Contacts of the helix formed by residues 321 - 342 (chain D) in PDB entry 3Q2K
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 321 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126D LEU 3.1 15.0 - - - +
128D VAL* 4.2 4.7 - - - +
318D PRO* 2.9 33.8 + - + +
320D THR* 1.3 77.7 - - - +
322D GLY* 1.3 60.2 + - - +
323D ARG* 3.7 15.7 + - - +
324D GLU* 2.9 24.3 + - - +
325D GLY* 3.0 21.1 + - - -
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Residues in contact with GLY 322 (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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105D MET* 3.6 8.7 - - - +
116D VAL* 3.9 8.3 - - - -
126D LEU* 2.8 37.5 + - - +
128D VAL* 4.1 7.4 - - - -
321D ASP* 1.3 77.3 - - - +
323D ARG* 1.3 58.3 + - - +
325D GLY* 2.9 3.5 + - - -
326D LEU* 2.9 25.1 + - - +
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Residues in contact with ARG 323 (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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179A GLU* 2.7 42.2 + - - +
180A TRP* 3.5 30.2 - - - +
116D VAL* 3.5 21.9 - - + +
120D ASP* 2.9 39.4 + - - -
321D ASP* 3.2 14.3 + - - +
322D GLY* 1.3 72.7 - - - +
324D GLU* 1.3 66.9 + - - +
326D LEU* 3.2 27.4 + - + +
327D GLN* 3.5 12.7 + - - +
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Residues in contact with GLU 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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130D LYS* 6.0 1.0 - - - +
133D ARG* 2.7 52.7 + - - +
194D ASP* 4.9 1.9 - - - +
197D ASP* 5.0 3.7 - - - +
198D TRP* 3.7 11.4 - - - +
319D GLU 4.3 5.6 - - - +
320D THR* 4.2 6.5 - - + +
321D ASP* 2.9 28.5 + - - +
323D ARG* 1.3 77.2 - - - +
325D GLY* 1.3 60.5 + - - +
327D GLN* 3.4 31.5 - - - +
328D SER* 4.1 3.3 + - - -
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Residues in contact with GLY 325 (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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105D MET* 3.2 21.1 - - - +
128D VAL* 4.3 17.9 - - - -
130D LYS* 5.9 3.4 - - - -
320D THR* 5.4 1.1 - - - -
321D ASP 3.0 9.1 + - - -
322D GLY 2.9 8.9 + - - -
324D GLU* 1.3 77.1 - - - +
326D LEU* 1.3 63.0 + - - +
327D GLN 3.1 1.4 + - - -
328D SER* 3.4 8.4 + - - -
329D LEU* 3.2 16.5 + - - +
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Residues in contact with LEU 326 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A GLU* 5.9 1.8 - - - +
105D MET* 3.4 11.6 - - - -
109D TRP* 3.5 26.4 - - + -
112D GLY* 3.6 31.4 - - - +
113D LYS* 4.0 16.4 - - + +
116D VAL* 3.9 21.5 - - + -
322D GLY 2.9 14.3 + - - +
323D ARG* 3.2 19.9 + - + +
325D GLY* 1.3 75.2 - - - +
327D GLN* 1.3 58.4 + - - +
328D SER 3.4 0.2 - - - -
329D LEU* 3.6 5.4 - - + -
330D ALA* 2.9 29.8 + - - +
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Residues in contact with GLN 327 (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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218A GLU* 3.8 21.7 + - - +
133D ARG* 5.7 2.5 - - - +
194D ASP* 5.8 1.3 - - - +
197D ASP* 2.6 41.9 - - + +
323D ARG 3.5 9.0 + - - +
324D GLU* 3.4 30.6 + - - +
325D GLY 3.1 0.6 - - - -
326D LEU* 1.3 79.5 - - - +
328D SER* 1.3 64.1 + - - +
330D ALA* 3.5 6.2 + - - +
331D LEU* 3.3 22.2 + - - +
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Residues in contact with SER 328 (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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130D LYS* 4.2 16.1 + - - +
190D SER 4.9 3.8 - - - -
193D VAL* 4.6 4.9 - - - -
194D ASP* 4.1 36.6 + - - +
197D ASP* 6.0 1.3 - - - -
324D GLU 4.1 1.4 + - - -
325D GLY* 3.4 11.3 + - - -
327D GLN* 1.3 81.5 - - - +
329D LEU* 1.3 66.4 + - - +
331D LEU* 3.6 8.2 - - - +
332D LEU* 2.9 34.2 + - - +
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Residues in contact with LEU 329 (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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104D PRO* 5.1 2.9 - - + -
105D MET* 4.1 8.1 - - + -
106D ALA* 3.5 35.2 - - + +
107D THR 4.8 4.0 - - - -
108D ARG 3.9 7.6 - - - +
109D TRP* 4.1 16.2 - - + -
112D GLY* 3.7 30.3 - - - -
186D MET* 4.7 9.2 - - + -
325D GLY 3.2 15.1 + - - +
326D LEU* 3.8 9.2 - - + +
327D GLN 3.3 0.4 - - - -
328D SER* 1.3 82.8 + - - +
330D ALA* 1.3 56.8 + - - +
332D LEU* 3.5 16.6 + - + +
333D THR* 2.9 38.3 + - - +
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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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109D TRP* 3.6 20.1 - - + -
326D LEU 2.9 18.2 + - - +
327D GLN* 3.7 9.2 - - - +
328D SER 3.2 0.2 - - - -
329D LEU* 1.3 73.1 - - - +
331D LEU* 1.3 63.9 + - - +
333D THR 3.1 1.2 + - - -
334D ALA* 3.0 22.9 + - - +
347D LEU* 4.3 13.0 - - + -
348D PRO* 6.3 0.4 - - + -
349D LEU* 3.5 25.0 - - + +
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Residues in contact with LEU 331 (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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193D VAL* 3.7 29.4 - - + +
196D LEU* 3.9 28.7 - - + -
197D ASP* 4.3 13.5 - - + +
203D VAL* 4.1 22.2 - - + -
206D VAL* 3.7 27.1 - - + -
227D LEU* 4.7 0.2 - - + -
327D GLN 3.3 10.8 + - - +
328D SER* 3.6 8.7 - - - +
330D ALA* 1.3 77.8 - - - +
332D LEU* 1.3 51.2 + - - +
334D ALA* 3.3 5.8 + - - +
335D ILE* 2.8 44.5 + - + +
347D LEU* 4.4 11.1 - - + +
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Residues in contact with LEU 332 (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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104D PRO* 4.8 5.8 - - + -
185D PHE* 3.3 37.9 - - + +
186D MET* 3.6 41.5 - - + +
190D SER* 4.4 13.7 - - - -
193D VAL* 4.0 19.5 - - + +
328D SER* 2.9 29.3 + - - +
329D LEU* 3.5 13.5 - - + +
331D LEU* 1.3 75.1 - - - +
333D THR* 1.3 57.3 + - - +
335D ILE* 3.3 7.0 + - + +
336D TYR* 2.9 35.5 + - + +
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Residues in contact with THR 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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107D THR 5.6 1.2 + - - -
109D TRP* 3.5 27.0 + - + +
186D MET* 5.7 3.3 - - - +
329D LEU* 2.9 25.6 + - - +
330D ALA 3.1 5.8 + - - -
332D LEU* 1.3 76.4 - - - +
334D ALA* 1.3 52.6 + - - +
336D TYR* 3.3 6.0 + - - +
337D ARG* 2.7 73.0 + - + +
349D LEU* 3.5 18.4 - - + -
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Residues in contact with ALA 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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206D VAL* 3.5 15.9 - - + +
330D ALA 3.0 12.0 + - - +
331D LEU* 3.5 9.0 - - - +
333D THR* 1.3 75.3 - - - +
335D ILE* 1.3 65.3 + - - +
337D ARG* 4.4 1.3 - - - -
338D SER* 3.0 25.6 + - - -
345D ILE* 3.5 31.9 - - + +
347D LEU* 3.9 18.4 - - + -
349D LEU* 4.5 2.0 - - + -
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Residues in contact with ILE 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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185D PHE* 3.9 40.8 - - + -
193D VAL* 4.5 14.1 - - + -
196D LEU* 5.4 0.7 - - + -
206D VAL* 4.0 15.7 - - + -
208D ALA* 3.6 18.5 - - + +
210D THR* 4.7 4.9 - - + -
225D ALA* 4.0 17.9 - - + -
227D LEU* 5.4 1.3 - - + -
237D ILE* 4.6 5.2 - - + -
331D LEU* 2.8 30.0 + - + +
332D LEU* 3.6 9.6 - - - +
334D ALA* 1.3 77.6 - - - +
336D TYR* 1.3 69.0 + - + +
338D SER* 3.1 2.8 + - - -
339D ALA* 2.9 27.5 + - - +
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Residues in contact with TYR 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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178D TRP* 3.9 27.1 - + + -
182D GLY* 4.6 0.9 - - - -
183D GLY 3.0 17.0 + - - -
185D PHE* 3.8 17.7 - + + -
186D MET* 3.2 47.3 + - + +
210D THR* 5.1 5.8 - - + -
220D GLU* 2.5 39.6 + - - -
332D LEU* 2.9 21.8 + - + +
333D THR* 3.8 5.8 - - - +
335D ILE* 1.3 79.9 - - + +
337D ARG* 1.3 61.9 + - + +
339D ALA* 4.0 3.8 - - + +
340D ARG* 3.0 25.5 + - - +
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Residues in contact with ARG 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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109D TRP* 3.9 21.4 - - - +
333D THR* 2.7 53.1 + - + +
334D ALA* 4.0 1.1 - - - +
335D ILE 3.3 0.2 - - - -
336D TYR* 1.3 73.4 - - + +
338D SER* 1.3 58.8 + - - +
340D ARG* 3.6 19.2 - - - +
341D ASP* 2.8 42.9 + - - +
345D ILE* 3.8 26.4 - - + +
349D LEU* 3.9 22.4 - - - +
350D ASP* 5.1 7.9 + - - +
350H ASP* 4.5 18.6 + - - +
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Residues in contact with SER 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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206D VAL* 4.3 7.0 - - - -
207D TYR* 3.3 7.3 - - - -
208D ALA 2.9 28.3 + - - +
334D ALA 3.0 19.2 + - - -
335D ILE 3.6 3.1 - - - -
337D ARG* 1.3 75.3 - - - +
339D ALA* 1.3 59.0 + - - +
342D GLY* 2.8 33.3 + - - +
343D VAL 2.8 22.7 + - - +
345D ILE* 3.5 12.6 - - - -
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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
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228C ARG* 5.6 4.0 + - - -
208D ALA* 3.3 16.7 + - + +
209D TYR* 4.5 2.0 - - - +
210D THR* 3.2 47.3 + - + +
335D ILE 2.9 17.0 + - - +
336D TYR* 4.0 5.8 - - - +
338D SER* 1.3 75.2 + - - +
340D ARG* 1.3 63.7 + - - +
342D GLY* 4.2 3.3 + - - -
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Residues in contact with ARG 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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336D TYR 3.0 19.1 + - - +
337D ARG* 3.6 18.3 + - - +
339D ALA* 1.3 80.0 - - - +
341D ASP* 1.3 86.4 + - - +
342D GLY 3.5 0.2 - - - -
204H GLU* 5.8 0.5 - - - +
230H ARG* 6.3 0.4 - - - +
344H ARG* 4.5 5.2 + - - -
346H PRO* 3.4 35.3 - - + +
347H LEU 3.8 16.4 - - - +
348H PRO* 2.8 34.3 + - + +
349H LEU* 4.0 1.4 - - - +
350H ASP* 3.2 44.2 + - - +
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Residues in contact with ASP 341 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337D ARG* 2.8 31.5 + - - +
338D SER 3.0 0.2 + - - -
340D ARG* 1.3 109.1 + - - +
342D GLY* 1.3 61.6 + - - +
343D VAL* 3.5 22.5 + - + +
345D ILE* 4.5 5.0 - - - +
344H ARG* 4.2 15.5 + - - -
346H PRO* 3.4 17.5 - - + +
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Residues in contact with GLY 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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344C ARG* 4.4 16.5 + - - +
207D TYR* 3.6 27.5 + - - -
208D ALA 5.7 0.2 - - - -
338D SER 2.8 13.3 + - - -
339D ALA 4.2 2.7 + - - -
340D ARG 3.5 1.8 - - - -
341D ASP* 1.3 77.9 - - - +
343D VAL* 1.3 61.1 + - - +
344H ARG* 5.3 4.7 - - - -
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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) + - + + + + + -
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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