Contacts of the helix formed by residues 171 - 192 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169C ASP* 3.1 11.2 - - - +
170C VAL* 1.3 87.2 - - - +
172C GLU* 1.3 55.3 + - - +
173C LYS* 2.9 9.0 - - + +
174C TRP* 2.7 68.3 + - + +
175C ALA 3.0 8.3 + - - -
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Residues in contact with GLU 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170C VAL 4.1 1.0 + - - -
171C PRO* 1.3 70.3 - - - +
173C LYS* 1.3 59.5 + - + +
174C TRP 3.4 0.2 - - - -
175C ALA* 3.5 1.7 - - - +
176C ARG* 3.2 29.8 + - - +
272C LEU* 3.9 27.3 - - + +
305C ILE* 3.9 8.7 - - - +
306C SER* 2.4 49.8 + - - -
309C ALA* 3.6 9.2 - - - +
337C PHE* 3.6 27.4 - - + -
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Residues in contact with LYS 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171C PRO* 2.8 6.9 + - + +
172C GLU* 1.3 78.3 - - + +
174C TRP* 1.3 68.3 + - + +
176C ARG* 3.7 38.3 + - - +
177C PHE* 3.7 12.8 + - - +
340C ASN* 5.7 0.6 - - - +
341C ASP* 5.8 1.0 + - - -
342C GLN* 4.0 20.6 + - - +
343C TRP* 5.0 3.1 + - - -
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Residues in contact with TRP 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164C LEU* 5.2 1.3 - - + -
168C TYR* 3.1 46.4 - + - -
169C ASP 4.8 0.7 - - - -
170C VAL* 3.3 29.8 - - + -
171C PRO* 2.7 50.4 + - + +
173C LYS* 1.3 74.3 - - + +
175C ALA* 1.3 55.9 + - - +
177C PHE* 2.7 33.6 + - - +
178C TYR* 2.9 12.0 + - + +
354C PRO* 3.3 51.4 + - + +
355C VAL* 3.6 7.2 - - + -
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Residues in contact with ALA 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C VAL* 3.4 11.6 - - + +
171C PRO 3.0 4.4 + - - -
172C GLU* 3.5 12.1 - - - +
173C LYS 3.3 0.2 - - - -
174C TRP* 1.3 73.9 - - - +
176C ARG* 1.3 66.5 + - - +
179C THR* 2.9 31.5 + - - -
268C LEU* 4.2 10.8 - - + -
271C MET* 3.8 16.2 - - - -
272C LEU* 3.6 28.9 - - + -
337C PHE* 4.4 2.5 - - + -
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Residues in contact with ARG 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172C GLU* 3.2 12.7 + - - +
173C LYS* 3.7 42.1 + - - +
174C TRP 3.3 0.2 - - - -
175C ALA* 1.3 79.0 - - - +
177C PHE* 1.3 56.5 + - - +
179C THR* 4.7 0.2 - - - -
180C ALA* 2.9 28.9 + - - +
337C PHE* 2.8 58.8 + - + +
338C PHE* 3.3 16.3 - - + -
339C LYS 3.5 10.3 + - - -
340C ASN* 2.9 36.2 - - - +
342C GLN* 3.5 21.8 + - - +
343C TRP* 3.5 5.5 - - + +
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Residues in contact with PHE 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173C LYS 3.7 7.3 + - - +
174C TRP* 2.7 16.2 + - + +
176C ARG* 1.3 77.3 - - - +
178C TYR* 1.3 87.0 + + - -
180C ALA* 3.1 5.8 + - - +
181C GLU* 3.0 46.7 + - - +
210C GLY 4.4 2.7 - - - -
211C HIS* 3.4 20.0 - + - -
343C TRP* 4.1 17.0 - + + +
348C LEU* 3.3 40.4 - - + -
351C THR* 3.9 7.6 - - - -
352C VAL 4.5 3.6 - - - -
353C ALA* 4.1 2.7 - - - -
354C PRO* 3.1 42.0 - - + -
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Residues in contact with TYR 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161C LEU* 3.8 21.1 - - + -
164C LEU* 3.1 43.8 - - + +
170C VAL* 4.0 10.3 - - + -
174C TRP* 2.9 14.8 + - + +
175C ALA 4.1 1.1 - - - +
177C PHE* 1.3 101.4 - + - +
179C THR* 1.3 66.4 + - - +
181C GLU* 2.9 10.3 + - - +
182C VAL* 2.9 27.8 + - - +
206C LEU* 3.9 16.2 - - + +
210C GLY 4.5 8.2 + - - -
212C LEU* 5.5 2.7 - - + -
267C PHE* 4.4 1.8 - - + -
271C MET* 3.3 35.9 - - + -
354C PRO* 3.6 21.2 - - + +
355C VAL* 4.2 6.1 + - - +
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Residues in contact with THR 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175C ALA 2.9 19.4 + - - -
176C ARG* 4.4 2.9 - - - -
178C TYR* 1.3 76.4 - - - +
180C ALA* 1.3 51.6 + - - +
182C VAL* 3.5 8.4 + - - +
183C VAL* 2.7 44.1 + - + +
264C VAL* 4.0 22.4 - - + -
267C PHE* 4.5 8.0 - - + -
268C LEU* 3.5 37.5 - - + +
271C MET* 4.4 6.2 - - - -
312C LEU* 5.1 6.7 - - + -
316C PHE* 5.9 0.4 - - + -
337C PHE* 5.0 1.3 - - + -
338C PHE* 4.3 10.8 - - + -
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Residues in contact with ALA 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176C ARG 2.9 23.3 + - - +
177C PHE 3.1 6.9 + - - +
178C TYR 3.0 0.8 - - - -
179C THR* 1.3 76.0 - - - +
181C GLU* 1.3 64.2 + - - +
183C VAL* 2.9 6.6 + - - +
184C LEU* 2.9 23.4 + - - +
338C PHE* 3.8 12.1 - - + -
343C TRP* 3.7 20.0 - - + -
345C TRP* 3.9 7.7 - - + -
348C LEU* 3.4 18.4 - - + -
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Residues in contact with GLU 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C TRP* 2.8 36.2 - - + -
177C PHE* 3.0 32.0 + - + +
178C TYR* 2.9 7.5 + - - +
180C ALA* 1.3 78.7 - - - +
182C VAL* 1.3 53.1 + - - +
184C LEU* 3.0 5.7 + - - +
185C ALA* 2.7 36.4 + - - +
211C HIS* 2.9 28.9 - - - -
212C LEU* 3.4 35.7 + - + +
348C LEU* 3.2 23.1 - - + -
349C ARG* 4.0 3.8 - - - +
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Residues in contact with VAL 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178C TYR 2.9 14.3 + - - +
179C THR* 3.7 9.9 - - - +
181C GLU* 1.3 74.8 - - - +
183C VAL* 1.3 63.5 + - - +
185C ALA* 4.0 2.6 - - - +
186C LEU* 3.1 45.3 + - + +
199C VAL* 4.6 0.9 - - + -
204C MET* 3.5 24.9 - - + -
212C LEU* 3.5 24.0 - - + -
214C LEU* 5.4 4.5 - - + -
264C VAL* 4.3 12.3 - - + -
267C PHE* 3.4 33.2 - - + -
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Residues in contact with VAL 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179C THR* 2.7 32.1 + - + +
180C ALA* 2.9 11.0 + - - +
182C VAL* 1.3 76.7 - - - +
184C LEU* 1.3 63.7 + - + +
187C ASP* 3.4 18.0 + - - +
261C TRP* 3.7 31.5 - - + -
264C VAL* 4.0 22.7 - - + -
316C PHE* 5.4 6.5 - - + -
338C PHE* 4.2 19.1 - - + -
345C TRP* 5.9 2.9 - - + -
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Residues in contact with LEU 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C TRP* 3.2 41.2 - - + +
180C ALA 2.9 17.1 + - - +
181C GLU 3.0 4.7 + - - +
183C VAL* 1.3 79.4 - - + +
185C ALA* 1.3 67.9 + - - +
187C ASP* 3.0 16.6 + - - +
188C ALA* 3.2 10.2 + - - +
345C TRP* 4.4 31.2 - - + +
348C LEU* 3.6 29.4 - - + -
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Residues in contact with ALA 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C TRP* 3.5 44.7 - - + +
136C VAL* 5.1 1.4 - - - +
181C GLU 2.7 19.3 + - - +
182C VAL 4.0 2.7 - - - +
184C LEU* 1.3 72.4 - - - +
186C LEU* 1.3 63.7 + - - +
188C ALA* 3.0 20.3 - - - +
189C ILE* 3.4 9.3 + - - +
212C LEU* 4.5 4.9 - - + -
214C LEU* 4.3 20.6 - - + -
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Residues in contact with LEU 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182C VAL* 3.1 43.1 + - + +
183C VAL 4.0 3.8 - - - +
185C ALA* 1.3 77.3 - - - +
187C ASP* 1.3 61.9 - - - +
189C ILE* 2.9 20.7 + - + +
190C HIS* 2.7 38.3 + - + +
196C HIS* 4.3 10.5 - - + -
199C VAL* 3.9 26.7 - - + -
214C LEU* 4.6 13.7 - - + -
260C ASP* 3.9 16.6 - - + +
261C TRP* 4.1 6.3 - - + -
264C VAL* 3.7 21.8 - - + -
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Residues in contact with ASP 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183C VAL 3.4 11.5 + - - +
184C LEU* 3.0 11.3 + - - +
186C LEU* 1.3 77.2 - - - +
188C ALA* 1.3 58.1 + - - +
190C HIS* 3.1 20.1 - - + +
191C SER* 2.7 42.7 + - - -
261C TRP* 4.4 9.1 - - + -
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Residues in contact with ALA 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133C SER* 4.6 17.9 - - - +
135C TRP* 4.7 7.0 - - + -
136C VAL* 5.0 7.2 - - + -
184C LEU 3.2 7.5 + - - +
185C ALA* 3.0 20.1 + - - +
186C LEU 3.0 0.2 - - - -
187C ASP* 1.3 78.7 - - - +
189C ILE* 1.3 60.0 + - - +
191C SER* 3.2 7.3 + - - -
192C MET* 3.1 28.8 + - + +
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Residues in contact with ILE 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127C ILE* 4.1 9.4 - - + -
136C VAL* 4.3 10.8 - - + -
185C ALA 3.9 11.2 - - - +
186C LEU* 2.9 14.0 + - + +
188C ALA* 1.3 74.6 - - - +
190C HIS* 1.3 59.9 + - + +
192C MET* 2.7 50.3 + - + +
194C PHE* 3.1 45.6 + - + +
195C ILE 4.4 0.2 - - - +
196C HIS* 4.5 15.7 - - + +
214C LEU* 4.6 8.5 - - + -
217C PHE* 3.5 32.5 - - + -
220C CYS* 5.3 1.1 - - - -
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Residues in contact with HIS 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186C LEU* 2.7 46.4 + - + +
187C ASP* 3.1 19.1 - - - +
189C ILE* 1.3 76.1 - - + +
191C SER* 1.3 53.9 + - - +
193C GLY* 2.5 28.4 + - - -
194C PHE 3.2 15.8 + - - -
195C ILE* 4.8 0.6 - - - -
196C HIS 5.2 0.4 - - - -
223C MET* 4.2 3.8 - - - +
257C ARG* 4.1 50.0 + - - +
260C ASP* 3.7 35.1 + - + +
261C TRP* 3.6 22.9 - + - -
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Residues in contact with SER 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187C ASP* 2.7 32.5 + - - -
188C ALA* 3.5 7.0 - - - -
190C HIS* 1.3 75.2 - - - +
192C MET* 1.3 59.3 + - - +
193C GLY* 3.1 1.4 + - - -
257C ARG* 5.2 4.3 - - - +
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Residues in contact with MET 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127C ILE* 3.8 25.6 - - + +
130C PHE 5.5 0.7 - - - +
131C ALA* 4.0 31.4 - - + +
136C VAL* 5.2 1.8 - - + -
188C ALA* 3.1 11.8 + - + +
189C ILE* 2.7 44.9 + - + +
191C SER* 1.3 77.3 - - - +
193C GLY* 1.3 58.6 + - - +
194C PHE* 3.2 22.6 - - + -
222C LYS* 3.8 8.7 + - - -
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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