Contacts of the helix formed by residues 284 - 307 (chain A) in PDB entry 5DGY
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 GLY 284 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A PRO* 4.4 4.9 - - - -
283A PHE* 1.3 76.6 - - - +
285A PRO* 1.3 74.7 - - - +
286A ILE 3.4 2.7 - - - -
287A PHE* 3.5 21.5 + - - +
288A MET* 3.5 12.3 + - - +
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Residues in contact with PRO 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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12A PRO* 4.1 19.0 - - + +
13A PHE* 6.1 1.8 - - + -
31A LEU* 4.1 31.0 - - + +
32A ALA* 5.0 0.4 - - + -
182A GLY* 3.2 38.8 - - - +
183A LEU* 3.9 17.5 - - + -
284A GLY* 1.3 82.0 - - - +
286A ILE* 1.3 67.9 + - + +
288A MET* 3.4 2.5 + - + -
289A THR* 2.6 30.7 + - - -
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Residues in contact with ILE 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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31A LEU 6.0 0.4 - - - +
32A ALA* 4.5 10.1 - - + -
36A GLN* 3.3 36.8 - - - +
183A LEU* 4.9 5.4 - - + -
284A GLY* 3.4 0.6 - - - -
285A PRO* 1.3 83.4 - - + +
287A PHE* 1.3 64.4 + - - +
289A THR* 3.1 21.0 + - - +
290A ILE* 3.3 22.5 + - + +
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Residues in contact with PHE 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A VAL* 3.9 36.5 - - + +
274A TYR* 5.3 9.4 - + + -
275A ILE* 5.1 0.4 - - + -
283A PHE* 3.6 40.2 - + + -
284A GLY* 3.5 21.6 + - - +
285A PRO 3.2 0.2 - - - -
286A ILE* 1.3 80.2 - - - +
288A MET* 1.3 62.2 - - + +
289A THR 3.5 0.2 + - - -
290A ILE* 3.6 18.6 + - + +
291A PRO* 3.3 17.0 - - - +
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Residues in contact with MET 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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10A TYR* 5.0 4.0 - - + -
12A PRO* 4.8 13.7 - - + -
181A GLU* 5.3 7.1 - - + +
182A GLY* 4.0 27.8 - - - +
191A TYR* 4.4 17.2 + - - +
192A TYR* 3.7 50.9 - - + -
268A TYR* 5.3 1.7 + - - -
271A VAL* 5.4 1.8 - - - -
275A ILE* 4.9 8.3 - - + -
283A PHE* 4.3 29.2 - - + +
284A GLY 3.5 9.4 + - - +
285A PRO 3.4 7.5 + - - +
286A ILE 3.3 0.2 - - - -
287A PHE* 1.3 79.5 - - + +
289A THR* 1.3 62.8 + - - +
290A ILE 3.3 0.2 - - - -
291A PRO* 3.5 13.1 - - - +
292A ALA* 3.9 10.2 + - - +
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Residues in contact with THR 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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40A LEU* 5.4 11.0 - - + -
182A GLY* 4.6 4.0 - - - -
183A LEU* 4.3 21.4 + - + +
285A PRO 2.6 22.3 + - - -
286A ILE* 3.1 17.7 + - - +
288A MET* 1.3 79.1 - - - +
290A ILE* 1.3 59.2 + - - +
291A PRO 3.4 0.2 - - - -
292A ALA* 3.1 10.8 + - + +
293A PHE* 2.9 29.7 + - + +
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Residues in contact with ILE 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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267A PRO* 5.5 3.1 - - + -
271A VAL* 6.1 1.1 - - + -
286A ILE* 3.3 21.7 + - + +
287A PHE* 3.8 20.4 - - + +
289A THR* 1.3 76.6 - - - +
291A PRO* 1.4 71.5 - - + +
293A PHE* 3.3 16.6 + - + +
294A PHE* 3.4 31.6 + - + -
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Residues in contact with PRO 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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191A TYR* 4.6 2.7 - - - +
264A CYS 4.9 0.2 - - - +
267A PRO* 3.6 29.7 - - + +
268A TYR* 3.7 39.1 - - + +
271A VAL* 3.6 22.4 - - + -
287A PHE 3.3 15.5 - - - +
288A MET 3.5 9.6 - - - +
290A ILE* 1.4 94.6 - - + +
292A ALA* 1.3 54.8 + - - +
294A PHE* 3.4 2.4 + - - +
295A ALA* 3.0 30.8 + - - +
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Residues in contact with ALA 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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181A GLU* 4.8 6.1 - - + +
186A SER* 5.4 1.3 - - - +
268A TYR* 3.8 22.8 - - - +
288A MET 3.9 7.2 + - - +
289A THR* 3.1 20.6 + - + +
291A PRO* 1.3 74.6 - - - +
293A PHE* 1.3 64.0 + - - +
295A ALA* 4.7 0.4 - - - -
296A LYS* 3.1 54.9 + - - +
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Residues in contact with PHE 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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43A TYR* 2.9 53.2 + + + -
289A THR* 2.9 15.4 + - + +
290A ILE* 3.4 10.8 - - + +
292A ALA* 1.3 76.9 - - - +
294A PHE* 1.3 94.9 + + - +
297A SER* 2.6 42.9 + - - -
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Residues in contact with PHE 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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263A ILE* 3.4 42.8 - - + +
264A CYS* 4.2 2.1 - - - +
267A PRO* 3.9 22.4 - - + -
290A ILE* 3.4 33.3 + - + -
291A PRO 3.4 3.6 + - - +
293A PHE* 1.3 106.8 - + - +
295A ALA* 1.3 58.3 + - - +
297A SER* 3.4 7.0 + - - -
298A ALA* 3.1 20.8 + - - +
301A TYR* 3.6 12.9 + + - -
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Residues in contact with ALA 295 (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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86A MET* 4.4 9.2 - - + +
264A CYS* 3.9 20.3 + - - +
265A TRP* 4.9 9.2 - - + -
268A TYR* 3.5 27.8 - - + -
291A PRO 3.0 17.1 + - - +
292A ALA* 4.3 2.0 - - - +
294A PHE* 1.3 77.3 - - - +
296A LYS* 1.3 62.0 + - + +
298A ALA* 3.2 22.3 + - - +
299A ALA 3.5 3.5 + - - -
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Residues in contact with LYS 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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40A LEU* 5.8 1.0 - - - +
43A TYR* 4.4 4.9 - - + +
44A MET* 3.8 24.2 - - + +
47A LEU* 4.0 18.4 - - + +
86A MET* 4.5 8.7 - - + -
91A PHE* 3.7 33.4 - - + -
94A THR* 4.9 1.2 + - - +
117A ALA* 6.5 0.9 - - - -
181A GLU* 4.6 6.6 + - - -
186A SER* 3.4 33.3 + - - -
268A TYR* 5.1 2.7 - - + -
292A ALA* 3.1 39.4 + - - +
293A PHE 4.3 1.1 - - - +
295A ALA* 1.3 76.0 - - + +
297A SER* 1.3 63.8 + - - +
299A ALA* 3.2 20.0 + - - +
300A ILE 3.8 1.7 + - - -
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Residues in contact with SER 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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43A TYR* 2.7 15.3 + - - -
47A LEU* 4.6 7.2 - - - +
293A PHE* 2.6 40.1 + - - -
294A PHE* 3.5 10.5 - - - -
296A LYS* 1.3 79.1 - - - +
298A ALA* 1.3 56.2 + - - +
300A ILE* 2.8 22.4 + - - +
301A TYR* 3.0 29.4 + - - -
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Residues in contact with ALA 298 (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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83A ASP* 4.9 0.2 - - - +
264A CYS* 3.4 28.3 - - - -
294A PHE 3.1 7.4 + - - +
295A ALA 3.2 14.4 - - - +
297A SER* 1.3 74.3 - - - +
299A ALA* 1.3 64.0 + - - +
301A TYR* 3.3 23.5 - - + +
302A ASN* 3.0 42.8 + - - +
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Residues in contact with ALA 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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51A GLY* 5.3 0.2 - - - -
55A ASN* 4.2 5.2 + - - -
83A ASP* 3.9 22.8 - - + +
86A MET* 3.9 28.4 - - + +
87A VAL* 6.0 1.3 - - + -
91A PHE* 4.0 20.0 - - + -
295A ALA 3.5 3.2 + - - -
296A LYS 3.2 16.0 + - - +
297A SER 3.1 0.4 - - - -
298A ALA* 1.3 78.5 - - - +
300A ILE* 1.3 60.1 + - + +
303A PRO* 3.3 21.0 - - - +
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Residues in contact with ILE 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 LEU* 3.5 38.6 - - + +
50A LEU* 3.8 29.4 - - + -
51A GLY* 3.3 38.8 - - - +
54A ILE* 4.8 11.5 - - + +
91A PHE* 5.6 1.3 - - + -
296A LYS 4.3 0.7 - - - +
297A SER* 2.8 11.0 + - - +
299A ALA* 1.3 81.7 - - + +
301A TYR* 1.3 63.4 + - + +
302A ASN 3.3 0.7 - - - -
303A PRO* 3.2 20.3 - - - +
304A VAL* 3.6 13.6 - - + +
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Residues in contact with TYR 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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260A ALA* 3.4 27.5 + - + -
263A ILE* 3.5 17.5 - - + +
264A CYS* 3.1 35.7 + - - -
294A PHE* 3.6 3.7 + + - -
297A SER* 3.0 38.7 + - - -
298A ALA* 3.3 20.0 - - + -
300A ILE* 1.3 73.1 - - + +
302A ASN* 1.3 80.7 + - - +
304A VAL* 3.5 14.3 - - + +
305A ILE* 3.3 32.5 + - + +
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Residues in contact with ASN 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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79A LEU* 5.0 12.8 - - + +
83A ASP* 5.0 2.9 - - - +
124A ALA* 5.5 5.3 - - - +
128A LEU* 3.6 26.9 - - - +
260A ALA* 4.6 6.8 + - - +
261A PHE* 6.4 0.2 - - - +
264A CYS* 5.2 5.7 - - - +
265A TRP* 6.0 0.8 - - - +
298A ALA* 3.0 28.5 + - - +
301A TYR* 1.3 97.5 - - - +
303A PRO* 1.4 65.1 - - + +
304A VAL 3.1 1.3 - - - -
305A ILE* 3.2 1.8 + - - -
306A TYR* 2.8 49.2 + - + +
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Residues in contact with PRO 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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54A ILE* 3.5 25.8 - - + -
55A ASN* 3.3 25.4 - - - +
79A LEU* 5.5 1.8 - - + -
83A ASP* 3.4 11.7 - - - +
298A ALA 3.9 0.2 - - - +
299A ALA 3.3 22.4 - - - +
300A ILE* 3.2 10.5 - - - +
302A ASN* 1.4 94.6 - - + +
304A VAL* 1.3 56.3 + - - +
307A ILE* 3.0 24.6 + - + +
308A MET* 2.8 28.0 + - - +
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Residues in contact with VAL 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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54A ILE* 4.8 13.9 - - + -
300A ILE* 3.6 20.4 + - + +
301A TYR* 3.5 17.7 + - + +
302A ASN 3.1 0.4 - - - -
303A PRO* 1.3 78.3 - - - +
305A ILE* 1.3 58.2 + - + +
308A MET* 3.2 17.4 - - + +
309A MET* 2.7 53.6 + - + +
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Residues in contact with ILE 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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253A MET* 5.1 3.9 - - - +
256A ILE* 3.7 28.5 - - + -
257A TYR* 3.6 38.7 + - + +
260A ALA* 3.5 31.0 - - + -
301A TYR* 3.3 24.3 + - + +
302A ASN* 3.2 3.2 + - - +
304A VAL* 1.3 81.6 - - + +
306A TYR* 1.3 66.5 + - + +
307A ILE 3.6 0.2 - - - -
309A MET* 3.4 33.2 + - + +
310A ASN 4.3 2.1 + - - -
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Residues in contact with TYR 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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76A LEU* 4.0 10.0 - - + +
79A LEU* 4.0 15.5 - - + -
128A LEU* 3.5 45.0 - - + +
131A LEU* 3.5 26.7 - - + -
135A ARG* 4.3 4.8 + - - -
219A ILE* 6.0 0.5 - - - +
223A TYR* 4.2 14.1 + - - -
257A TYR* 3.4 53.4 + + - +
260A ALA* 5.2 8.0 - - + +
261A PHE* 5.4 2.6 - - - +
302A ASN* 2.8 40.4 + - + +
305A ILE* 1.3 79.4 - - + +
307A ILE* 1.3 65.0 + - - +
310A ASN* 3.6 22.8 + - - +
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Residues in contact with ILE 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ILE* 5.9 0.2 - - + -
55A ASN* 5.9 0.9 - - - +
58A THR* 3.7 24.5 - - + +
76A LEU* 3.8 44.2 - - + +
79A LEU* 4.7 6.5 - - + -
80A ALA* 5.8 3.1 - - + -
303A PRO* 3.0 26.2 + - + +
306A TYR* 1.3 89.9 - - + +
308A MET* 1.3 67.3 + - + +
309A MET 3.4 1.1 - - - -
310A ASN* 3.2 18.0 + - - +
313A PHE* 3.2 27.3 - - + +
317A MET* 3.7 28.7 - - + -
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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) + - + + + + + -
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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