Contacts of the helix formed by residues 283 - 311 (chain A) in PDB entry 3M6L
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 PRO 283 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A GLU* 3.5 29.2 - - + +
12A THR* 3.4 21.1 - - + +
274A PHE* 3.6 29.4 - - + -
281A HIS* 3.6 13.8 - - + +
282A ILE* 1.4 85.8 - - - +
284A GLN* 1.3 61.0 + - - +
285A ALA 3.4 0.2 - - - -
286A SER* 3.4 1.2 + - - -
287A LYS* 2.9 26.0 + - - +
633A PO4 3.6 26.2 - - - +
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Residues in contact with GLN 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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282A ILE 3.6 1.7 + - - +
283A PRO* 1.3 71.2 - - - +
285A ALA* 1.3 63.8 + - - +
287A LYS* 3.2 23.3 + - - +
288A ILE* 3.0 53.1 + - + +
633A PO4 3.1 21.3 + - - +
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Residues in contact with ALA 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ILE* 3.8 16.2 - - + +
8A GLU* 3.2 17.8 + - - +
283A PRO 3.4 0.6 - - - -
284A GLN* 1.3 80.0 - - - +
286A SER* 1.3 57.5 + - - +
288A ILE* 3.4 8.5 + - - +
289A ARG* 3.0 30.7 + - - +
633A PO4 5.2 1.0 + - - -
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Residues in contact with SER 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ILE* 4.5 0.6 - - - +
8A GLU* 2.7 38.8 + - - +
9A GLN* 3.2 31.9 + - - +
12A THR* 3.5 21.5 - - - -
282A ILE* 4.9 0.7 - - - -
283A PRO* 3.7 7.6 - - - -
284A GLN 3.2 0.2 - - - -
285A ALA* 1.3 72.5 - - - +
287A LYS* 1.3 64.4 + - - +
290A PHE* 3.0 33.7 + - - -
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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
----------------------------------------------------------
77A HIS* 5.2 7.9 + - - -
78A LEU* 4.6 6.2 - - + +
282A ILE* 3.8 35.9 - - + +
283A PRO 2.9 19.1 + - - +
284A GLN* 3.5 23.1 - - - +
286A SER* 1.3 75.0 - - - +
288A ILE* 1.3 63.1 + - + +
290A PHE* 4.2 1.0 - - - +
291A GLU* 3.1 51.2 + - + +
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Residues in contact with ILE 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 GLN* 3.0 50.8 + - + +
285A ALA* 3.9 7.0 - - - +
287A LYS* 1.3 77.4 - - + +
289A ARG* 1.3 65.6 + - - +
291A GLU* 3.4 20.9 + - + +
292A SER* 3.1 23.1 + - - -
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Residues in contact with ARG 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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1A MSE 3.4 24.7 - - - +
2A ASN* 5.8 0.6 + - - -
5A ILE* 3.9 24.0 - - + +
9A GLN* 3.4 17.7 - - - +
44A TYR* 3.1 42.0 + - - +
285A ALA 3.0 18.9 + - - +
286A SER 4.0 0.9 - - - +
288A ILE* 1.3 78.9 - - - +
290A PHE* 1.3 59.8 + - - +
292A SER* 2.7 31.5 + - - -
2001A GOL 3.0 16.1 + - - +
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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
----------------------------------------------------------
9A GLN* 3.6 49.4 - - + -
12A THR* 4.8 0.4 - - - -
13A LEU* 3.8 29.6 - - + -
39A LEU 5.4 0.2 - - - -
40A SER* 4.4 3.8 - - - -
43A SER* 4.0 20.9 - - - -
75A PHE* 4.3 18.2 - + - -
78A LEU* 3.4 47.3 - - + +
79A SER* 3.6 7.0 - - - +
286A SER* 3.0 29.7 + - - +
287A LYS 4.4 0.9 - - - +
289A ARG* 1.3 76.9 - - - +
291A GLU* 1.3 62.9 + - - +
293A ALA* 3.2 13.7 + - - +
2001A GOL 3.0 20.9 + - - -
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Residues in contact with GLU 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A LEU 3.4 11.6 + - - +
79A SER 4.5 5.8 - - - -
80A GLY* 5.6 1.6 - - - +
287A LYS* 3.1 50.7 + - - +
288A ILE* 3.5 26.5 + - + +
290A PHE* 1.3 71.7 - - - +
292A SER* 1.3 58.3 + - - +
293A ALA 2.9 11.0 + - - -
294A VAL* 3.0 25.2 + - + +
295A GLU 4.4 0.5 + - - -
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Residues in contact with SER 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A ILE* 3.1 13.2 + - - -
289A ARG* 2.7 27.3 + - - -
290A PHE 3.1 0.2 - - - -
291A GLU* 1.3 77.8 - - - +
293A ALA* 1.3 60.8 + - - +
294A VAL 3.1 0.8 + - - -
295A GLU* 3.4 9.0 + - - +
296A LEU* 3.1 34.2 + - - +
2001A GOL 3.4 15.1 + - - -
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Residues in contact with ALA 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A HIS* 4.1 22.9 - - + +
50A PRO* 3.5 15.6 - - + +
79A SER* 3.7 16.4 - - - +
290A PHE 3.2 16.6 + - - +
291A GLU 2.9 0.4 + - - -
292A SER* 1.3 79.1 + - - +
294A VAL* 1.3 57.5 + - - +
296A LEU* 4.2 4.4 - - - +
297A GLY* 2.8 27.0 + - - -
2001A GOL 3.8 15.1 + - - +
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Residues in contact with VAL 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ASN* 4.5 2.6 - - - +
50A PRO* 4.1 10.1 - - + -
51A LYS* 4.0 35.2 - - + +
79A SER 3.4 20.6 - - - +
80A GLY* 3.8 14.4 - - - -
291A GLU* 3.0 17.9 + - + +
293A ALA* 1.3 74.6 - - - +
295A GLU* 1.3 66.7 + - - +
298A ASP* 3.0 25.9 + - + +
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Residues in contact with GLU 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A GLU 4.4 0.6 + - - -
292A SER* 3.4 9.8 + - - +
294A VAL* 1.3 82.4 - - - +
296A LEU* 1.3 70.3 + - + +
298A ASP* 3.3 5.6 + - - +
299A LEU* 3.2 39.7 + - + +
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Residues in contact with LEU 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A SER* 3.1 26.7 + - - +
293A ALA* 4.2 4.0 - - - +
295A GLU* 1.3 83.8 - - + +
297A GLY* 1.3 57.6 + - - +
299A LEU* 3.4 14.4 + - + +
300A GLU* 3.1 32.5 + - + +
2001A GOL 3.9 27.4 - - - +
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Residues in contact with GLY 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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48A HIS 3.2 28.2 - - - -
49A ASN* 3.7 12.6 - - - +
55A TRP* 5.0 0.2 - - - -
293A ALA 2.8 18.7 + - - -
294A VAL 3.9 0.2 - - - -
296A LEU* 1.3 69.4 - - - +
298A ASP* 1.3 60.1 + - - +
300A GLU* 3.9 6.8 - - - +
301A GLU* 2.9 31.0 + - - +
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Residues in contact with ASP 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ASN* 4.0 15.7 + - - +
51A LYS* 6.4 0.9 - - + -
294A VAL* 3.0 20.3 + - + +
295A GLU* 3.3 7.2 + - - +
297A GLY* 1.3 77.9 - - - +
299A LEU* 1.3 63.9 + - - +
301A GLU* 3.9 1.7 - - - +
302A ALA* 3.0 28.6 + - - +
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Residues in contact with LEU 299 (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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295A GLU* 3.2 36.6 + - + +
296A LEU* 3.8 15.3 - - + +
298A ASP* 1.3 79.7 - - - +
300A GLU* 1.3 60.4 + - - +
302A ALA* 3.2 10.5 + - + +
303A LYS* 2.9 30.9 + - - +
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Residues in contact with GLU 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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47A LYS* 3.3 42.4 - - + +
48A HIS 5.6 0.2 - - - +
55A TRP* 3.7 23.1 - - + -
296A LEU* 3.1 23.1 + - + +
297A GLY* 3.4 7.4 + - - +
299A LEU* 1.3 74.1 - - - +
301A GLU* 1.3 63.9 + - - +
303A LYS* 3.4 21.4 + - - +
304A TRP* 3.1 22.0 + - - +
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Residues in contact with GLU 301 (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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49A ASN* 2.7 33.3 + - - +
52A ASN* 2.8 34.5 + - - +
55A TRP* 3.8 37.6 - - + +
297A GLY 2.9 17.1 + - - +
298A ASP* 4.0 1.8 - - - +
300A GLU* 1.3 78.9 - - - +
302A ALA* 1.3 62.5 + - - +
304A TRP* 3.1 3.6 + - - +
305A LYS* 3.0 49.2 + - + +
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Residues in contact with ALA 302 (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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298A ASP* 3.0 21.0 + - - +
299A LEU* 3.2 13.9 + - + +
301A GLU* 1.3 76.8 - - - +
303A LYS* 1.3 61.7 + - - +
305A LYS* 3.2 15.3 + - - +
306A ASP* 3.1 30.0 + - - +
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Residues in contact with LYS 303 (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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299A LEU 2.9 15.9 + - - +
300A GLU* 3.7 22.7 - - - +
302A ALA* 1.3 74.3 - - - +
304A TRP* 1.4 61.9 + - - +
306A ASP* 3.3 11.7 + - - +
307A LYS* 2.3 64.7 + - - +
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Residues in contact with TRP 304 (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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55A TRP* 3.5 30.5 - + + +
56A LEU* 4.3 27.8 - - + -
57A ASN* 3.5 23.4 - - + +
137A LEU* 6.0 0.4 - - + -
140A ASP 4.7 3.8 - - - -
141A LEU* 2.7 55.6 + - + +
142A ILE* 5.1 0.7 - - + -
300A GLU 3.1 13.9 + - - +
301A GLU* 3.1 8.5 + - - +
303A LYS* 1.4 75.1 - - - +
305A LYS* 1.3 76.0 + - + +
307A LYS* 3.0 12.3 + - + +
308A LEU* 2.8 51.3 + - + -
317A LEU* 4.1 14.8 - - + -
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Residues in contact with LYS 305 (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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301A GLU* 3.0 42.2 + - + +
302A ALA* 3.2 14.1 + - - +
304A TRP* 1.3 93.6 - - + +
306A ASP* 1.3 60.4 + - - +
308A LEU* 3.3 8.7 + - + +
309A GLU* 2.9 28.2 + - - +
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Residues in contact with ASP 306 (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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302A ALA* 3.1 19.9 + - - +
303A LYS* 3.5 12.0 - - - +
305A LYS* 1.3 78.1 - - - +
307A LYS* 1.3 61.9 + - + +
309A GLU* 3.3 8.3 + - - +
310A LYS* 3.2 28.0 + - + +
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Residues in contact with LYS 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A ASP* 3.4 35.5 - - + +
141A LEU* 3.9 12.9 - - + +
303A LYS* 2.3 60.5 + - - +
304A TRP* 3.0 14.6 + - + +
306A ASP* 1.3 74.4 - - + +
308A LEU* 1.3 65.0 + - - +
310A LYS* 3.2 19.9 + - + +
311A SER* 3.2 13.5 + - - -
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Residues in contact with LEU 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A LEU* 3.7 29.3 - - + +
304A TRP* 2.8 39.5 + - + +
305A LYS* 3.6 13.2 - - + +
307A LYS* 1.3 76.7 - - - +
309A GLU* 1.3 63.9 + - - +
311A SER* 3.0 17.7 + - - -
313A LYS 4.9 0.2 - - - -
314A LYS* 3.4 35.8 - - + +
317A LEU* 3.8 27.6 - - + -
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Residues in contact with GLU 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A LYS 2.9 16.5 + - - +
306A ASP* 3.7 8.5 - - - +
307A LYS 3.3 0.4 - - - -
308A LEU* 1.3 76.4 - - - +
310A LYS* 1.4 56.9 + - + +
314A LYS* 2.7 43.3 + - - +
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Residues in contact with LYS 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A ASP* 3.2 17.1 + - + +
307A LYS* 3.2 13.1 + - + +
308A LEU 3.1 0.6 - - - -
309A GLU* 1.4 76.3 - - + +
311A SER* 1.3 61.9 + - - +
312A ALA 3.9 0.9 + - - -
314A LYS* 4.4 0.4 - - - -
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Residues in contact with SER 311 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A ASP* 4.3 9.1 + - - -
141A LEU* 3.4 20.3 - - - +
307A LYS 3.2 10.2 + - - -
308A LEU* 3.0 16.8 + - - -
309A GLU 3.3 0.2 - - - -
310A LYS* 1.3 80.0 - - - +
312A ALA* 1.3 58.2 + - - +
313A LYS* 3.0 33.5 + - - +
314A LYS* 2.9 26.6 + - - +
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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