Contacts of the helix formed by residues 336 - 358 (chain D) in PDB entry 1ML3
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 GLU 336 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A VAL* 5.1 5.2 - - - +
12D ARG* 2.9 42.2 + - + +
13D ILE* 4.0 9.9 - - + +
16D MET* 4.4 10.0 - - + +
55D VAL* 4.1 2.0 - - - +
56D HIS* 2.4 36.1 + - - +
253D PRO 4.2 9.2 - - - +
254D ASP* 3.1 22.1 - - - +
334D ASP* 2.8 8.5 + - - +
335D ASN* 1.3 83.6 + - - +
337D TRP* 1.3 57.8 + - - +
338D GLY 3.6 0.4 - - - -
340D SER* 2.8 37.6 + - - -
1361D NAD 4.0 13.2 + - - +
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Residues in contact with TRP 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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16D MET* 3.6 27.1 - - + -
19D GLN* 3.0 41.5 - - + -
23D GLU* 3.4 28.2 + - - -
56D HIS* 3.6 20.4 - + + -
303D ASN* 3.2 54.5 + - + -
304D ASP 3.3 13.0 - - - -
305D ASN* 3.7 5.2 + - - +
334D ASP* 2.9 29.9 + - + +
336D GLU* 1.3 72.1 - - - +
338D GLY* 1.3 65.0 + - - +
340D SER* 3.3 3.2 + - - -
341D HIS* 3.0 55.1 + + - -
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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
----------------------------------------------------------
304D ASP 3.8 7.0 + - - -
305D ASN 3.7 8.5 - - - -
306D ARG 3.5 23.8 - - - -
307D SER* 5.1 2.7 - - - -
333D TYR* 6.4 0.4 - - - -
334D ASP* 3.0 12.6 + - - -
337D TRP* 1.3 76.7 - - - +
339D TYR* 1.3 63.4 + - - +
341D HIS* 3.1 6.9 + - - +
342D ARG* 3.1 28.5 + - - +
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Residues in contact with TYR 339 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D ILE* 4.3 7.4 - - + -
134D SER* 2.9 37.9 - - - -
135D ALA 3.1 0.7 + - - -
163D ASN* 3.4 30.5 - - - +
164D ALA 2.7 29.6 + - - -
165D SER 3.5 26.9 - - - -
166D CYS* 3.7 8.1 - - + -
169D ASN* 3.5 9.4 - - + -
307D SER* 5.7 0.6 - - - +
334D ASP 4.1 3.2 + - - -
335D ASN* 3.6 20.2 - - - +
336D GLU 3.9 1.0 + - - +
337D TRP 3.4 0.2 - - - -
338D GLY* 1.3 74.2 - - - +
340D SER* 1.3 63.7 + - - +
342D ARG* 3.1 10.3 + - - +
343D VAL* 3.0 38.0 + - + +
1361D NAD 3.4 17.5 - + + -
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Residues in contact with SER 340 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D ILE* 3.7 15.2 + - - +
16D MET* 3.2 40.2 - - - +
17D VAL* 3.6 14.1 + - - +
20D ALA* 4.6 0.9 - - - -
336D GLU 2.8 23.8 + - - -
337D TRP* 3.7 5.4 - - - -
338D GLY 3.2 0.4 - - - -
339D TYR* 1.3 78.1 - - - +
341D HIS* 1.3 63.5 + - - +
343D VAL* 3.4 11.0 + - - +
344D VAL* 3.4 18.8 + - - +
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Residues in contact with HIS 341 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D MET 5.4 0.4 - - - -
20D ALA* 3.6 29.7 - - + +
23D GLU* 3.1 23.1 + - - -
24D ASP* 3.7 19.1 + - - -
305D ASN* 3.7 20.9 + - + +
337D TRP* 3.0 57.8 + + - -
338D GLY 3.1 8.8 + - - +
340D SER* 1.3 75.5 - - - +
342D ARG* 1.3 76.3 + - - +
344D VAL* 3.4 4.4 + - - +
345D ASP* 2.8 35.2 + - - +
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Residues in contact with ARG 342 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146D MET* 3.9 16.7 - - + +
163D ASN* 3.8 14.8 - - - +
169D ASN* 4.0 14.6 - - - +
287D GLY 3.9 9.1 + - - -
288D ILE* 3.6 24.0 - - - +
305D ASN* 2.7 34.1 + - - +
306D ARG* 3.5 2.0 - - - +
307D SER* 2.9 44.9 + - - +
338D GLY 3.1 14.6 + - - +
339D TYR* 3.1 14.8 + - - +
341D HIS* 1.3 87.3 - - - +
343D VAL* 1.3 60.1 + - - +
345D ASP* 2.8 33.5 + - - +
346D LEU* 2.8 30.0 + - - +
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Residues in contact with VAL 343 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D ILE* 5.0 0.2 - - + -
17D VAL* 4.0 17.9 - - + -
108D ILE* 3.4 39.9 - - + -
132D VAL* 4.6 6.7 - - + -
134D SER* 4.5 9.6 - - - -
163D ASN* 3.5 26.7 - - + +
339D TYR* 3.0 33.0 + - + +
340D SER 3.6 7.9 - - - +
341D HIS 3.3 0.4 - - - -
342D ARG* 1.3 75.9 - - - +
344D VAL* 1.3 62.7 + - - +
346D LEU* 3.1 4.9 + - - +
347D VAL* 3.0 22.6 + - + +
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Residues in contact with VAL 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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17D VAL* 3.7 32.3 - - + +
20D ALA* 3.8 11.0 - - + -
21D LEU* 3.7 17.7 - - + -
24D ASP* 5.2 4.0 - - - +
26D LEU* 3.6 31.4 - - + -
31D ILE* 4.1 5.6 - - + -
108D ILE* 6.0 0.2 - - - -
340D SER 3.5 13.9 - - - +
341D HIS* 3.4 7.8 + - - +
342D ARG 3.3 0.2 - - - -
343D VAL* 1.3 77.2 - - - +
345D ASP* 1.3 65.8 + - - +
347D VAL* 3.2 8.1 + - - +
348D ARG* 3.0 30.2 + - + +
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Residues in contact with ASP 345 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D ASP* 5.7 1.0 - - - +
146D MET* 4.0 22.3 - - + +
288D ILE* 4.9 2.2 - - - +
341D HIS* 2.8 20.0 + - - +
342D ARG* 2.8 43.8 + - - +
344D VAL* 1.3 78.7 - - - +
346D LEU* 1.3 62.6 + - - +
348D ARG* 3.5 19.6 + - - +
349D HIS* 3.0 23.9 + - - +
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Residues in contact with LEU 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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132D VAL* 3.7 17.3 - - + -
144D LEU* 3.6 33.7 - - + -
146D MET* 3.7 19.7 - - + -
150D HIS* 4.7 3.8 - - + -
161D VAL* 4.4 9.4 - - + -
163D ASN* 3.3 41.1 - - + +
342D ARG 2.8 12.8 + - - +
343D VAL 3.4 9.4 - - - +
345D ASP* 1.3 75.1 - - - +
347D VAL* 1.3 65.9 + - - +
349D HIS* 3.2 7.2 + - + +
350D MET* 3.0 38.4 + - + +
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Residues in contact with VAL 347 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D ILE* 4.7 5.4 - - + -
5D VAL* 4.5 14.1 - - + -
31D ILE* 4.7 10.8 - - + -
106D TYR* 4.0 31.5 - - + -
108D ILE* 3.4 29.8 - - + -
132D VAL* 4.2 12.8 - - + -
343D VAL 3.0 15.9 + - - +
344D VAL* 3.2 8.3 + - - +
346D LEU* 1.3 74.6 - - - +
348D ARG* 1.3 60.6 + - - +
350D MET* 3.1 10.4 + - - +
351D ALA* 2.8 28.2 + - + +
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Residues in contact with ARG 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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26D LEU* 3.1 36.8 - - - +
30D GLU* 2.8 43.1 + - - +
31D ILE* 4.0 19.3 - - + -
344D VAL* 3.0 19.0 + - + +
345D ASP* 3.8 17.5 + - - +
347D VAL* 1.3 75.4 - - - +
349D HIS* 1.3 61.9 + - - +
351D ALA* 3.4 7.6 + - - +
352D SER* 3.2 23.0 + - - -
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Residues in contact with HIS 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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146D MET* 4.4 9.4 - - + -
150D HIS* 3.0 45.9 + - + -
151D HIS* 3.6 24.4 + + - -
153D TYR* 4.2 11.0 - - + -
345D ASP 3.0 18.1 + - - +
346D LEU* 3.2 11.0 + - + +
348D ARG* 1.3 77.3 - - - +
350D MET* 1.3 61.5 + - - +
352D SER* 2.8 23.6 + - - -
353D LYS* 3.1 44.0 + - + +
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Residues in contact with MET 350 (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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106D TYR* 4.2 7.4 - - + -
130D LYS* 4.2 24.7 - - + -
131D VAL 4.8 2.9 - - - +
132D VAL* 3.5 29.6 - - + -
153D TYR* 3.5 52.3 - - + +
158D HIS 4.8 0.2 - - - +
159D HIS 5.0 0.9 - - - +
161D VAL* 4.0 24.0 - - + -
346D LEU* 3.0 28.1 + - + +
347D VAL* 3.1 8.7 + - - +
349D HIS* 1.3 76.7 - - + +
351D ALA* 1.3 58.5 + - - +
353D LYS 3.4 0.3 + - - -
354D ASP* 2.8 37.7 + - - +
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Residues in contact with ALA 351 (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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3D ILE* 3.6 38.9 - - + +
106D TYR* 3.3 16.1 + - + +
347D VAL* 2.8 16.3 + - + +
348D ARG* 3.7 9.0 - - - +
349D HIS 3.3 0.2 - - - -
350D MET* 1.3 78.4 - - - +
352D SER* 1.3 59.7 + - - +
354D ASP* 3.9 1.6 - - - +
355D ARG* 3.3 26.2 + - - +
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Residues in contact with SER 352 (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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348D ARG 3.2 10.8 + - - -
349D HIS* 2.8 28.9 + - - -
351D ALA* 1.3 73.8 - - - +
353D LYS* 1.3 67.1 + - - +
355D ARG* 3.2 7.4 + - - +
356D SER* 3.0 26.2 + - - -
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Residues in contact with LYS 353 (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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151D HIS* 3.8 25.4 + - - -
153D TYR* 3.0 46.9 + - + +
155D PRO* 3.5 17.1 - - + +
349D HIS* 3.1 49.8 + - + +
352D SER* 1.3 83.9 + - - +
354D ASP* 1.3 57.0 + - - +
356D SER* 3.2 10.6 + - - +
357D ALA 2.9 24.8 + - - -
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Residues in contact with ASP 354 (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 GLU* 5.2 0.9 - - - +
106D TYR* 2.3 37.4 + - - +
130D LYS* 3.6 13.8 - - - +
153D TYR* 2.5 31.1 + - - -
155D PRO* 3.5 14.8 - - - +
350D MET 2.8 19.5 + - - +
351D ALA 3.9 3.1 - - - +
352D SER 3.2 0.2 - - - -
353D LYS* 1.3 77.2 - - - +
355D ARG* 1.3 74.9 + - - +
357D ALA* 3.5 2.1 + - - +
358D ARG* 3.2 37.9 + - - +
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Residues in contact with ARG 355 (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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3D ILE* 6.1 4.4 - - + +
105D GLU* 4.0 10.5 + - - -
106D TYR* 5.5 0.2 + - - -
351D ALA 3.3 13.5 + - - +
352D SER* 3.2 11.2 + - - +
354D ASP* 1.3 84.7 + - - +
356D SER* 1.3 67.1 + - - +
358D ARG* 2.8 84.0 + - - +
359D LEU* 3.4 17.4 + - + +
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Residues in contact with SER 356 (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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352D SER* 3.0 15.2 + - - -
353D LYS* 3.4 14.6 - - - -
355D ARG* 1.3 77.4 - - - +
357D ALA* 1.3 60.5 + - - +
359D LEU* 3.2 36.7 + - - +
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Residues in contact with ALA 357 (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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155D PRO* 3.5 33.7 - - + -
156D SER* 5.4 4.7 - - - +
353D LYS 2.9 8.1 + - - +
354D ASP 3.9 3.8 - - - +
356D SER* 1.3 76.8 - - - +
358D ARG* 1.3 63.0 + - + +
359D LEU 3.2 3.3 + - - -
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Residues in contact with ARG 358 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105D GLU* 3.9 8.3 + - - -
129D ARG* 3.1 57.2 - - - +
130D LYS* 5.6 5.1 - - - +
354D ASP* 3.2 19.1 + - - +
355D ARG* 2.8 62.1 + - - +
357D ALA* 1.3 78.7 - - + +
359D LEU* 1.3 67.2 + - - +
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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) + - + + + + + -
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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