Contacts of the helix formed by residues 313 - 334 (chain D) in PDB entry 4IL6
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 THR 313 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A VAL* 4.0 8.3 - - - -
68A SER 3.4 12.3 - - - +
75A ASN* 3.3 29.4 - - - +
79A THR* 4.6 1.6 - - - -
301D GLN* 2.8 19.8 + - - +
311D PHE* 3.6 29.6 - - + -
312D GLU* 1.3 79.9 - - - +
314D PHE* 1.3 63.2 + - - +
315D TYR* 3.3 11.5 + - - +
316D THR* 2.9 25.3 + - - +
317D LYS* 3.1 13.4 + - - +
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Residues in contact with PHE 314 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ILE* 4.1 21.5 - - + -
67A VAL* 4.2 8.2 - - + +
68A SER 4.7 1.9 + - - -
69A GLY* 5.8 0.2 - - - -
79A THR 4.4 5.6 + - - +
81A ALA* 3.8 25.6 - - + -
83A VAL* 4.0 20.4 - - + -
84A PRO* 4.1 3.1 - - + -
173A PRO* 3.5 35.7 - - + -
177A SER* 3.8 6.5 - - - -
178A GLY* 3.5 28.9 - - - +
181A ASN* 3.8 17.0 - - + -
313D THR* 1.3 75.1 - - - +
315D TYR* 1.3 61.1 + - - +
317D LYS* 3.7 31.9 - - + +
318D ASN* 3.1 29.1 + - - +
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Residues in contact with TYR 315 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A THR* 3.3 26.3 - - + -
177A SER* 4.0 11.5 - - - +
190D ASN* 5.0 0.9 - - - -
193D LEU* 4.0 15.7 - - + -
296D TYR 3.8 15.0 - - - -
297D ASP* 3.0 9.9 - - - +
298D PHE* 2.9 44.2 + + + -
301D GLN* 3.5 33.7 - - + -
302D GLU* 2.6 32.3 + - - -
313D THR* 3.1 6.0 + - - +
314D PHE* 1.3 78.8 - - - +
316D THR* 1.3 71.0 + - + +
318D ASN* 3.5 5.9 + - - +
319D LEU* 3.4 38.8 + - + +
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Residues in contact with THR 316 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301D GLN* 4.6 4.9 - - - +
302D GLU* 5.0 0.7 - - - +
305D ALA* 4.3 13.9 - - + -
311D PHE* 5.0 5.6 - - + +
312D GLU* 3.6 12.0 - - - +
313D THR* 2.9 35.1 + - - +
315D TYR* 1.3 91.9 - - + +
317D LYS* 1.3 65.5 + - - +
319D LEU* 3.4 15.7 + - - +
320D LEU* 3.5 16.6 + - - +
159O PRO* 4.0 17.8 + - - +
160O LYS* 4.2 20.3 + - + +
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Residues in contact with LYS 317 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ILE* 5.3 3.8 - - - +
61A ASP* 4.1 18.2 + - - -
65A GLU* 6.0 0.2 + - - -
67A VAL* 4.2 21.8 - - + +
181A ASN* 3.9 11.8 + - - +
333A GLU* 4.4 6.9 + - - +
334A ARG* 4.9 4.5 - - - +
1003A CL 3.1 27.0 - - + +
312D GLU* 3.4 24.8 + - - +
313D THR 3.1 16.9 + - - +
314D PHE* 3.7 39.9 - - + +
315D TYR 3.3 0.2 - - - -
316D THR* 1.3 77.0 + - - +
318D ASN* 1.3 61.7 + - - +
320D LEU* 3.3 22.4 + - - +
321D LEU* 3.4 16.0 + - - +
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Residues in contact with ASN 318 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A SER* 3.0 33.1 + - - -
180A PHE* 3.8 10.3 - - - +
181A ASN* 3.1 38.5 + - - +
184A ILE* 4.1 12.2 - - + +
186D GLN* 5.2 0.7 - - - +
190D ASN* 5.1 9.6 - - - +
193D LEU* 6.3 0.4 - - - +
314D PHE 3.1 16.8 + - - +
315D TYR* 3.9 5.3 - - - +
316D THR 3.3 0.2 - - - -
317D LYS* 1.3 73.9 - - - +
319D LEU* 1.3 65.1 + - + +
321D LEU* 3.3 12.9 + - - +
322D ASN* 3.0 27.4 + - - +
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Residues in contact with LEU 319 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190D ASN* 3.6 24.0 - - - +
296D TYR* 3.5 37.2 + - + +
302D GLU* 2.9 29.4 - - - +
315D TYR* 3.4 29.2 + - + +
316D THR* 3.8 7.4 - - - +
317D LYS 3.4 0.6 - - - -
318D ASN* 1.3 77.9 - - + +
320D LEU* 1.3 57.4 + - - +
322D ASN* 3.2 7.9 + - - +
323D GLU* 2.9 46.3 + - - +
160O LYS* 3.6 16.4 - - - +
173O ALA* 5.5 0.9 - - + -
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Residues in contact with LEU 320 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A MET* 3.4 39.6 - - + +
334A ARG* 3.5 35.9 - - - +
312D GLU* 5.0 0.2 - - - +
316D THR 3.5 11.2 + - - +
317D LYS* 3.3 13.6 + - - +
318D ASN 3.3 0.4 - - - -
319D LEU* 1.3 76.8 - - + +
321D LEU* 1.3 58.3 + - + +
323D GLU* 3.4 21.8 + - - +
324D GLY 3.1 22.0 + - - -
159O PRO 3.4 19.7 - - - +
160O LYS* 4.1 4.7 - - - +
161O GLY* 3.8 28.7 - - - +
168O TYR* 4.7 1.1 - - + -
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Residues in contact with LEU 321 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A ASN* 3.7 25.8 - - - +
184A ILE* 3.6 36.1 - - + -
185A VAL* 4.2 7.6 - - + -
327A GLY 4.2 2.1 - - - +
328A MET* 3.6 16.6 - - + +
331A MET* 4.1 5.8 - - - -
332A HIS* 3.5 39.9 - - + +
1003A CL 4.2 2.9 - - + -
317D LYS 3.5 9.9 - - - +
318D ASN* 3.3 17.5 + - - +
319D LEU 3.3 0.2 - - - -
320D LEU* 1.3 75.7 - - + +
322D ASN* 1.3 60.7 + - - +
324D GLY* 3.2 2.9 + - - -
325D ILE* 2.8 33.9 + - - +
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Residues in contact with ASN 322 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A ILE* 4.9 0.5 - - - +
186D GLN* 2.8 42.6 + - - +
187D GLY* 3.4 16.6 - - - +
190D ASN* 3.3 31.7 + - - +
296D TYR* 3.5 18.9 + - - +
318D ASN 3.0 18.3 + - - +
319D LEU* 3.3 13.1 - - - +
321D LEU* 1.3 75.4 - - - +
323D GLU* 1.3 58.2 + - - +
325D ILE* 3.2 4.1 + - - +
326D ARG* 2.9 35.3 + - - +
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Residues in contact with GLU 323 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A MET* 5.6 0.4 - - + -
365B SER* 4.1 6.7 - - - +
296D TYR* 4.8 2.5 + - - +
319D LEU* 2.9 34.5 + - - +
320D LEU* 3.5 22.2 - - - +
321D LEU 3.2 0.2 - - - -
322D ASN* 1.3 75.3 - - - +
324D GLY* 1.3 61.2 + - - +
326D ARG* 3.4 29.0 + - - +
327D ALA* 3.2 25.1 + - - +
347D PRO* 4.1 6.3 - - + +
160O LYS* 4.6 8.7 + - - +
168O TYR* 2.9 38.5 + - - +
172O ILE* 3.6 15.1 - - - +
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Residues in contact with GLY 324 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327A GLY* 3.3 27.2 - - - -
331A MET* 3.6 13.6 - - - +
320D LEU 3.1 11.3 + - - -
321D LEU 3.2 1.1 + - - -
323D GLU* 1.3 73.9 - - - +
325D ILE* 1.3 63.7 + - - +
327D ALA 3.4 0.3 + - - -
328D TRP* 3.0 34.0 + - - -
347D PRO* 4.6 3.1 - - - -
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Residues in contact with ILE 325 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A ILE* 4.7 3.6 - - + -
324A ALA* 3.7 13.7 - - + +
327A GLY* 3.8 5.8 - - - -
328A MET* 3.6 39.5 - - + -
183D LEU 3.9 8.3 - - - +
186D GLN* 4.3 14.4 - - + -
187D GLY* 3.9 29.6 - - - +
188D PHE* 5.0 0.9 - - + -
321D LEU 2.8 23.8 + - - +
322D ASN* 3.5 9.6 - - - +
324D GLY* 1.3 70.7 - - - +
326D ARG* 1.3 59.3 + - - +
329D MET* 2.9 56.2 + - - +
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Residues in contact with ARG 326 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362B PHE 4.8 0.2 - - - -
363B PHE* 4.1 18.8 - - + +
364B GLU* 4.0 13.3 - - - +
365B SER* 2.9 41.8 + - - +
187D GLY 2.8 35.0 + - - +
188D PHE* 3.6 45.6 - - + +
296D TYR* 2.8 32.7 + - - -
322D ASN* 2.9 23.9 + - - +
323D GLU* 3.4 24.3 + - - +
325D ILE* 1.3 76.7 - - - +
327D ALA* 1.3 57.7 + - - +
330D ALA* 3.0 36.4 + - - +
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Residues in contact with ALA 327 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A ARG* 5.3 0.2 + - - -
363B PHE* 5.8 0.7 - - - -
367B PRO* 6.1 5.6 - - + -
323D GLU 3.2 14.6 + - - +
326D ARG* 1.3 78.0 - - - +
328D TRP* 1.3 65.8 + - + +
331D PRO* 3.3 18.2 - - - +
341D PHE* 3.4 22.7 - - + -
346D LEU* 4.0 10.5 - - + +
347D PRO* 3.6 28.9 - - + -
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Residues in contact with TRP 328 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A ARG* 2.9 65.0 + - - +
326A LEU* 3.8 19.5 - - + -
327A GLY* 3.7 11.4 - - - -
330A VAL* 3.5 21.8 - - + +
324D GLY* 3.0 23.4 + - - +
327D ALA* 1.3 88.0 - - + +
329D MET* 1.3 59.0 + - - +
331D PRO* 4.1 4.0 - - - +
332D GLN 5.5 0.3 + - - -
346D LEU* 3.9 23.9 - - + +
347D PRO 3.2 21.0 + - - -
348D ARG* 3.7 27.1 - - + -
134V LYS* 3.8 19.1 - - + -
135V VAL* 3.7 41.1 - - + -
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Residues in contact with MET 329 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A ILE* 4.0 14.2 - - + +
323A ARG* 3.7 9.1 - - + +
324A ALA* 3.8 30.3 - - + +
180D ARG* 4.0 22.4 - - + +
184D PHE* 4.3 10.8 - - + -
188D PHE* 4.2 19.3 - - + -
325D ILE* 2.9 39.2 + - - +
328D TRP* 1.3 77.9 - - - +
330D ALA* 1.3 64.7 + - - +
331D PRO 3.3 1.7 - - - -
332D GLN* 3.4 4.9 + - - +
333D ASP* 2.9 59.6 + - + +
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Residues in contact with ALA 330 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363B PHE* 3.8 27.8 - - + -
188D PHE* 4.5 1.1 - - + -
326D ARG 3.0 20.7 + - - +
329D MET* 1.3 80.4 - - - +
331D PRO* 1.4 64.8 - - + +
333D ASP* 4.4 1.8 - - - -
334D GLN* 2.8 44.7 + - - +
339D PHE* 3.9 11.7 - - + -
341D PHE* 4.4 3.6 - - + -
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Residues in contact with PRO 331 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A ARG* 5.8 4.0 - - - +
327D ALA 3.3 16.8 - - - +
328D TRP 4.1 5.2 - - - +
329D MET 3.6 3.1 - - - -
330D ALA* 1.4 92.9 - - + +
332D GLN* 1.3 62.8 + - + +
334D GLN 3.9 0.9 - - - +
335D PRO* 3.8 19.1 - - - +
339D PHE* 3.9 33.2 + - + +
341D PHE* 3.7 27.8 - - + +
346D LEU* 6.2 0.2 - - + -
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Residues in contact with GLN 332 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A ASN* 3.3 30.6 + - - +
319A ASP* 4.6 3.0 + - - +
320A ILE* 3.8 22.1 - - + +
323A ARG* 3.5 43.9 + - + +
61D HIS 4.6 5.9 - - - +
328D TRP 5.5 0.2 + - - -
329D MET 3.4 5.3 + - - +
330D ALA 3.3 0.2 - - - -
331D PRO* 1.3 80.2 - - + +
333D ASP* 1.3 62.7 + - - +
334D GLN 3.3 0.6 + - - -
335D PRO* 3.6 14.6 - - - +
136V TYR 5.2 0.9 - - - +
137V TYR* 3.5 12.5 + - - +
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Residues in contact with ASP 333 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A TRP* 4.0 6.4 - - - -
320A ILE* 3.3 24.1 - - + +
61D HIS* 5.5 0.2 + - - -
168D PHE* 3.3 24.9 - - - -
180D ARG* 2.8 45.1 + - - -
184D PHE* 3.4 17.0 - - - -
329D MET* 2.9 35.0 + - + +
330D ALA* 4.2 2.2 - - - +
332D GLN* 1.3 78.2 - - - +
334D GLN* 1.3 61.1 + - + +
335D PRO* 3.5 1.5 - - - +
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Residues in contact with GLN 334 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B PRO* 5.5 0.5 - - - +
362B PHE* 4.3 6.7 - - - -
363B PHE* 3.8 22.7 - - - -
169D PHE* 3.9 27.6 - - + -
184D PHE* 3.9 9.3 - - - -
188D PHE* 3.4 36.0 - - - -
330D ALA* 2.8 21.2 + - - +
331D PRO 3.9 2.1 - - - +
333D ASP* 1.3 88.8 + - + +
335D PRO* 1.3 65.4 - - - +
336D HIS* 3.2 17.0 - - + -
337D GLU* 3.0 34.9 + - + +
338D ASN 4.2 1.0 + - - -
339D PHE* 4.3 4.6 + - + -
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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