Contacts of the helix formed by residues 306 - 335 (chain A) in PDB entry 1NOY
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 ILE 306 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A TYR* 4.5 14.8 - - + +
304A GLY 3.1 10.4 + - - +
305A PRO* 1.3 69.2 - - + +
307A ASN* 1.3 59.3 + - - +
308A LYS 2.8 11.3 + - - -
309A LEU* 2.9 38.2 + - + +
317A TYR* 5.6 2.6 - - - -
320A TYR* 5.3 7.2 - - + -
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Residues in contact with ASN 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A THR* 4.5 16.1 - - - +
117A GLY 5.2 8.2 + - - +
305A PRO* 3.6 20.1 - - - +
306A ILE* 1.3 74.9 + - - +
308A LYS* 1.3 71.0 + - - +
309A LEU 3.6 0.2 - - - -
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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
----------------------------------------------------------
116A THR* 6.0 1.6 - - - -
305A PRO* 2.9 25.5 + - + +
306A ILE 2.9 1.0 - - - -
307A ASN* 1.3 91.9 - - - +
309A LEU* 1.3 60.1 + - - +
310A ARG 3.2 3.6 - - - -
311A GLU* 3.0 35.9 + - + +
312A THR* 2.9 36.6 + - + -
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Residues in contact with LEU 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A TYR* 3.5 41.1 - - + +
305A PRO 3.4 3.1 + - - -
306A ILE* 2.9 26.9 + - + +
307A ASN 3.6 0.4 - - - -
308A LYS* 1.3 77.1 - - - +
310A ARG* 1.3 55.7 + - - +
311A GLU 3.4 0.2 - - - -
312A THR* 3.5 6.3 - - - -
313A ASN* 2.7 51.9 + - + +
314A HIS* 3.9 0.2 - - - -
316A ARG* 4.2 7.9 - - + -
317A TYR* 3.5 29.8 - - + -
320A TYR* 3.5 31.0 - - + -
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Residues in contact with ARG 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A THR* 4.0 17.8 + - + +
131A ASP* 3.8 30.6 + - - +
148A LEU 2.6 31.7 + - - -
149A LEU 4.2 2.2 + - - -
151A SER* 3.5 26.9 + - - +
153A TYR* 4.5 7.9 - - - +
154A GLY* 2.4 37.4 + - - +
156A VAL* 3.8 22.0 - - + +
308A LYS 3.0 1.4 + - - -
309A LEU* 1.3 75.7 - - - +
311A GLU* 1.3 65.1 + - - +
314A HIS* 3.1 48.1 + - + +
317A TYR* 3.8 23.6 - - + -
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Residues in contact with GLU 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A TYR 5.1 11.0 - - - +
154A GLY* 6.5 0.9 - - - -
156A VAL* 5.5 4.0 - - - -
308A LYS* 3.0 45.3 + - + +
310A ARG* 1.3 81.4 - - - +
312A THR* 1.3 77.5 + - - +
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Residues in contact with THR 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A TYR* 2.6 27.3 + - - -
305A PRO* 4.7 9.3 + - + +
308A LYS* 2.9 25.1 + - + +
309A LEU* 3.5 6.1 + - - -
311A GLU* 1.3 99.7 - - - +
313A ASN* 1.3 63.7 + - - +
314A HIS 4.1 0.2 - - - -
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Residues in contact with ASN 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A ASP* 5.1 1.6 - - - +
302A TYR* 4.0 20.9 - - + +
309A LEU* 2.7 26.6 + - + +
312A THR* 1.3 78.5 + - - +
314A HIS* 1.3 58.7 + - - +
315A GLN* 3.0 27.7 + - - +
316A ARG* 3.0 34.7 + - - +
317A TYR 3.1 6.9 + - - -
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Residues in contact with HIS 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A ASP 5.9 0.2 - - - -
147A ASP* 2.9 41.6 + - - -
148A LEU 4.4 0.2 + - - -
149A LEU* 4.2 5.6 - - + +
156A VAL* 3.1 33.6 - - + +
157A SER* 3.1 25.9 + - - -
158A LYS 4.4 1.0 + - - -
159A TRP* 4.2 11.4 + - + -
309A LEU 3.2 1.6 + - - -
310A ARG* 3.1 36.5 + - + +
311A GLU 5.3 0.2 + - - -
313A ASN* 1.3 70.4 - - - +
315A GLN* 1.3 67.2 + - - +
317A TYR* 3.5 10.8 - - - +
318A ILE* 3.3 22.6 + - + +
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Residues in contact with GLN 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A LYS 4.5 2.3 - - - +
159A TRP* 3.4 24.7 - - - +
160A ASP* 2.9 54.5 + - - +
163A LEU* 3.7 21.7 - - + +
164A ALA* 3.2 11.9 - - - +
171A GLY 5.3 0.7 - - - +
173A ASP* 3.1 26.3 + - - +
313A ASN* 3.0 13.5 + - - +
314A HIS* 1.3 84.3 + - - +
316A ARG* 1.3 63.1 + - - +
319A SER* 3.3 17.2 + - - -
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Residues in contact with ARG 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A ASP* 3.4 20.9 + - - -
172A GLY 2.8 28.3 + - - -
173A ASP* 3.3 27.4 + - - +
300A LEU* 3.0 29.6 - - - +
301A PRO 3.3 22.6 + - - -
302A TYR* 4.7 10.3 - - + -
309A LEU* 4.2 9.6 - - + -
313A ASN* 3.0 26.9 + - - +
315A GLN* 1.3 76.7 - - - +
317A TYR* 1.3 66.3 + - - +
319A SER* 3.2 0.9 + - - -
320A TYR* 2.9 62.7 + - + +
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Residues in contact with TYR 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A GLU* 3.1 40.7 + - + +
115A VAL 3.9 2.1 + - - -
116A THR* 3.1 15.9 + - - -
131A ASP* 2.4 31.4 + - - -
132A ALA* 4.3 7.9 - - + -
306A ILE 5.6 2.0 - - - -
309A LEU* 3.5 32.9 - - + +
310A ARG* 3.8 30.7 - - + -
313A ASN 3.1 6.6 + - - +
314A HIS* 3.5 18.8 - - - +
316A ARG* 1.3 78.1 - - - +
318A ILE* 1.3 80.0 + - + +
320A TYR* 3.5 3.5 + - - +
321A ASN* 3.2 19.9 + - - +
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Residues in contact with ILE 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A ASP 5.0 0.4 - - - +
132A ALA* 4.3 14.1 - - + -
145A VAL* 4.0 22.7 - - + -
147A ASP* 3.4 40.4 - - + +
159A TRP* 3.4 41.3 - - + +
314A HIS* 3.3 14.8 + - + +
316A ARG 3.3 0.4 - - - -
317A TYR* 1.3 99.7 - - + +
319A SER* 1.3 64.3 + - - +
321A ASN* 3.3 7.7 + - + +
322A ILE* 3.1 25.0 + - + +
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Residues in contact with SER 319 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A TRP* 3.1 17.7 + - - +
164A ALA* 3.5 9.0 - - - +
173A ASP* 2.8 34.3 + - - -
175A VAL* 3.6 19.1 - - - +
315A GLN 3.3 2.2 + - - -
316A ARG* 3.2 8.3 + - - -
318A ILE* 1.3 76.3 - - - +
320A TYR* 1.3 66.3 + - - +
322A ILE* 3.4 7.6 + - - +
323A ILE* 3.0 30.6 + - - +
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Residues in contact with TYR 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A GLU* 6.0 0.7 - - - +
299A LYS* 3.7 36.6 - - + +
300A LEU* 2.5 33.9 + - + -
302A TYR* 3.7 18.0 - - + +
306A ILE* 5.3 6.3 - - + -
309A LEU* 3.5 31.2 - - + -
316A ARG* 2.9 49.5 + - + +
317A TYR 3.7 4.5 - - - +
319A SER* 1.3 75.7 - - - +
321A ASN* 1.3 56.7 + - - +
323A ILE* 2.9 16.1 + - + +
324A ASP* 2.9 35.4 + - - +
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Residues in contact with ASN 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ASP* 3.2 22.4 + - - +
114A GLU* 3.2 35.0 + - + +
132A ALA* 4.1 7.4 - - + +
133A ILE 3.9 9.9 - - - +
134A THR* 2.4 37.3 + - - +
145A VAL* 5.1 3.4 - - - +
317A TYR 3.2 11.0 + - - +
318A ILE* 3.3 12.7 + - - +
320A TYR* 1.3 80.3 - - - +
322A ILE* 1.3 60.9 + - - +
324A ASP* 3.4 6.1 + - - +
325A VAL* 3.2 25.8 + - - +
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Residues in contact with ILE 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A THR* 3.9 26.7 - - + +
143A PHE* 4.4 7.0 - - + -
145A VAL* 4.0 17.3 - - + -
159A TRP* 5.5 3.8 - - + -
175A VAL* 4.5 11.4 - - + -
179A ILE* 3.1 33.8 - - + +
180A LEU* 4.9 6.1 - - + -
183A VAL* 3.5 24.9 - - + -
318A ILE* 3.1 25.0 + - + +
319A SER* 3.4 8.5 + - - +
320A TYR 3.3 0.2 - - - -
321A ASN* 1.3 74.0 - - - +
323A ILE* 1.3 67.7 + - - +
325A VAL* 3.9 2.1 - - - +
326A GLU* 3.1 23.2 + - - +
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Residues in contact with ILE 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A ASP 5.0 6.1 - - - +
174A GLU 5.9 0.4 - - - +
175A VAL* 4.0 33.9 - - + -
176A PRO* 5.7 2.7 - - + -
179A ILE* 5.5 4.7 - - + -
298A GLY 5.8 1.6 - - - +
299A LYS* 3.7 37.2 - - + -
300A LEU 5.9 0.4 - - - +
319A SER* 3.0 25.3 + - - +
320A TYR* 2.9 17.1 + - + +
322A ILE* 1.3 78.9 - - - +
324A ASP* 1.3 58.4 + - - +
326A GLU* 3.2 6.3 + - - +
327A SER* 2.9 37.9 + - - +
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Residues in contact with ASP 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ASP* 3.7 22.6 - - - +
114A GLU* 4.4 11.4 - - - +
287A LEU* 3.7 25.2 - - + +
288A GLU* 4.1 2.8 - - - +
299A LYS* 2.8 38.2 + - - +
320A TYR* 2.9 14.9 + - - +
321A ASN* 3.6 8.3 - - - +
323A ILE* 1.3 75.4 - - - +
325A VAL* 1.3 63.5 + - - +
327A SER* 3.0 21.9 + - - -
328A VAL* 3.6 6.2 + - - +
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Residues in contact with VAL 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ASN* 3.0 43.7 + - - +
111A CYS 4.2 1.3 - - - -
112A ASP* 3.5 26.7 - - + +
134A THR* 3.5 33.7 - - + +
136A TYR* 3.7 27.4 - - + +
143A PHE* 4.2 4.0 - - + -
321A ASN 3.2 17.1 + - - +
322A ILE 4.0 2.7 - - - +
323A ILE 3.3 0.2 - - - -
324A ASP* 1.3 76.7 - - - +
326A GLU* 1.3 61.8 + - - +
327A SER 3.4 0.5 + - - -
328A VAL* 3.6 5.7 + - - -
329A GLN* 3.9 5.4 + - - +
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Residues in contact with GLU 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A PHE* 3.6 30.0 - - + -
179A ILE* 3.7 30.2 - - + +
182A ARG* 4.6 8.6 + - - +
322A ILE 3.1 19.0 + - - +
323A ILE* 3.2 4.4 + - - +
325A VAL* 1.3 76.5 - - - +
327A SER* 1.3 65.5 + - - +
328A VAL 3.3 0.2 - - - -
329A GLN* 3.4 11.0 + - + +
330A ALA* 3.1 31.6 + - - +
333A LYS* 6.1 0.5 - - - +
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Residues in contact with SER 327 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A LEU* 4.3 11.2 - - - +
291A ALA* 4.3 23.4 - - - +
295A THR* 4.9 1.9 - - - +
323A ILE* 2.9 29.5 + - - +
324A ASP* 3.0 17.6 + - - -
326A GLU* 1.3 80.5 + - - +
328A VAL* 1.3 55.0 + - - +
330A ALA* 3.2 6.4 + - - +
331A ILE* 2.9 34.5 + - - +
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Residues in contact with VAL 328 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ASN* 3.7 30.7 - - + +
211A THR* 4.7 4.0 - - + -
212A GLY* 4.3 22.7 - - - +
213A TRP* 4.5 17.5 - - + +
270A TYR* 3.9 32.0 - - + -
287A LEU* 4.6 6.1 - - + -
324A ASP 3.6 10.1 + - - +
325A VAL* 5.2 0.4 - - - -
326A GLU 3.3 0.4 - - - -
327A SER* 1.3 72.5 - - - +
329A GLN* 1.3 65.5 + - - +
331A ILE* 3.3 9.1 + - - +
332A ASP* 2.9 27.5 + - + +
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Residues in contact with GLN 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A ARG* 5.4 4.3 + - - -
108A VAL* 4.5 19.3 + - - +
110A ASN* 2.7 30.1 + - - +
136A TYR* 3.5 40.6 + - + -
138A SER* 5.4 2.8 - - - -
143A PHE* 6.0 0.7 - - + -
211A THR* 4.9 3.0 - - - +
325A VAL 3.9 5.4 + - - +
326A GLU* 3.4 15.7 + - + +
327A SER 3.4 0.2 - - - -
328A VAL* 1.3 78.7 - - - +
330A ALA* 1.3 56.6 + - - +
332A ASP* 4.4 9.1 - - - +
333A LYS* 2.7 56.8 + - + +
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Residues in contact with ALA 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A THR* 3.7 22.4 - - + -
326A GLU* 3.1 29.6 + - - +
327A SER* 3.5 10.3 - - - +
328A VAL 3.2 0.2 - - - -
329A GLN* 1.3 77.5 - - - +
331A ILE* 1.3 63.2 + - - +
333A LYS* 3.1 18.8 + - - +
334A ILE* 3.2 17.8 + - - +
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Residues in contact with ILE 331 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A TRP* 4.4 11.7 - - + -
270A TYR* 3.7 24.9 - - + -
274A TYR* 4.4 13.2 - - + -
287A LEU* 4.4 9.0 - - + -
290A VAL* 3.8 23.6 - - + -
291A ALA* 4.1 16.4 - - - +
294A GLU* 4.2 17.9 - - + -
295A THR* 4.6 3.6 - - + -
327A SER 2.9 24.1 + - - +
328A VAL* 3.6 6.5 - - - +
330A ALA* 1.3 74.6 - - - +
332A ASP* 1.3 58.2 + - - +
334A ILE* 3.0 12.0 + - - +
335A ARG* 2.9 38.4 + - + +
----------------------------------------------------------
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Residues in contact with ASP 332 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A ARG* 3.2 26.5 + - - -
270A TYR* 2.4 38.8 + - + +
328A VAL* 2.9 17.7 + - + +
329A GLN* 3.8 11.8 - - - +
331A ILE* 1.3 77.1 - - - +
333A LYS* 1.3 64.2 + - - +
336A GLY* 2.8 28.3 + - - +
337A PHE 3.2 3.6 + - - -
338A ILE* 3.2 27.5 + - - +
----------------------------------------------------------
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Residues in contact with LYS 333 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A ARG* 5.2 4.0 - - - +
326A GLU* 6.1 0.7 - - - +
329A GLN* 2.7 52.6 + - + +
330A ALA* 3.2 15.0 - - - +
332A ASP* 1.3 86.0 + - - +
334A ILE* 1.3 64.3 + - + +
336A GLY* 4.8 0.9 + - - -
----------------------------------------------------------
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Residues in contact with ILE 334 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A GLU* 3.4 51.4 - - + +
295A THR* 4.2 13.7 - - + -
330A ALA* 3.2 13.9 + - + +
331A ILE* 3.0 6.5 + - - +
333A LYS* 1.3 81.7 - - + +
335A ARG* 1.3 70.0 + - + +
----------------------------------------------------------
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Residues in contact with ARG 335 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A TYR* 4.4 3.4 - - - +
274A TYR* 4.2 2.7 - - + -
278A ALA* 3.4 31.4 + - - +
280A THR* 3.2 27.7 - - - +
293A HIS* 5.2 1.2 - - - -
294A GLU* 2.9 41.9 + - - +
331A ILE* 2.9 30.0 + - + +
334A ILE* 1.3 81.3 - - + +
336A GLY* 1.3 60.5 + - - +
337A PHE* 3.5 42.7 - - + -
40B HIS* 4.2 14.8 + - - -
56B ALA* 4.3 8.7 - - - +
----------------------------------------------------------
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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).
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