Contacts of the helix formed by residues 316 - 339 (chain A) in PDB entry 4M8J
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 TRP 316 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A TRP* 3.7 27.1 - + - -
111A GLU* 5.0 2.5 - - + -
114A TYR* 3.4 58.0 + + + +
115A TYR* 3.9 26.2 - + + -
141A HIS* 4.2 8.1 - - + -
312A PHE* 3.0 27.9 + + + +
315A ALA* 1.3 93.7 - - + +
317A THR* 1.3 67.9 + - - +
318A VAL 3.3 1.8 - - - -
319A PHE* 4.0 11.2 - + - +
320A TYR* 3.0 66.1 + + + -
469A LEU* 5.1 4.9 - - + -
473A GLN* 4.6 7.4 - - - -
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Residues in contact with THR 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A GLU* 3.2 20.9 - - - +
137A TYR* 4.0 11.8 + - - -
140A PHE* 4.2 2.0 - - + -
141A HIS* 3.5 28.3 + - + +
300A MET 4.0 17.0 + - - +
303A TYR* 5.3 0.3 - - - +
312A PHE* 4.1 3.5 - - - -
313A PRO* 2.7 32.4 + - + +
316A TRP* 1.3 72.7 - - - +
318A VAL* 1.3 57.3 + - - -
320A TYR* 4.2 0.9 - - - +
321A TRP* 3.0 47.5 + - + +
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Residues in contact with VAL 318 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A THR* 3.5 27.6 - - + +
52A GLY* 3.9 33.0 - - - +
55A PHE* 4.4 11.9 - - + -
56A GLU* 4.2 10.1 - - - +
304A THR* 6.5 0.9 - - + -
313A PRO* 2.8 25.0 + - + +
314A GLN* 3.3 22.9 - - + +
317A THR* 1.3 73.7 - - - +
319A PHE* 1.3 64.1 - - - +
320A TYR 3.3 0.2 - - - -
321A TRP* 3.4 9.3 + - - +
322A ALA* 2.9 27.2 + - - +
477A ILE* 4.3 3.1 - - + +
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Residues in contact with PHE 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A PHE* 4.5 1.1 - - + -
107A TRP* 3.8 28.3 - + - -
314A GLN 4.2 1.3 + - - +
315A ALA 3.5 19.1 - - - +
316A TRP* 3.4 11.4 + + - -
318A VAL* 1.3 77.6 - - - +
320A TYR* 1.3 95.5 + + - +
322A ALA 3.3 0.7 + - - -
323A TRP* 3.1 24.3 + + - +
472A ILE* 5.0 3.6 - - + -
473A GLN* 3.4 44.4 - - + +
476A ILE* 3.1 39.2 - - + +
477A ILE* 3.7 22.7 - - + -
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Residues in contact with TYR 320 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A TRP* 3.7 16.3 - + - -
111A GLU* 2.6 39.5 + - - +
115A TYR* 3.2 16.4 - - - -
141A HIS* 3.3 28.9 - + + -
142A TRP* 3.4 26.0 - + - -
316A TRP* 3.0 46.6 + + - +
317A THR 4.2 3.1 - - - +
319A PHE* 1.3 99.0 - + - +
321A TRP* 1.3 60.6 + - + +
323A TRP* 2.8 22.9 + + + +
324A TRP* 2.8 30.1 + - + +
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Residues in contact with TRP 321 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A PHE* 4.0 13.0 - - + -
56A GLU* 3.8 34.6 + - + +
59A MET* 3.6 38.0 - - + +
140A PHE* 3.6 35.9 - + - -
141A HIS* 4.2 12.3 - + + -
145A LEU* 4.1 17.5 - - + -
146A PRO* 3.5 33.4 - - + -
301A LEU* 4.5 6.5 + - + +
317A THR* 3.0 34.9 + - + +
318A VAL* 3.6 7.4 - - - +
319A PHE 3.3 0.6 - - - -
320A TYR* 1.3 79.7 - - + +
322A ALA* 1.3 52.6 + - - +
324A TRP* 3.2 14.5 + + - +
325A VAL* 2.8 40.0 + - + +
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Residues in contact with ALA 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A PHE* 4.2 19.2 - - + -
318A VAL 2.9 17.2 + - - +
319A PHE 3.5 6.3 - - - +
320A TYR 3.1 0.2 - - - -
321A TRP* 1.3 76.1 - - - +
323A TRP* 1.3 58.6 + - - +
324A TRP 3.2 0.2 - - - -
325A VAL* 3.9 7.7 - - - +
326A ILE* 3.2 31.4 + - - +
476A ILE* 3.4 14.3 - - + +
477A ILE* 3.8 23.1 - - + -
480A GLY* 4.2 2.6 - - - -
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Residues in contact with TRP 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A SER* 5.7 0.2 - - - -
103A ALA* 4.3 24.2 - - + -
104A VAL* 6.4 0.9 - - + -
107A TRP* 5.2 11.0 - + - +
142A TRP* 3.4 40.6 - + - -
150A TYR* 4.2 0.2 + - - -
203A ALA* 6.0 0.7 - - + -
206A THR* 4.8 6.8 + - - -
207A SER* 4.9 5.1 + - - -
210A LEU* 5.5 5.5 - - + +
319A PHE* 3.1 19.0 + + + +
320A TYR* 2.8 17.2 + + + +
322A ALA* 1.3 76.1 - - - +
324A TRP* 1.3 61.3 + - - +
326A ILE* 4.1 2.3 - - + +
327A TYR* 3.3 64.2 + + - -
363A TRP* 6.2 0.2 - + - -
472A ILE* 6.3 1.9 - - + +
476A ILE* 3.2 28.7 - - + +
601A NM2 3.5 44.2 - - + -
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Residues in contact with TRP 324 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A TYR* 6.0 0.2 - - - -
59A MET* 4.4 13.0 - - + -
141A HIS 3.2 20.3 + - - -
142A TRP* 3.5 40.1 - + - -
146A PRO* 3.4 37.7 - - + -
147A TRP* 3.6 45.1 - + - -
150A TYR* 2.5 55.5 + + + -
320A TYR* 2.8 32.3 + - + +
321A TRP* 3.2 18.1 + + - +
323A TRP* 1.3 78.4 - + + +
325A VAL* 1.3 65.1 + - - +
326A ILE 3.2 0.6 + - - -
328A ALA 3.6 1.4 + - - -
601A NM2 3.5 23.3 - - - -
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Residues in contact with VAL 325 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A PHE* 4.4 15.7 - - + -
58A TYR* 3.7 32.1 - - + +
59A MET* 4.9 2.2 - - - -
321A TRP* 2.8 27.9 + - + +
322A ALA* 3.9 7.0 - - - +
323A TRP 3.5 0.2 - - - -
324A TRP* 1.3 73.4 - - - +
326A ILE* 1.3 63.0 + - - +
328A ALA* 3.3 3.5 - - - +
480A GLY* 3.6 11.4 - - - +
483A LEU* 3.5 34.2 - - + +
484A PHE* 3.5 9.6 - - + +
487A ASN* 2.5 32.2 + - - +
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Residues in contact with ILE 326 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A TYR* 4.8 1.7 - - - -
199A ALA 4.3 5.2 - - - +
200A LEU* 4.7 9.7 - - + +
203A ALA* 3.5 33.9 - - + -
322A ALA 3.2 13.6 + - - +
323A TRP* 4.1 5.2 - - - +
324A TRP 3.2 0.8 - - - -
325A VAL* 1.3 74.1 - - - +
327A TYR* 1.3 69.7 + - + +
328A ALA* 3.0 10.1 + - - -
329A ILE* 4.3 4.5 + - - +
330A GLN* 4.6 4.3 + - - +
476A ILE* 3.3 41.3 - - + +
479A GLY* 3.9 11.2 - - - +
480A GLY* 3.8 18.4 - - - +
483A LEU* 3.6 26.9 - - + +
487A ASN* 5.1 0.5 - - - +
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Residues in contact with TYR 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A TYR* 3.5 13.0 - - + +
200A LEU* 5.6 3.1 - - + -
203A ALA* 2.7 46.8 + - + +
204A MET* 4.8 5.6 - - + -
207A SER* 3.1 15.0 + - - -
323A TRP* 3.3 59.1 + + - -
324A TRP 3.8 0.4 + - - -
325A VAL 3.6 0.4 - - - -
326A ILE* 1.3 81.3 - - + +
328A ALA* 1.3 54.7 + - - +
329A ILE 3.7 0.7 - - - -
330A GLN* 3.8 25.8 - - + -
331A MET* 2.7 38.2 + - + +
601A NM2 3.4 23.8 - - - -
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Residues in contact with ALA 328 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A TYR* 4.9 2.5 - - - +
150A TYR* 3.5 30.1 + - + -
153A LEU* 4.2 11.2 - - + -
324A TRP 3.6 0.4 + - - +
325A VAL* 3.3 2.9 - - - +
326A ILE 3.0 3.4 + - - -
327A TYR* 1.3 77.3 - - - +
329A ILE* 1.3 54.8 + - - +
332A SER* 2.5 43.2 + - - +
487A ASN* 3.3 33.0 - - - +
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Residues in contact with ILE 329 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A LEU* 3.9 19.0 - - + +
157A PHE* 3.5 24.7 - - + -
169A ILE 6.1 0.2 - - - +
171A PRO* 4.0 23.8 - - + -
196A TYR* 3.6 26.7 - - + +
326A ILE 4.3 2.0 + - - +
327A TYR 3.7 0.2 - - - -
328A ALA* 1.3 78.0 - - - +
330A GLN* 1.3 61.6 - - - +
332A SER* 4.3 5.8 - - - -
333A ILE* 3.0 36.4 + - + +
486A VAL* 4.0 14.6 - - + -
487A ASN* 4.0 11.9 - - - +
490A VAL* 3.9 25.1 - - + -
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Residues in contact with GLN 330 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A TYR* 3.7 8.7 + - - +
200A LEU* 3.6 24.8 - - + +
204A MET* 4.8 9.2 - - - +
326A ILE 4.6 2.4 + - - +
327A TYR* 3.4 36.4 - - + +
328A ALA 3.1 0.2 - - - -
329A ILE* 1.3 80.3 - - - +
331A MET* 1.3 59.5 + - + +
333A ILE* 4.1 6.0 - - - +
334A PHE* 3.9 12.8 + - - +
425A ALA* 5.5 1.0 + - - +
426A CYS* 5.5 5.1 - - - +
429A THR* 3.6 37.9 + - - +
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Residues in contact with MET 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A SER* 3.7 29.6 - - - +
147A TRP* 4.5 17.3 - - + -
150A TYR* 4.1 20.9 - - + -
327A TYR* 2.7 25.4 + - + +
328A ALA 3.9 0.2 - - - +
330A GLN* 1.3 71.7 - - + +
332A SER* 1.3 60.5 + - - +
333A ILE 3.2 1.8 - - - -
334A PHE* 3.1 29.9 + - + +
335A LEU* 2.9 49.0 + - + +
355A LEU* 4.7 4.0 - - + -
601A NM2 4.6 12.3 - - - +
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Residues in contact with SER 332 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A TYR* 3.3 26.7 + - - +
153A LEU* 3.4 17.6 - - - +
154A SER* 3.4 31.1 - - - -
157A PHE* 4.6 3.6 - - - -
328A ALA* 2.5 29.7 + - - -
329A ILE* 4.3 2.5 - - - -
331A MET* 1.3 69.9 - - - +
333A ILE* 1.3 58.8 + - - +
335A LEU* 3.6 3.3 + - - -
336A ALA* 2.9 30.0 + - - +
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Residues in contact with ILE 333 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A PHE* 3.5 36.3 - - + -
161A PHE* 4.5 5.4 - - + -
168A VAL* 4.8 6.7 - - + +
169A ILE* 4.7 13.9 - - - +
196A TYR* 5.6 1.1 - - - +
329A ILE* 3.0 32.8 + - + +
330A GLN* 4.1 6.3 - - - +
332A SER* 1.3 76.9 - - - +
334A PHE* 1.3 54.5 + - - +
336A ALA* 3.0 7.6 + - - +
337A ARG* 2.8 67.6 + - + +
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Residues in contact with PHE 334 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A MET* 4.4 21.1 - - + -
95A MET* 5.4 0.7 - - - -
98A SER* 4.3 21.5 - - - -
330A GLN 3.9 8.1 + - - +
331A MET* 3.1 33.5 + - + +
333A ILE* 1.3 80.7 - - - +
335A LEU* 1.3 68.5 + - + +
337A ARG* 3.2 17.7 + - + +
338A ILE* 3.3 43.9 + - + +
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Residues in contact with LEU 335 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A MET* 4.1 34.5 - - + -
150A TYR* 4.9 4.5 - - + -
154A SER* 3.9 19.5 - - - -
331A MET* 2.9 47.9 + - + +
332A SER* 4.6 1.3 - - - -
334A PHE* 1.3 81.4 - - + +
336A ALA* 1.3 55.4 + - - +
338A ILE* 3.2 6.4 - - + +
339A SER* 2.2 40.6 + - - +
347A LEU* 5.3 2.9 - - + -
351A MET* 3.6 32.5 - - + -
355A LEU* 4.2 14.4 - - + -
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Residues in contact with ALA 336 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A SER 3.3 10.7 + - - +
157A PHE* 3.6 10.5 - - + -
158A ALA* 3.3 34.9 - - - +
161A PHE* 4.2 4.3 - - + -
162A PHE* 3.0 21.4 - - - -
332A SER 2.9 19.9 + - - +
333A ILE 3.0 4.9 + - - +
335A LEU* 1.3 75.6 - - - +
337A ARG* 1.3 65.3 + - - +
338A ILE 3.1 1.0 + - - -
339A SER* 3.2 9.3 + - - -
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Residues in contact with ARG 337 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A PHE* 5.4 1.4 - - - -
161A PHE* 3.1 39.7 - - - -
162A PHE* 3.9 18.6 - - - -
167A GLU* 3.1 26.1 + - - -
168A VAL 3.6 10.5 + - - -
169A ILE* 5.6 2.6 - - - +
333A ILE* 2.8 39.5 + - + +
334A PHE* 3.2 10.7 + - + +
336A ALA* 1.3 73.3 - - - +
338A ILE* 1.3 63.9 - - + +
340A LYS* 4.2 5.4 - - - +
440A GLU* 5.0 5.6 + - - -
----------------------------------------------------------
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Residues in contact with ILE 338 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A GLU 5.6 0.5 + - - -
86A PHE* 3.9 24.4 - - + -
91A TRP* 3.6 30.8 + - + +
94A MET* 3.7 31.6 - - + -
95A MET* 4.5 11.4 - - + -
334A PHE* 3.5 40.6 - - + +
335A LEU* 3.2 28.3 - - + +
337A ARG* 1.3 79.9 - - + +
339A SER* 1.3 58.2 + - - +
340A LYS* 2.9 13.7 + - - +
342A ARG* 3.8 5.7 + - - -
----------------------------------------------------------
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Residues in contact with SER 339 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A LEU* 3.2 18.2 - - - +
91A TRP* 3.6 21.1 + - - +
95A MET* 4.6 0.9 - - - +
158A ALA* 5.1 0.7 - - - -
335A LEU* 2.2 27.0 + - - -
336A ALA* 3.2 9.3 + - - -
338A ILE* 1.3 74.7 - - - +
340A LYS* 1.3 62.6 + - - +
341A GLY 3.5 0.2 + - - -
342A ARG* 3.6 12.2 + - - +
347A LEU* 3.2 42.7 - - - +
----------------------------------------------------------
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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).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il