Contacts of the helix formed by residues 327 - 350 (chain D) in PDB entry 2QJK
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 ASP 327 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168C PRO* 3.6 25.3 - - + +
315D VAL* 4.9 2.2 - - - -
319D ASN* 4.4 13.5 - - - +
324D GLY 3.5 12.7 + - - +
325D ILE 3.5 6.0 + - - +
326D ILE* 1.3 77.1 - - - +
328D ALA* 1.3 67.0 + - - +
329D LYS* 3.0 18.8 + - - +
330D PHE* 3.1 14.0 + - - +
331D PHE* 3.0 20.9 + - - +
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Residues in contact with ALA 328 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166C PRO* 4.0 16.6 - - + +
168C PRO* 6.3 0.4 - - + -
308D PHE 4.1 9.4 - - - +
309D THR 3.8 6.3 - - - -
310D ALA* 3.6 38.8 - - + +
315D VAL* 4.2 11.8 - - + +
327D ASP* 1.3 76.7 - - - +
329D LYS* 1.3 68.1 + - - +
331D PHE* 2.9 8.8 + - - +
332D GLY* 2.8 19.6 + - - -
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Residues in contact with LYS 329 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C THR 3.5 17.0 + - - +
131C HIS* 2.7 47.4 + - + +
132C LEU* 4.5 6.5 - - + -
166C PRO* 3.8 16.9 + - - +
168C PRO* 4.1 12.8 - - + +
164D GLY 4.9 1.3 + - - -
167D GLY* 4.3 11.7 + - - -
168D ALA* 4.0 29.2 - - + +
305D LEU* 5.3 0.3 - - - +
327D ASP* 3.0 12.9 + - - +
328D ALA* 1.3 82.0 - - - +
330D PHE* 1.3 60.8 + - - +
332D GLY* 3.0 13.9 + - - -
333D VAL* 3.1 14.1 + - + +
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Residues in contact with PHE 330 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168D ALA* 3.5 29.8 - - + +
169D ILE* 4.0 14.8 - - + -
170D PRO* 3.5 35.2 - - + -
325D ILE* 4.4 3.4 - - + +
326D ILE* 4.3 23.6 - - + -
327D ASP* 3.1 15.0 + - - +
329D LYS* 1.3 75.7 - - + +
331D PHE* 1.3 59.8 + - - +
333D VAL* 3.4 13.9 + - + -
334D LEU* 2.9 69.7 + - + +
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Residues in contact with PHE 331 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308D PHE* 3.3 53.2 - + + -
314D VAL* 3.5 32.5 - - + -
315D VAL* 3.6 11.2 - - + -
318D ALA* 4.2 14.8 - - + -
326D ILE* 4.1 19.5 - - + +
327D ASP 3.0 19.2 + - - +
328D ALA* 2.9 8.6 + - - +
330D PHE* 1.3 75.5 - - - +
332D GLY* 1.3 53.1 + - - +
334D LEU* 2.9 13.0 + - + +
335D ALA* 2.6 39.9 + - + +
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Residues in contact with GLY 332 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305D LEU* 3.5 37.7 - - - +
308D PHE* 4.4 5.8 - - - +
328D ALA 2.8 12.5 + - - -
329D LYS 3.4 4.9 - - - -
331D PHE* 1.3 78.8 - - - +
333D VAL* 1.3 61.1 + - - +
335D ALA* 3.3 8.8 + - - +
336D MET* 3.0 18.4 + - - +
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Residues in contact with VAL 333 (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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131C HIS* 6.0 0.4 - - - +
132C LEU* 5.3 2.7 - - + -
165D LEU* 4.1 31.6 - - + +
168D ALA* 3.5 28.0 - - + -
169D ILE* 6.0 2.0 - - + +
305D LEU* 3.7 9.6 - - + +
329D LYS* 3.1 13.9 + - + +
330D PHE* 3.5 17.5 - - + +
332D GLY* 1.3 75.9 - - - +
334D LEU* 1.3 63.7 + - + +
336D MET* 3.1 13.0 + - - +
337D PHE* 3.1 40.5 + - + -
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Residues in contact with LEU 334 (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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326D ILE* 4.4 15.0 - - + -
330D PHE* 2.9 65.4 + - + +
331D PHE* 3.3 12.1 - - + +
333D VAL* 1.3 77.1 - - + +
335D ALA* 1.3 58.9 + - - +
337D PHE* 4.4 4.0 - - + +
338D GLY* 2.7 30.7 + - - -
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Residues in contact with ALA 335 (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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304D ILE* 4.0 6.1 - - + -
308D PHE* 3.4 37.5 - - + -
331D PHE* 2.6 21.6 + - + +
332D GLY 3.4 9.4 - - - +
334D LEU* 1.3 73.3 - - - +
336D MET* 1.3 56.2 + - - +
338D GLY* 4.9 0.2 - - - -
339D ALA* 2.8 25.8 + - - +
401D PHE* 3.2 18.3 - - + -
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Residues in contact with MET 336 (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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2D SMA 3.1 60.8 - - + +
165D LEU* 3.6 24.0 - - + -
301D PHE* 3.4 40.5 - - + +
304D ILE* 4.2 7.2 - - - -
305D LEU* 4.1 12.6 - - + -
332D GLY 3.0 12.4 + - - +
333D VAL* 3.1 6.9 + - - +
335D ALA* 1.3 73.5 - - - +
337D PHE* 1.3 83.5 + - + +
338D GLY 2.9 0.9 - - - -
339D ALA* 2.7 20.6 + - - +
340D ILE* 3.3 8.2 + - - +
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Residues in contact with PHE 337 (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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2D SMA 3.6 42.0 - - + -
137D LEU* 5.6 5.6 - - + -
165D LEU* 4.5 14.1 - - + -
166D PHE* 4.7 19.1 - + - -
333D VAL* 3.1 42.7 + - + +
334D LEU* 4.4 2.5 - - - +
336D MET* 1.3 94.0 - - + +
338D GLY* 1.3 57.2 + - - +
340D ILE* 3.1 12.2 + - + +
341D LEU* 2.8 28.8 + - - +
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Residues in contact with GLY 338 (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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334D LEU 2.7 19.1 + - - -
335D ALA 3.7 0.7 - - - -
337D PHE* 1.3 74.1 - - - +
339D ALA* 1.3 65.8 + - - +
340D ILE 2.8 2.3 + - - -
341D LEU* 2.9 11.1 + - - -
342D VAL* 2.8 29.5 + - - +
401D PHE* 4.0 9.6 - - - -
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Residues in contact with ALA 339 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301D PHE* 4.5 9.4 - - + -
304D ILE* 3.8 20.9 - - + -
335D ALA 2.8 13.9 + - - +
336D MET* 2.7 16.1 + - - +
338D GLY* 1.3 70.7 - - - +
340D ILE* 1.3 58.1 + - - +
342D VAL* 3.2 12.1 - - - +
343D MET* 3.9 1.6 + - - +
400D TRP* 2.9 34.9 + - - +
401D PHE* 3.6 20.6 - - + -
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Residues in contact with ILE 340 (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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2D SMA 3.7 29.8 - - - -
133D MET* 3.8 21.7 - - + +
136D TYR* 4.5 8.3 - - + -
137D LEU* 5.4 13.0 - - + -
140D MET* 3.9 15.5 - - + -
301D PHE* 3.2 35.0 - - + -
336D MET 3.8 8.1 - - - +
337D PHE* 3.1 13.9 + - + +
338D GLY 2.9 0.6 - - - -
339D ALA* 1.3 76.3 - - - +
341D LEU* 1.3 68.1 + - - +
343D MET* 2.8 30.2 + - + +
344D ALA 3.2 4.3 + - - -
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Residues in contact with LEU 341 (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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337D PHE 2.8 19.3 + - - +
338D GLY* 3.5 10.3 - - - +
340D ILE* 1.3 75.0 - - - +
342D VAL* 1.3 66.5 + - + +
344D ALA* 2.9 19.2 + - + +
345D LEU* 3.2 37.4 + - + +
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Residues in contact with VAL 342 (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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338D GLY* 2.8 22.0 + - - +
339D ALA* 3.2 19.7 - - - +
341D LEU* 1.3 74.7 - - + +
343D MET* 1.3 69.9 + - - +
345D LEU* 2.8 30.3 + - + +
346D VAL* 3.1 9.9 + - - -
349D LEU* 4.7 3.4 - - + +
400D TRP* 4.0 7.0 - - + +
401D PHE* 4.1 20.0 - - + -
404D PHE* 3.9 35.7 - - + -
405D LEU* 4.3 22.2 - - + -
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Residues in contact with MET 343 (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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109D TYR* 6.5 0.2 - - + -
112D ILE* 4.3 27.1 - - + -
116D LEU* 4.9 4.9 - - + -
129D TRP* 3.2 20.5 + - + -
133D MET* 3.9 23.1 - - + -
136D TYR* 4.4 19.5 - - + -
301D PHE* 4.8 10.3 - - + -
339D ALA 4.1 6.7 - - - +
340D ILE* 2.8 23.0 + - + +
342D VAL* 1.3 81.3 - - - +
344D ALA* 1.3 55.2 - - - +
346D VAL* 2.9 27.3 - - - +
400D TRP* 4.2 20.6 - - + -
404D PHE* 3.9 25.1 - - + -
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Residues in contact with ALA 344 (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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129D TRP* 3.6 15.0 + - - +
130D ILE* 5.2 3.6 - - + +
133D MET* 3.9 27.5 - - + +
340D ILE 3.2 3.4 + - - +
341D LEU* 2.9 22.7 + - + +
343D MET* 1.3 77.6 - - - +
345D LEU* 1.3 60.1 + - + +
346D VAL 3.1 0.4 - - - -
347D PRO* 3.0 17.5 - - - +
348D TRP* 3.7 7.1 - - - -
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Residues in contact with LEU 345 (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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341D LEU* 3.3 41.7 - - + +
342D VAL* 2.8 12.6 + - + +
344D ALA* 1.3 77.4 - - + +
346D VAL* 1.3 53.1 + - - +
347D PRO* 3.0 4.3 - - - -
348D TRP* 2.6 48.2 + - + +
349D LEU* 3.1 23.5 + - + -
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Residues in contact with VAL 346 (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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116D LEU* 4.1 5.8 - - + -
121D TYR* 3.7 32.4 - - + +
129D TRP* 3.4 21.5 - - + +
342D VAL 3.1 5.6 + - - -
343D MET 2.9 24.9 - - - +
345D LEU* 1.3 77.9 - - - +
347D PRO* 1.3 72.4 - - + +
348D TRP 3.0 1.8 + - - -
349D LEU* 3.7 8.3 - - - +
350D ASP* 3.2 20.5 + - + +
404D PHE* 4.1 25.4 - - + -
408D LEU* 4.3 12.8 - - + -
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Residues in contact with PRO 347 (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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121D TYR* 3.7 33.5 - - + +
122D LYS* 5.3 4.4 - - - +
126D GLU* 4.1 15.4 - - + +
129D TRP* 3.8 21.3 - - + -
344D ALA 3.0 15.5 - - - +
345D LEU 3.0 4.3 - - - +
346D VAL* 1.3 98.5 - - + +
348D TRP* 1.3 81.6 + - + +
350D ASP* 3.9 11.5 - - - +
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Residues in contact with TRP 348 (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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18A TRP* 4.8 12.6 - + - -
126D GLU* 4.4 23.2 + - + +
130D ILE* 3.8 30.3 - - + -
344D ALA 3.7 18.2 - - - -
345D LEU* 2.6 38.6 + - + +
347D PRO* 1.3 97.5 - - + +
349D LEU* 1.3 69.5 + - + +
350D ASP 3.3 4.0 - - - +
351D THR* 4.7 7.8 - - - +
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Residues in contact with LEU 349 (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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342D VAL* 4.7 9.4 - - + +
345D LEU* 3.1 25.9 + - + +
346D VAL* 3.4 5.8 + - - +
348D TRP* 1.3 85.5 - - + +
350D ASP* 1.3 61.2 + - - +
351D THR* 3.2 8.4 + - - +
404D PHE* 2.9 43.7 - - + +
405D LEU* 3.6 24.0 - - + -
408D LEU* 4.4 3.8 - - + -
409D PRO* 3.2 33.5 - - + +
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Residues in contact with ASP 350 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121D TYR* 2.8 26.0 + - + +
122D LYS* 3.0 40.1 + - - -
346D VAL* 3.2 18.9 + - + +
347D PRO 3.9 11.9 - - - +
348D TRP 4.6 1.5 - - - -
349D LEU* 1.3 74.8 - - - +
351D THR* 1.3 59.9 + - - +
352D SER* 3.0 17.2 + - - +
360D ARG* 3.1 13.4 + - - -
408D LEU* 3.7 24.0 - - + +
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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