE* 1.3 62.2 + - - +
268L TYR* 3.7 12.1 + - - +
269L LEU* 3.9 16.8 + - - +
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Residues in contact with PHE 266 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127L ILE* 5.6 3.4 - - + -
130L VAL* 3.7 31.9 - - + -
131L GLN* 5.0 15.7 - - + -
134L VAL* 5.0 6.4 - - + +
256L PHE* 6.3 3.1 - + - -
261L LEU* 3.2 28.4 - - + +
262L VAL 2.9 5.4 + - - -
263L PRO* 2.8 25.6 + - + +
265L GLN* 1.3 78.9 - - - +
267L ASP* 1.3 65.6 + - + -
269L LEU* 4.1 1.9 + - - +
270L VAL* 3.0 43.0 + - + +
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Residues in contact with ASP 267 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263L PRO* 2.5 29.9 + - - +
264L LYS* 2.6 32.0 + - - +
266L PHE* 1.3 80.1 - - + +
268L TYR* 1.3 63.5 + - - +
270L VAL* 3.7 8.7 - - + -
271L ASN* 2.3 57.6 + - - +
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Residues in contact with TYR 268 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143L TYR* 3.3 52.5 + + + -
147L GLN* 5.2 2.5 - - - -
264L LYS 2.9 14.5 + - - +
265L GLN* 3.9 11.2 - - - +
266L PHE 3.3 0.4 - - - -
267L ASP* 1.3 82.4 + - - +
269L LEU* 1.3 57.5 + - + +
271L ASN* 3.3 3.3 - - - +
272L SER* 2.4 47.8 + - - -
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Residues in contact with LEU 269 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134L VAL* 4.3 16.8 - - + +
137L TYR* 5.2 7.1 - - + -
139L GLU 4.6 0.9 - - - +
140L ALA* 2.9 43.7 - - + +
143L TYR* 3.6 41.5 - - + -
144L LEU* 4.1 8.5 - - + +
265L GLN* 3.9 13.6 + - - +
266L PHE 4.7 0.9 - - - +
268L TYR* 1.3 80.6 - - + +
270L VAL* 1.3 51.9 + - - +
272L SER* 3.2 11.0 - - - +
273L MET* 2.2 38.6 + - - +
276L MET* 5.5 0.3 - - - +
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Residues in contact with VAL 270 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130L VAL* 4.5 4.5 - - + -
134L VAL* 3.9 13.9 - - + -
266L PHE* 3.0 46.3 + - + +
267L ASP* 3.3 8.5 + - + +
268L TYR 3.1 0.6 - - - -
269L LEU* 1.3 76.9 - - - +
271L ASN* 1.3 61.6 + - - +
273L MET* 2.7 26.9 + - + +
274L ARG* 2.3 47.5 + - + +
365L MET* 5.1 4.7 - - - -
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Residues in contact with ASN 271 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267L ASP* 2.3 47.6 + - - +
268L TYR* 3.3 3.4 - - - +
270L VAL* 1.3 77.3 - - - +
272L SER* 1.3 55.6 + - - +
274L ARG* 3.7 16.2 - - + +
275L VAL* 2.9 30.2 + - - +
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Residues in contact with SER 272 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268L TYR* 2.4 41.7 + - - -
269L LEU* 3.4 17.4 - - - +
271L ASN* 1.3 68.9 - - - +
273L MET* 1.3 52.3 + - - -
275L VAL* 2.8 12.3 + - - +
276L MET* 2.5 37.8 + - - +
279L ARG* 4.8 7.6 + - - -
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Residues in contact with MET 273 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133L SER 4.7 4.9 - - - +
134L VAL* 3.2 45.3 - - + -
137L TYR* 5.6 3.8 - - + -
269L LEU 2.2 27.5 + - - +
270L VAL* 2.7 23.2 + - + +
272L SER* 1.3 67.3 - - - +
274L ARG* 1.3 69.6 + - - +
276L MET* 3.1 33.9 + - + +
277L MET* 3.3 7.8 + - - +
358L VAL* 6.3 0.4 - - + -
361L ILE* 4.9 2.9 - - - -
362L ASN* 3.9 15.7 + - + -
365L MET* 3.4 43.1 - - + +
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Residues in contact with ARG 274 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270L VAL* 2.3 40.8 + - + +
271L ASN* 3.7 21.1 - - + +
273L MET* 1.3 94.8 + - - +
275L VAL* 1.3 60.8 + - + +
277L MET* 3.9 14.8 - - - +
278L ASP* 2.8 39.2 + - - +
281L ARG* 4.2 14.1 - - - +
362L ASN* 3.3 23.2 - - - +
365L MET* 4.4 11.0 - - - +
366L SER* 4.9 10.3 + - - -
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Residues in contact with VAL 275 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271L ASN 2.9 25.0 + - - +
272L SER* 2.8 14.9 + - - +
274L ARG* 1.3 76.7 - - + +
276L MET* 1.3 63.9 + - - +
278L ASP* 3.5 4.8 + - - +
279L ARG* 2.9 58.0 + - + +
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Residues in contact with MET 276 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137L TYR* 3.3 56.5 - - + -
272L SER 2.5 16.1 + - - +
273L MET* 3.1 30.7 + - + +
275L VAL* 1.3 74.1 - - - +
277L MET* 1.3 62.2 + - - +
279L ARG* 3.5 20.3 + - - +
280L VAL* 3.2 23.9 + - + +
347L ILE* 5.0 4.4 - - + +
350L GLU* 5.0 2.7 - - + +
351L THR* 4.0 24.2 - - + -
358L VAL* 4.2 16.8 - - + -
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Residues in contact with MET 277 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273L MET 3.3 3.8 + - - -
274L ARG* 3.9 13.0 - - - +
275L VAL 3.4 0.2 - - - -
276L MET* 1.3 76.7 - - - +
278L ASP* 1.3 58.1 + - - +
280L VAL* 3.1 18.8 - - + +
281L ARG* 2.6 77.6 + - + +
355L ILE* 5.5 0.7 - - - -
358L VAL* 4.9 5.8 - - - +
359L LYS* 3.3 42.0 - - + -
362L ASN* 3.1 41.7 - - - +
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Residues in contact with ASP 278 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274L ARG* 2.8 31.5 + - - +
275L VAL* 3.5 6.0 + - + +
276L MET 3.4 0.4 - - - -
277L MET* 1.3 77.2 - - - +
279L ARG* 1.3 56.9 + - - +
281L ARG* 3.8 19.9 + - - +
282L THR* 2.5 40.1 + - - +
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Residues in contact with ARG 279 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272L SER* 4.8 7.7 + - - -
275L VAL* 2.9 47.4 + - + +
276L MET* 3.7 21.8 - - - +
277L MET 3.2 0.2 - - - -
278L ASP* 1.3 77.9 - - + +
280L VAL* 1.3 58.7 + - - +
282L THR* 3.7 2.9 - - - -
283L GLN* 2.9 37.7 + - - +
346L GLN* 5.9 0.2 - - - +
347L ILE* 3.8 11.2 - - + +
350L GLU* 2.8 41.9 + - - +
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Residues in contact with VAL 280 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276L MET* 3.2 13.9 + - + +
277L MET* 3.1 43.5 - - + +
279L ARG* 1.3 77.4 - - - +
281L ARG* 1.3 62.9 + - - +
283L GLN* 2.9 24.6 + - - +
284L GLU* 3.3 5.9 + - - +
344L LEU* 3.5 19.6 - - + +
347L ILE* 3.3 23.6 - - + -
355L ILE* 3.3 31.2 - - + -
358L VAL* 6.4 0.9 - - + -
359L LYS* 5.7 0.4 - - + -
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Residues in contact with ARG 281 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274L ARG* 4.2 11.5 - - - +
277L MET* 2.6 62.4 + - + +
278L ASP* 3.8 24.0 + - - +
280L VAL* 1.3 73.5 - - - +
282L THR* 1.3 61.8 + - - +
284L GLU* 3.3 11.9 + - + +
285L ARG* 3.1 43.9 + - + +
362L ASN* 4.9 0.8 - - - +
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Residues in contact with THR 282 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278L ASP* 2.5 27.0 + - - +
279L ARG* 3.7 6.3 - - - -
281L ARG* 1.3 77.9 - - - +
283L GLN* 1.3 61.8 + - - +
285L ARG* 3.1 14.6 + - + +
286L LEU* 2.9 25.5 + - + +
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Residues in contact with GLN 283 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279L ARG* 2.9 31.5 + - - +
280L VAL 2.9 9.5 + - - +
282L THR* 1.3 82.7 - - - +
284L GLU* 1.3 48.8 - - - +
286L LEU* 2.6 16.5 + - - +
287L ILE* 2.2 50.2 + - + +
340L ALA* 4.0 9.2 - - - +
343L LYS* 3.4 33.5 - - + +
344L LEU* 4.2 7.6 - - + -
346L GLN* 5.7 0.8 + - - -
347L ILE* 3.4 22.5 - - + +
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Residues in contact with GLU 284 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280L VAL 3.3 5.5 + - - +
281L ARG* 3.3 13.0 + - + +
283L GLN* 1.3 78.2 - - - +
285L ARG* 1.3 59.8 + - + +
287L ILE* 3.3 13.8 - - + +
288L MET* 2.2 80.2 + - + +
289L LYS 3.0 5.0 + - - -
302L PHE* 3.2 18.4 - - + -
303L ILE* 5.3 2.1 - - - +
306L PHE* 4.4 16.7 - - + -
344L LEU* 6.3 0.2 - - + -
359L LYS* 5.5 7.1 + - - +
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Residues in contact with ARG 285 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281L ARG* 3.1 35.3 + - + +
282L THR* 3.1 20.0 - - + +
283L GLN 3.1 0.2 - - - -
284L GLU* 1.3 78.2 - - - +
286L LEU* 1.3 55.7 + - - +
288L MET* 5.9 6.2 - - - +
289L LYS* 3.0 50.1 + - + +
290L LEU* 3.7 7.1 + - - +
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Residues in contact with LEU 286 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282L THR* 2.9 11.0 + - + +
283L GLN* 2.6 24.0 + - - +
285L ARG* 1.3 72.9 - - - +
287L ILE* 1.3 58.5 + - - -
290L LEU* 3.2 31.3 - - + +
336L GLU* 4.1 27.6 - - + +
337L VAL* 2.9 24.3 - - - +
339L ARG* 5.1 4.9 - - + +
340L ALA* 3.5 25.8 - - + +
343L LYS* 5.5 3.8 - - + -
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Residues in contact with ILE 287 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283L GLN 2.2 32.9 + - - +
284L GLU* 3.3 13.2 - - + +
286L LEU* 1.3 72.8 - - - +
288L MET* 1.3 64.4 + - - +
291L CYS* 3.7 16.6 + - - +
302L PHE* 3.3 31.9 - - + -
306L PHE* 5.4 1.3 - - + -
315L TRP* 3.5 19.3 - - + -
337L VAL* 3.3 22.8 - - + +
340L ALA* 3.2 24.9 - - + +
344L LEU* 3.2 41.1 - - + -
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Residues in contact with MET 288 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284L GLU* 2.2 62.1 + - + +
285L ARG* 5.9 6.1 - - - +
287L ILE* 1.3 68.1 - - - +
289L LYS* 1.3 53.7 + - + +
290L LEU 3.1 1.6 - - - -
291L CYS 2.6 6.5 + - - +
292L VAL* 2.4 58.1 + - + -
293L GLU* 3.1 8.2 - - - +
299L LYS* 3.4 27.8 - - - +
302L PHE* 3.4 29.2 - - + -
303L ILE* 4.7 5.4 - - - -
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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
------------------------------------------------------------
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