Contacts of the helix formed by residues 171 - 192 (chain D) in PDB entry 3NDM
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 PRO 171 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169D ASP 3.7 4.7 - - - +
170D VAL* 1.3 89.9 - - - +
172D GLU* 1.3 56.6 + - - +
173D LYS* 4.5 5.8 - - + +
174D TRP* 2.8 73.1 + - + +
175D ALA 3.0 9.2 + - - -
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Residues in contact with GLU 172 (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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170D VAL* 4.0 1.6 + - - +
171D PRO* 1.3 69.1 - - - +
173D LYS* 1.3 61.8 + - - +
175D ALA* 3.2 8.9 + - - +
176D ARG* 3.0 31.0 + - - +
272D LEU* 4.4 17.4 - - - +
304D ASP 4.6 4.0 - - - +
305D ILE* 4.4 6.9 - - - +
306D SER* 3.1 41.4 + - - +
309D ALA* 3.6 16.1 - - - +
337D PHE* 4.1 13.2 - - + -
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Residues in contact with LYS 173 (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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171D PRO* 3.0 7.0 + - + +
172D GLU* 1.3 73.6 - - + +
174D TRP* 1.3 74.4 + - + +
176D ARG* 3.0 38.5 + - - +
177D PHE* 3.0 12.7 + - - +
341D ASP* 5.4 0.4 + - - -
342D GLN* 3.2 34.7 + - + +
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Residues in contact with TRP 174 (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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164D LEU* 5.4 1.8 - - + -
168D TYR* 3.7 45.3 - + + -
170D VAL* 4.3 13.9 - - + -
171D PRO* 2.8 46.4 + - + +
173D LYS* 1.3 81.9 - - + +
175D ALA* 1.3 63.0 + - - +
177D PHE* 3.0 6.2 + - - +
178D TYR* 2.9 34.0 + + + +
354D PRO* 3.1 49.9 - - + +
355D VAL* 3.7 22.0 - - + -
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Residues in contact with ALA 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170D VAL* 3.6 23.3 - - + +
171D PRO 3.0 6.3 + - - +
172D GLU 3.5 9.4 - - - +
174D TRP* 1.3 75.7 - - - +
176D ARG* 1.3 65.0 - - - +
177D PHE 3.0 0.2 + - - -
178D TYR* 4.5 0.9 - - - +
179D THR* 2.7 33.3 + - - +
268D LEU* 4.7 4.5 - - + -
271D MET* 4.2 17.7 - - - -
272D LEU* 4.2 18.8 - - + -
337D PHE* 4.6 2.2 - - + -
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Residues in contact with ARG 176 (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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172D GLU* 3.0 19.0 + - - +
173D LYS* 3.0 39.9 + - - +
175D ALA* 1.3 75.2 - - - +
177D PHE* 1.3 55.8 + - - +
179D THR* 3.9 0.3 - - - -
180D ALA* 2.9 32.1 + - - +
337D PHE* 2.9 47.0 + - + +
338D PHE* 3.2 38.2 - - + -
339D LYS 4.0 4.6 + - - -
340D ASN* 3.6 12.6 - - - +
342D GLN* 3.1 26.2 + - - +
343D TRP* 4.1 9.8 - - + +
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Residues in contact with PHE 177 (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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173D LYS 3.0 10.7 + - - +
174D TRP 3.1 7.4 - - - +
175D ALA 3.0 0.8 - - - -
176D ARG* 1.3 75.0 - - - +
178D TYR* 1.3 98.9 + + - +
180D ALA* 3.2 3.8 + - - +
181D GLU* 2.7 53.3 + - - +
210D GLY 4.4 1.3 - - - -
211D HIS* 4.1 11.2 - + - -
343D TRP* 4.0 19.7 - + + +
348D LEU* 3.5 30.0 - - + +
351D THR* 4.5 5.2 - - - -
352D VAL 4.6 1.8 - - - -
353D ALA* 3.8 15.7 - - + -
354D PRO* 2.9 44.6 - - + -
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Residues in contact with TYR 178 (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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161D LEU* 3.8 15.9 - - + -
164D LEU* 2.7 50.9 - - + +
170D VAL* 5.2 3.4 - - + -
174D TRP* 2.9 26.7 + + - +
177D PHE* 1.3 104.2 - + - +
179D THR* 1.3 64.8 + - - +
181D GLU* 3.0 9.0 + - - +
182D VAL* 2.9 29.3 + - - +
206D LEU* 4.3 13.8 - - + +
210D GLY 4.3 11.7 + - - -
212D LEU* 5.0 3.6 - - + -
271D MET* 3.5 29.2 - - + -
354D PRO* 4.5 8.7 - - + -
355D VAL* 3.5 19.6 + - - +
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Residues in contact with THR 179 (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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175D ALA 2.7 29.5 + - - -
176D ARG 3.9 2.9 - - - -
178D TYR* 1.3 72.6 - - - +
180D ALA* 1.3 62.0 + - - +
182D VAL* 3.3 7.6 + - - +
183D VAL* 2.9 38.1 + - + +
264D VAL* 5.0 9.2 - - + -
267D PHE* 5.1 6.3 - - + -
268D LEU* 4.0 19.6 + - + +
271D MET* 3.7 16.4 - - - +
312D LEU* 4.6 10.1 - - + -
337D PHE* 4.1 17.9 - - + -
338D PHE* 4.4 6.7 - - + -
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Residues in contact with ALA 180 (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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176D ARG 2.9 22.2 + - - +
177D PHE 3.5 1.6 - - - +
178D TYR 3.2 0.2 - - - -
179D THR* 1.3 75.0 - - - +
181D GLU* 1.3 64.0 + - - +
183D VAL* 3.0 5.5 + - - +
184D LEU* 3.0 24.4 + - - +
338D PHE* 3.8 11.0 - - + -
343D TRP* 3.4 29.4 - - + -
345D TRP* 3.5 12.4 - - + -
348D LEU* 3.4 12.8 - - + -
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Residues in contact with GLU 181 (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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135D TRP* 2.8 34.0 - - + -
177D PHE* 2.7 47.9 + - + +
178D TYR* 3.4 9.3 - - - +
180D ALA* 1.3 74.3 - - - +
182D VAL* 1.3 56.6 + - - +
184D LEU* 3.2 3.4 + - - +
185D ALA* 2.8 30.7 + - - +
211D HIS* 3.4 19.5 - - - +
212D LEU* 3.1 42.1 + - + +
348D LEU* 3.5 20.4 - - + +
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Residues in contact with VAL 182 (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 TYR 2.9 15.3 + - - +
179D THR* 3.7 4.9 - - - +
181D GLU* 1.3 73.2 - - - +
183D VAL* 1.3 63.6 + - + +
185D ALA* 4.2 6.2 - - - +
186D LEU* 3.2 40.8 + - + +
199D VAL* 4.7 3.1 - - + -
204D MET* 3.6 21.3 - - + -
212D LEU* 3.2 30.1 - - + -
214D LEU* 5.3 5.8 - - + -
264D VAL* 5.0 8.5 - - + -
267D PHE* 3.3 27.4 - - + -
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Residues in contact with VAL 183 (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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179D THR* 2.9 32.6 + - + +
180D ALA* 3.0 8.0 + - - +
182D VAL* 1.3 78.2 - - + +
184D LEU* 1.3 59.9 + - - +
187D ASP* 3.5 10.9 + - - +
261D TRP* 3.5 34.3 - - + -
264D VAL* 4.8 12.1 - - + -
316D PHE* 5.6 0.9 - - + -
329D VAL* 4.9 4.6 - - + +
332D ILE* 3.9 27.8 - - + -
333D LYS* 4.7 17.3 - - - -
338D PHE* 3.9 18.6 - - + -
345D TRP* 4.6 4.0 - - + -
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Residues in contact with LEU 184 (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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135D TRP* 3.3 41.0 - - + +
180D ALA 3.0 12.0 + - - +
181D GLU 3.2 6.5 + - - +
183D VAL* 1.3 75.4 - - - +
185D ALA* 1.3 66.0 + - - +
186D LEU 3.2 1.3 - - - -
187D ASP* 3.2 17.0 + - + +
188D ALA* 3.2 9.0 + - - +
329D VAL* 6.3 0.2 - - + -
333D LYS* 2.7 39.7 - - - +
345D TRP* 4.0 27.6 - - + +
348D LEU* 4.1 16.4 - - + -
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Residues in contact with ALA 185 (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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135D TRP* 3.5 41.4 - - + +
136D VAL* 5.1 0.7 - - - +
181D GLU 2.8 20.7 + - - +
182D VAL* 4.2 6.5 - - - +
184D LEU* 1.3 71.3 - - - +
186D LEU* 1.3 63.3 + - - +
188D ALA* 3.0 18.4 - - - +
189D ILE* 3.2 12.2 - - - +
212D LEU* 4.7 5.6 - - + -
214D LEU* 4.0 18.8 - - + -
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Residues in contact with LEU 186 (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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182D VAL* 3.2 31.5 + - + +
184D LEU 3.2 1.0 - - - -
185D ALA* 1.3 74.9 - - - +
187D ASP* 1.3 59.2 + - - +
188D ALA 3.0 2.0 - - - -
189D ILE* 2.8 27.6 + - + +
190D HIS* 2.9 38.3 + - + +
196D HIS* 3.9 25.4 - - + +
199D VAL* 4.0 21.8 - - + -
214D LEU* 4.2 15.5 - - + -
260D ASP* 4.0 16.8 - - + +
261D TRP* 4.1 22.2 - - + -
264D VAL* 4.2 3.4 - - + -
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Residues in contact with ASP 187 (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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183D VAL 3.5 12.8 + - - +
184D LEU* 3.2 13.7 + - + +
186D LEU* 1.3 73.2 - - - +
188D ALA* 1.3 60.5 + - - +
190D HIS* 3.8 16.0 - - + +
191D SER* 2.5 36.9 + - - -
261D TRP* 4.4 2.4 - - + -
329D VAL* 3.8 38.4 - - + +
333D LYS* 6.0 0.3 + - - -
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Residues in contact with ALA 188 (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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133D SER* 4.7 9.4 - - - +
135D TRP* 4.4 18.4 - - + -
136D VAL* 5.3 3.1 - - + -
184D LEU 3.2 10.1 + - - +
185D ALA* 3.0 15.0 - - - +
187D ASP* 1.3 78.9 - - - +
189D ILE* 1.3 65.6 + - + +
191D SER* 3.1 7.1 + - - -
192D MET* 3.1 28.6 + - + +
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Residues in contact with ILE 189 (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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127D ILE* 4.3 9.2 - - + -
136D VAL* 3.9 17.3 - - + -
185D ALA 3.2 17.3 - - - +
186D LEU* 2.8 12.5 + - + +
188D ALA* 1.3 72.6 - - + +
190D HIS* 1.3 66.8 + - - +
192D MET* 2.9 31.3 + - + +
194D PHE* 3.1 41.8 + - + +
196D HIS* 5.0 14.1 - - + +
214D LEU* 4.0 11.9 - - + -
217D PHE* 3.9 30.1 - - + -
220D CYS* 5.5 0.9 - - - -
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Residues in contact with HIS 190 (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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186D LEU* 2.9 32.7 + - + +
187D ASP* 3.9 11.2 - - - +
189D ILE* 1.3 74.1 - - + +
191D SER* 1.3 55.6 + - - +
193D GLY* 2.7 26.0 + - - -
194D PHE 3.2 16.6 + - - -
195D ILE* 4.3 1.9 - - - -
196D HIS 4.6 0.7 - - - -
223D MET* 4.4 2.1 - - - +
257D ARG* 2.8 51.5 + - + +
260D ASP* 3.1 41.2 - - + +
261D TRP* 4.0 30.1 - + - -
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Residues in contact with SER 191 (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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187D ASP* 2.5 35.7 + - - -
188D ALA* 3.2 8.0 - - - -
190D HIS* 1.3 75.0 - - - +
192D MET* 1.3 57.6 + - - +
193D GLY* 3.0 3.7 + - - -
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Residues in contact with MET 192 (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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127D ILE* 4.5 18.2 - - + -
130D PHE* 6.4 0.2 - - - -
131D ALA* 4.0 37.9 - - + +
136D VAL* 4.9 2.9 - - + -
188D ALA* 3.1 11.8 + - + +
189D ILE* 2.9 60.9 + - + +
191D SER* 1.3 76.0 - - - +
193D GLY* 1.3 60.8 + - - +
194D PHE* 3.6 18.7 - - + +
222D LYS* 4.5 5.7 - - - -
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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
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Atomic class I II III IV V VI VII VIII
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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