Contacts of the helix formed by residues 292 - 313 (chain D) in PDB entry 1R4N
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 VAL 292 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C GLN* 3.3 26.7 - - + +
19C LEU* 3.5 25.6 - - + -
20C TRP* 4.1 16.2 - - + -
52C PRO* 5.7 1.8 - - + -
89D ASN* 4.5 4.7 - - - +
90D ARG* 4.1 9.4 - - - +
182D THR* 5.9 0.2 - - - +
184D GLY 4.9 1.8 + - - +
185D PHE* 4.4 12.3 - - + -
291D ALA* 1.3 82.1 - - - +
293D ALA* 1.3 66.2 + - - +
294D SER* 3.4 27.1 - - - +
295D THR* 3.8 13.7 + - - +
296D ASN* 3.7 13.5 + - - -
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Residues in contact with ALA 293 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C LYS* 5.7 0.2 - - - -
48C ASN* 3.7 33.7 - - - +
51C LEU* 4.3 16.2 - - + -
52C PRO* 4.7 5.6 - - + +
62D GLU* 5.0 3.3 - - - +
89D ASN 4.4 5.1 + - - +
90D ARG* 3.7 22.9 - - + +
292D VAL* 1.3 72.9 - - - +
294D SER* 1.3 69.6 + - - +
295D THR 2.9 1.7 + - - -
296D ASN* 2.9 18.3 + - - +
297D ALA* 3.0 9.6 + - - -
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Residues in contact with SER 294 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C ASN* 4.3 10.4 + - - +
52C PRO* 5.4 1.0 - - - +
499C GLY* 3.6 15.3 - - - -
502C ALA* 5.0 0.7 - - - -
503C GLN* 3.4 43.6 + - - +
506C ILE* 4.3 8.7 - - - +
185D PHE* 4.9 0.4 - - - -
292D VAL* 3.4 17.9 - - - +
293D ALA* 1.3 77.0 - - - +
295D THR* 1.3 64.6 + - - +
297D ALA* 3.1 17.3 - - - +
298D VAL* 3.3 12.1 + - - +
326D ASP* 4.9 1.8 - - - -
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Residues in contact with THR 295 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182D THR* 3.3 23.6 - - - +
184D GLY 3.0 26.6 + - - +
185D PHE* 3.5 22.7 + - - +
186D LYS 3.8 19.1 - - - +
187D GLY* 4.6 0.2 - - - -
292D VAL* 3.8 9.0 + - - +
293D ALA 2.9 3.6 + - - -
294D SER* 1.3 71.7 - - - +
296D ASN* 1.3 67.3 + - - -
298D VAL* 2.8 20.2 + - - +
299D ILE* 3.1 17.2 + - + -
324D PHE* 4.9 5.3 - - + -
326D ASP* 4.4 5.5 + - - -
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Residues in contact with ASN 296 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58D GLY* 3.6 30.2 - - - +
59D LEU* 3.8 14.4 - - + +
62D GLU* 4.6 4.9 - - - +
90D ARG* 3.6 33.6 - - - +
182D THR* 3.0 35.3 + - - +
291D ALA* 4.9 0.8 - - - +
292D VAL 3.7 9.8 + - - -
293D ALA* 2.9 10.0 + - - +
295D THR* 1.3 75.9 - - - +
297D ALA* 1.3 65.9 + - - +
299D ILE* 4.0 0.6 - - - +
300D ALA* 2.8 29.8 + - - +
176J GLY* 3.8 4.8 + - - +
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Residues in contact with ALA 297 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C GLU* 5.9 0.7 - - - +
48C ASN* 3.7 25.6 - - - +
495C ALA* 4.5 6.9 - - + +
499C GLY* 3.8 13.7 - - - +
62D GLU* 3.7 25.1 + - - +
293D ALA 3.0 6.6 + - - +
294D SER 3.1 12.6 - - - +
296D ASN* 1.3 75.9 - - - +
298D VAL* 1.3 58.2 + - - +
300D ALA* 3.9 0.9 - - - +
301D ALA* 2.8 34.2 + - - +
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Residues in contact with VAL 298 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496C PHE* 3.3 40.7 - - + +
499C GLY 3.8 1.3 - - - -
500C ALA* 3.6 24.7 - - + +
294D SER 3.4 15.7 - - - +
295D THR 2.8 12.4 + - - +
297D ALA* 1.3 67.6 - - - +
299D ILE* 1.3 73.0 + - + +
301D ALA* 3.0 5.5 + - - +
302D VAL* 3.0 22.6 + - + +
324D PHE* 3.5 43.5 - - + -
326D ASP* 5.2 0.4 - - - +
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Residues in contact with ILE 299 (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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59D LEU* 3.9 11.7 - - + -
180D GLY* 3.9 11.2 - - - -
181D GLY 3.4 24.5 - - - +
182D THR* 4.2 5.6 - - - +
187D GLY* 3.5 13.2 - - - +
188D ASN* 3.3 43.5 - - - +
189D ALA* 4.1 6.5 - - + +
295D THR* 3.1 10.8 + - + +
296D ASN 4.0 3.8 - - - +
298D VAL* 1.3 79.9 - - + +
300D ALA* 1.3 56.2 + - - +
302D VAL* 2.7 29.5 + - + +
303D CYS* 3.0 16.7 + - - -
322D LEU* 5.3 3.4 - - + +
324D PHE* 4.3 13.2 - - + -
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Residues in contact with ALA 300 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D LEU* 3.9 17.0 - - + +
62D GLU* 3.5 30.5 - - + -
63D LEU* 3.7 18.4 - - + +
66D ASN* 3.6 4.8 + - - +
296D ASN 2.8 22.4 + - - +
299D ILE* 1.3 74.3 - - - +
301D ALA* 1.3 57.2 + - - +
303D CYS* 3.4 3.3 + - - -
304D ALA* 2.8 31.5 + - - +
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Residues in contact with ALA 301 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492C THR* 3.5 12.7 - - - +
495C ALA* 3.6 10.5 - - + -
496C PHE* 3.4 31.4 - - + +
522C TYR* 5.2 1.1 + - - -
66D ASN* 3.4 11.6 - - - +
297D ALA 2.8 20.7 + - - +
298D VAL 3.4 4.7 - - - +
300D ALA* 1.3 76.7 - - - +
302D VAL* 1.3 61.3 + - - +
304D ALA* 3.5 2.5 - - - +
305D THR* 3.2 23.7 + - - -
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Residues in contact with VAL 302 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496C PHE* 3.8 24.7 - - + -
522C TYR* 4.3 2.7 - - - +
527C GLN* 3.0 30.7 - - + +
189D ALA* 3.9 20.9 - - + -
298D VAL* 3.0 18.8 + - + +
299D ILE* 2.7 13.5 + - + +
301D ALA* 1.3 74.0 - - - +
303D CYS* 1.3 69.7 + - - +
304D ALA 3.0 0.9 - - - -
305D THR* 2.9 17.8 + - - -
306D GLU* 3.1 15.4 + - + +
318D LEU* 4.9 4.0 - - + -
322D LEU* 4.2 17.5 - - + -
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Residues in contact with CYS 303 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D LEU* 5.8 0.7 - - - -
63D LEU* 4.2 13.0 - - + -
142D VAL* 4.2 3.6 - - + -
143D CYS 5.3 2.0 - - - -
178D ILE* 3.3 24.6 - - + +
179D ASP 3.8 22.7 - - - -
180D GLY* 4.0 13.5 - - - -
189D ALA* 3.9 12.8 - - - -
299D ILE* 3.0 17.0 + - - -
300D ALA* 3.9 5.4 - - - +
302D VAL* 1.3 79.8 - - - +
304D ALA* 1.3 66.9 + - - +
306D GLU* 3.1 7.3 + - - +
307D VAL* 3.0 24.5 + - - +
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Residues in contact with ALA 304 (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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492C THR* 3.5 9.6 - - + -
63D LEU* 4.1 9.4 - - + +
66D ASN* 3.4 32.5 - - + +
67D LEU* 4.7 8.3 - - + +
70D SER* 5.6 0.4 + - - -
300D ALA 2.8 18.9 + - - +
301D ALA 3.5 8.7 - - - +
303D CYS* 1.3 79.6 - - - +
305D THR* 1.3 64.9 + - - +
307D VAL* 3.0 15.5 + - - +
308D PHE* 3.1 11.3 + - - +
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Residues in contact with THR 305 (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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158C LEU* 5.1 12.8 - - + -
492C THR* 2.8 35.3 + - - +
493C ILE* 4.8 4.4 - - + +
522C TYR* 4.9 0.7 + - - -
524C GLY* 5.0 1.8 - - - +
527C GLN* 3.8 17.1 + - - +
301D ALA 3.2 6.2 + - - -
302D VAL 2.9 8.8 + - - -
304D ALA* 1.3 79.3 - - - +
306D GLU* 1.3 52.7 + - - +
308D PHE* 2.8 13.9 + - + +
309D LYS* 2.7 60.2 + - + +
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Residues in contact with GLU 306 (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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527C GLN* 3.2 27.9 + - - +
178D ILE* 4.3 6.7 - - + -
191D VAL* 3.2 34.8 - - + -
302D VAL* 3.1 10.9 + - + +
303D CYS* 3.1 13.0 + - - +
305D THR* 1.3 76.4 - - - +
307D VAL* 1.3 54.2 + - - +
309D LYS* 2.9 29.8 + - - +
310D ILE* 2.6 39.9 + - + +
317D PRO* 3.4 3.1 - - + +
318D LEU* 2.5 36.1 + - + +
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Residues in contact with VAL 307 (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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51D VAL* 4.6 4.0 - - + -
67D LEU* 3.7 16.8 - - + -
72D PHE* 3.7 19.3 - - + -
140D ILE* 3.6 34.3 - - + -
142D VAL* 3.4 37.0 - - + -
178D ILE* 4.2 5.4 - - + +
303D CYS 3.0 13.8 + - - +
304D ALA* 3.2 7.6 - - - +
306D GLU* 1.3 75.3 - - - +
308D PHE* 1.3 57.5 + - - +
310D ILE* 3.0 7.3 + - - +
311D ALA* 2.7 33.4 + - - +
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Residues in contact with PHE 308 (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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492C THR* 5.7 1.1 - - + +
20D VAL* 3.6 29.2 - - + -
23D PHE* 4.5 16.6 - + + -
24D LEU* 3.7 21.8 - - + -
45D LEU* 4.2 3.4 - - + -
70D SER* 3.6 25.6 - - - +
72D PHE* 3.9 21.9 - + + -
304D ALA 3.1 6.3 + - - +
305D THR* 2.8 17.1 + - + +
307D VAL* 1.3 80.5 - - - +
309D LYS* 1.3 59.2 + - + +
312D THR* 2.6 63.7 + - + +
314D ALA* 4.3 11.0 - - + -
315D TYR* 5.7 2.5 - + - -
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Residues in contact with LYS 309 (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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158C LEU* 5.2 2.0 - - - -
524C GLY 3.0 28.3 + - - -
525C MET* 3.1 14.6 + - - +
527C GLN* 3.6 10.1 - - - +
305D THR* 2.7 36.2 + - + +
306D GLU* 3.1 34.1 + - - +
308D PHE* 1.3 75.7 - - + +
310D ILE* 1.3 61.1 + - - +
312D THR* 4.1 3.4 - - - -
313D SER* 2.4 37.2 + - - +
314D ALA* 4.7 2.7 - - - +
315D TYR* 3.9 42.0 - - + +
316D ILE 3.7 14.4 + - - +
317D PRO* 4.7 4.3 - - + -
318D LEU 4.6 0.6 - - - +
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Residues in contact with ILE 310 (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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140D ILE* 3.9 12.6 - - + -
176D PRO* 3.7 31.6 - - + -
178D ILE* 3.6 31.9 - - + -
191D VAL* 4.3 19.3 - - + -
193D LEU* 4.9 4.0 - - + -
306D GLU* 2.6 20.3 + - + +
307D VAL 3.4 6.1 - - - +
309D LYS* 1.3 75.7 - - - +
311D ALA* 1.3 62.9 + - - +
313D SER* 3.7 12.4 + - - +
317D PRO* 4.0 24.7 - - + +
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Residues in contact with ALA 311 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D LEU* 4.0 11.7 - - + +
49D CYS* 4.1 8.5 - - - -
72D PHE* 3.7 24.7 - - + -
140D ILE* 3.6 19.5 - - + -
307D VAL 2.7 19.2 + - - +
308D PHE 4.1 0.7 - - - +
310D ILE* 1.3 76.4 - - - +
312D THR* 1.3 60.8 + - - +
313D SER* 4.6 1.2 + - - -
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Residues in contact with THR 312 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D LEU* 3.4 31.4 - - + -
35D PHE* 4.1 9.9 - - - -
41D SER 6.1 0.4 - - - +
45D LEU* 3.9 22.4 - - + -
308D PHE* 2.6 44.3 + - + +
309D LYS* 4.1 0.2 - - - -
311D ALA* 1.3 78.0 - - - +
313D SER* 1.3 73.9 + - - +
314D ALA* 3.3 17.5 + - - +
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Residues in contact with SER 313 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D HIS* 3.5 28.9 - - - +
34D ASP* 4.8 12.8 - - - +
35D PHE* 3.1 23.2 - - - +
309D LYS 2.4 26.8 + - - -
310D ILE* 3.7 11.6 + - - +
311D ALA 3.5 1.2 + - - -
312D THR* 1.3 71.6 - - - +
314D ALA* 1.3 56.4 + - - +
315D TYR 3.3 10.3 - - - +
317D PRO* 6.3 0.2 - - - -
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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