Contacts of the helix formed by residues 284 - 316 (chain D) in PDB entry 2VT4
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 ARG 284 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285D GLU* 1.3 71.5 + - - +
286D HIS* 3.2 4.5 - - - +
287D LYS* 3.1 59.9 + - + +
288D ALA* 3.3 11.8 + - - +
347D PRO* 5.8 7.4 - - - +
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Residues in contact with GLU 285 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139D ARG* 5.6 3.8 + - - -
284D ARG* 1.3 83.6 - - - +
286D HIS* 1.3 66.8 + - + +
288D ALA* 3.2 12.6 + - - +
289D LEU* 2.9 32.5 + - + +
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Residues in contact with HIS 286 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234D ALA* 2.6 47.5 + - + +
237D GLN* 3.5 17.9 + - - -
238D ILE* 3.0 42.9 - - + +
284D ARG* 3.2 2.7 - - - +
285D GLU* 1.3 85.1 - - + +
287D LYS* 1.3 59.5 + - + +
288D ALA 3.4 0.2 - - - -
289D LEU* 3.7 11.3 - - + +
290D LYS* 3.0 28.1 + - - +
405D SOG 5.0 24.8 + - + +
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Residues in contact with LYS 287 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284D ARG* 3.1 62.6 + - + +
285D GLU 3.1 0.6 - - - -
286D HIS* 1.3 79.6 - - + +
288D ALA* 1.3 62.7 + - - +
290D LYS* 3.4 4.7 + - - -
291D THR* 3.3 24.8 + - - -
345D ARG* 3.4 12.9 + - - +
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Residues in contact with ALA 288 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284D ARG 3.3 8.0 + - - +
285D GLU* 3.2 15.4 + - - +
287D LYS* 1.3 79.6 - - - +
289D LEU* 1.3 63.3 + - + +
291D THR* 3.5 7.3 + - - -
292D LEU* 3.3 28.1 + - + +
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Residues in contact with LEU 289 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139D ARG* 4.0 36.3 - - + -
143D ILE* 4.3 13.7 - - + -
230D VAL* 4.3 18.2 - - + -
234D ALA* 3.9 27.4 - - + -
285D GLU* 2.9 20.4 + - + +
286D HIS* 3.8 14.1 - - + +
288D ALA* 1.3 76.5 - - + +
290D LYS* 1.3 60.0 + - - +
292D LEU* 3.5 8.8 + - + +
293D GLY 3.0 21.3 + - - -
405D SOG 3.1 28.7 - - + +
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Residues in contact with LYS 290 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286D HIS 3.0 18.8 + - - +
287D LYS* 3.8 7.0 - - - +
288D ALA 3.3 0.4 - - - -
289D LEU* 1.3 75.0 - - - +
291D THR* 1.3 60.2 + - - +
293D GLY* 3.4 1.3 + - - +
294D ILE* 2.9 42.4 + - + +
345D ARG* 3.9 26.3 - - - +
405D SOG 3.4 49.0 + - + +
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Residues in contact with THR 291 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287D LYS 3.3 10.8 + - - -
288D ALA* 3.8 10.7 - - - -
289D LEU 3.3 0.2 - - - -
290D LYS* 1.3 76.3 - - - +
292D LEU* 1.3 63.2 + - + +
294D ILE* 3.1 5.0 + - - +
295D ILE* 2.8 29.4 + - + +
342D ILE* 3.8 24.7 - - + +
343D TYR* 4.0 26.5 - - + -
345D ARG* 3.0 27.3 + - - +
346D SER* 5.1 6.4 + - - +
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Residues in contact with LEU 292 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D THR* 4.1 17.3 - - + -
80D ILE* 4.2 22.0 - - + -
135D ILE* 4.2 17.5 - - + -
139D ARG* 3.7 34.8 - - + -
288D ALA* 3.3 16.7 + - + +
289D LEU* 3.7 14.6 - - + +
290D LYS 3.4 0.2 - - - -
291D THR* 1.3 80.8 - - + +
293D GLY* 1.3 61.7 + - - +
295D ILE* 3.4 10.6 + - + +
296D MET* 3.1 32.5 + - + +
343D TYR* 5.8 0.9 - - + -
405D SOG 4.1 14.1 - - + -
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Residues in contact with GLY 293 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289D LEU 3.0 11.8 + - - -
290D LYS 3.7 4.3 - - - -
291D THR 3.2 0.2 - - - -
292D LEU* 1.3 77.6 - - - +
294D ILE* 1.3 54.8 + - - +
296D MET* 3.3 6.5 + - - +
297D GLY* 3.0 25.1 + - - -
405D SOG 3.7 23.6 - - - +
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Residues in contact with ILE 294 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290D LYS* 2.9 34.6 + - + +
291D THR* 3.1 5.8 + - - +
293D GLY* 1.3 71.1 - - - +
295D ILE* 1.3 66.2 + - - +
297D GLY* 3.2 2.4 + - - +
298D VAL* 2.9 37.5 + - + +
342D ILE* 3.5 33.0 - - + -
345D ARG* 3.6 40.4 - - - +
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Residues in contact with ILE 295 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80D ILE* 5.8 2.5 - - + -
83D LEU* 4.6 2.9 - - + -
132D LEU* 3.8 24.2 - - + -
291D THR 2.8 21.0 + - - +
292D LEU* 3.5 14.6 - - + +
294D ILE* 1.3 73.5 - - - +
296D MET* 1.3 56.9 + - - +
298D VAL* 4.1 1.4 - - - +
299D PHE* 3.2 26.9 + - - +
335D ASN* 5.2 0.2 - - - +
339D ASN* 2.9 53.7 - - + +
342D ILE* 3.7 22.7 - - + -
343D TYR* 3.9 22.4 - - + +
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Residues in contact with MET 296 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132D LEU* 3.7 34.8 - - + +
135D ILE* 3.9 14.6 - - + -
136D ALA* 3.9 12.6 - - + +
223D MET* 3.7 39.3 - - + +
227D ALA* 4.2 11.2 - - + -
292D LEU* 3.1 16.1 + - + +
293D GLY* 3.8 5.2 - - - +
294D ILE 3.2 0.4 - - - -
295D ILE* 1.3 74.1 - - - +
297D GLY* 1.3 63.5 + - - +
299D PHE* 3.9 5.7 - - - +
300D THR* 2.9 27.0 + - - -
405D SOG 3.0 38.4 - - + -
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Residues in contact with GLY 297 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293D GLY 3.0 14.4 + - - -
294D ILE* 3.2 2.4 + - - -
296D MET* 1.3 75.9 - - - +
298D VAL* 1.3 58.1 + - - +
299D PHE 3.2 0.2 - - - -
300D THR* 3.2 6.7 + - - -
301D LEU* 2.9 37.3 + - - +
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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
----------------------------------------------------------
294D ILE* 2.9 25.6 + - + +
295D ILE 4.3 2.2 - - - +
297D GLY* 1.3 72.7 - - - +
299D PHE* 1.3 65.5 + - - +
301D LEU* 3.8 11.7 - - + +
302D CYS* 3.0 26.5 + - - +
335D ASN* 3.6 3.4 - - - +
338D MET* 3.1 41.7 - - + -
339D ASN* 6.0 0.7 - - - +
342D ILE* 3.9 17.9 - - + -
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Residues in contact with PHE 299 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83D LEU* 6.4 0.2 - - + -
125D VAL* 4.3 9.6 - - + -
128D SER* 3.8 22.0 - - - -
129D ILE* 3.6 43.3 - - + -
132D LEU* 3.6 23.1 - - + -
216D PHE* 4.0 19.7 - + - -
220D LEU* 4.8 2.0 - - + -
223D MET* 5.6 0.9 - - + -
295D ILE* 3.2 20.1 + - + +
296D MET 3.9 3.6 - - - +
297D GLY 3.2 0.2 - - - -
298D VAL* 1.3 78.0 - - - +
300D THR* 1.3 69.9 + - - +
302D CYS* 3.1 10.7 + - - +
303D TRP* 3.2 39.4 + + - +
335D ASN* 3.2 30.0 + - - +
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Residues in contact with THR 300 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216D PHE* 5.5 1.1 - - - -
220D LEU* 3.7 31.0 - - + +
223D MET* 4.0 5.4 - - - +
224D ILE* 4.9 9.8 - - + +
296D MET 2.9 15.4 + - - -
297D GLY* 3.2 9.9 + - - -
299D PHE* 1.3 81.5 - - - +
301D LEU* 1.3 67.1 + - + +
303D TRP* 5.4 0.2 - - - -
304D LEU* 3.0 54.0 + - + +
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Residues in contact with LEU 301 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297D GLY* 2.9 27.6 + - - +
298D VAL* 3.9 11.0 - - + +
300D THR* 1.3 76.3 - - + +
302D CYS* 1.3 60.4 + - - +
304D LEU* 5.2 2.0 - - + -
305D PRO* 3.4 18.7 - - - +
331D LEU* 3.7 6.8 - - - +
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Residues in contact with CYS 302 (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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298D VAL* 3.0 24.5 + - - +
299D PHE 3.7 3.4 - - - +
300D THR 3.0 0.6 - - - -
301D LEU* 1.3 81.4 - - - +
303D TRP* 1.3 59.5 + - + +
305D PRO* 3.9 3.1 - - - +
306D PHE 5.2 0.2 + - - -
328D PHE 4.1 4.0 - - - +
331D LEU* 3.5 35.9 - - - +
332D GLY* 3.1 22.6 + - - -
335D ASN* 3.7 21.8 - - + -
338D MET* 3.7 34.1 - - - -
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Residues in contact with TRP 303 (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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125D VAL* 3.6 28.5 - - + +
216D PHE* 3.7 20.2 - + + -
299D PHE* 3.2 49.4 + + - +
302D CYS* 1.3 83.2 - - + +
304D LEU* 1.3 66.6 + - - +
305D PRO* 3.2 2.7 - - - -
306D PHE* 3.1 34.5 + + + +
307D PHE* 3.2 29.9 + + - -
329D ASN* 3.7 22.4 - - - -
332D GLY* 3.3 39.4 + - - -
333D TYR* 4.0 10.5 - + - -
335D ASN* 4.4 4.0 - - + +
400D P32 3.6 21.3 - - - -
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Residues in contact with LEU 304 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216D PHE* 3.9 15.2 - - + -
217D TYR* 4.1 22.7 - - + +
220D LEU* 4.8 6.7 - - + -
300D THR* 3.0 36.8 + - + +
301D LEU* 5.2 1.8 - - + -
303D TRP* 1.3 78.6 - - - +
305D PRO* 1.3 67.6 - - + +
307D PHE 3.3 0.2 + - - -
308D LEU* 2.9 54.8 + - + +
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Residues in contact with PRO 305 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301D LEU* 3.4 25.1 - - - +
302D CYS 3.9 0.4 - - - -
303D TRP 3.3 6.5 - - - +
304D LEU* 1.3 92.7 - - + +
306D PHE* 1.3 62.8 + - - +
308D LEU* 3.0 9.7 + - + +
309D VAL* 3.0 25.5 + - - +
328D PHE* 3.5 36.6 - - + +
331D LEU* 3.9 15.0 - - + -
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Residues in contact with PHE 306 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303D TRP* 3.1 20.7 + + + +
305D PRO* 1.3 79.9 - - - +
307D PHE* 1.3 85.1 + + - +
309D VAL* 3.6 6.9 - - - +
310D ASN* 3.3 33.7 + - - +
325D PHE* 4.0 22.2 - + - -
328D PHE* 3.8 25.7 + - + +
329D ASN* 3.5 42.2 - - + -
400D P32 3.5 50.0 - + + -
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Residues in contact with PHE 307 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125D VAL* 4.1 6.7 - - + -
212D SER* 4.1 21.3 - - - -
216D PHE* 3.3 54.5 - + + -
217D TYR* 2.9 27.8 + + + +
303D TRP* 3.2 44.7 + + - +
304D LEU 4.1 1.3 - - - +
306D PHE* 1.3 83.6 - + - +
308D LEU* 1.3 64.8 + - - +
310D ASN* 3.4 7.3 - - + +
311D ILE* 3.2 19.4 + - - +
400D P32 3.7 50.3 - + - -
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Residues in contact with LEU 308 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217D TYR* 3.4 18.8 - - + +
304D LEU* 2.9 44.0 + - + +
305D PRO* 3.6 6.3 - - + +
307D PHE* 1.3 75.2 - - - +
309D VAL* 1.3 64.7 + - + +
310D ASN 3.0 4.9 + - - -
311D ILE* 3.1 20.2 + - + +
312D VAL* 3.1 17.7 + - + +
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Residues in contact with VAL 309 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305D PRO 3.0 8.3 + - - +
306D PHE* 3.6 13.0 - - - +
308D LEU* 1.3 75.2 - - + +
310D ASN* 1.3 58.8 + - - +
312D VAL* 3.7 10.9 - - + +
313D ASN* 3.1 32.2 + - - -
320D VAL* 4.3 17.0 - - + -
324D LEU* 4.5 11.7 - - + +
325D PHE* 3.6 30.7 - - + +
328D PHE* 3.5 38.8 - - + -
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Residues in contact with ASN 310 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208D ALA* 4.3 7.3 + - - +
212D SER* 3.7 14.2 + - - +
306D PHE* 3.3 31.0 + - - +
307D PHE* 3.4 14.1 - - + +
308D LEU 3.0 1.0 - - - -
309D VAL* 1.3 77.8 - - - +
311D ILE* 1.3 63.8 + - + +
313D ASN* 3.6 10.3 + - - +
314D VAL* 3.7 15.8 + - - +
325D PHE* 3.5 24.2 - - - -
400D P32 3.4 35.2 + - - -
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Residues in contact with ILE 311 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209D ILE* 5.7 9.6 - - + -
212D SER* 5.5 5.4 - - - -
217D TYR* 3.1 40.8 - - + +
307D PHE 3.2 8.7 + - - +
308D LEU* 3.1 15.0 + - + +
310D ASN* 1.3 76.8 - - + +
312D VAL* 1.3 64.7 + - + +
314D VAL* 3.1 23.0 + - + +
315D PHE* 3.4 27.8 - - + -
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Residues in contact with VAL 312 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308D LEU* 3.1 15.1 + - + +
309D VAL* 3.7 13.5 - - + +
310D ASN 3.2 0.2 - - - -
311D ILE* 1.3 75.1 - - + +
313D ASN* 1.3 61.1 + - - +
314D VAL 3.0 5.8 + - - -
315D PHE* 3.2 7.1 + - - +
316D ASN* 3.2 20.5 + - - +
319D LEU* 4.0 31.8 - - + +
320D VAL* 4.4 19.5 - - + -
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Residues in contact with ASN 313 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309D VAL 3.1 20.0 + - - +
310D ASN* 3.6 6.3 + - - +
311D ILE 3.4 0.4 - - - -
312D VAL* 1.3 75.5 - - - +
314D VAL* 1.3 61.7 + - + +
315D PHE 3.4 0.2 - - - -
316D ASN 3.5 8.5 - - - -
317D ARG* 3.2 56.8 + - + +
320D VAL* 3.5 23.9 + - - +
325D PHE* 2.7 39.5 - - + -
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Residues in contact with VAL 314 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205D ARG* 3.4 48.0 + - + +
208D ALA* 3.8 27.1 - - + -
209D ILE* 3.6 35.9 - - + -
310D ASN 3.7 14.8 + - - +
311D ILE* 3.1 13.4 + - - +
312D VAL 3.0 0.4 - - - -
313D ASN* 1.3 81.2 - - + +
315D PHE* 1.3 74.4 + - + +
317D ARG* 5.3 0.8 - - - +
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Residues in contact with PHE 315 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152C LEU* 3.7 34.1 - - + -
205D ARG* 4.4 13.2 + - - +
209D ILE* 5.1 6.5 - - + -
311D ILE* 3.4 29.8 - - + -
312D VAL* 3.2 9.4 + - + +
314D VAL* 1.3 94.1 - - + +
316D ASN* 1.3 62.4 + - + +
319D LEU* 6.2 2.5 - - + -
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Residues in contact with ASN 316 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205D ARG* 5.8 1.1 - - - +
312D VAL 3.2 15.8 + - - +
313D ASN* 3.5 8.1 - - - +
315D PHE* 1.3 80.5 - - + +
317D ARG* 1.3 66.1 + - - +
318D ASP* 3.0 24.1 + - - +
319D LEU* 3.4 46.4 + - + +
----------------------------------------------------------
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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