Contacts of the helix formed by residues 171 - 192 (chain A) in PDB entry 4YVE
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A ASP 3.1 10.0 - - - +
170A VAL* 1.3 88.1 - - - +
172A GLU* 1.3 66.1 + - - +
173A LYS* 4.2 18.2 - - + +
174A TRP* 3.1 60.1 + - + +
175A ALA 3.1 8.8 + - - -
272A LEU* 4.5 0.2 - - - -
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Residues in contact with GLU 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A VAL 3.8 0.8 + - - -
171A PRO* 1.3 71.9 - - - +
173A LYS* 1.4 58.4 + - - +
175A ALA* 3.1 2.9 + - - +
176A ARG* 2.8 41.3 + - - +
272A LEU* 3.8 24.0 - - + +
304A ASP 3.5 9.2 - - - +
305A ILE* 3.9 4.3 - - - -
306A SER* 2.0 46.3 + - - -
308A GLU* 5.2 0.3 - - - +
309A ALA* 4.0 9.1 - - - +
337A PHE* 3.8 25.3 - - + -
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Residues in contact with LYS 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A PRO* 4.2 14.8 - - + +
172A GLU* 1.4 78.7 - - - +
174A TRP* 1.4 86.8 + - + +
176A ARG* 3.5 28.9 + - - +
177A PHE* 3.5 17.2 + - - +
342A GLN* 6.5 0.7 - - + -
343A TRP* 5.5 1.0 + - - -
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Residues in contact with TRP 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A LEU* 4.7 3.8 - - + -
168A TYR* 3.6 46.0 - + + -
170A VAL* 3.8 12.6 - - + -
171A PRO* 3.1 40.4 + - + +
173A LYS* 1.4 94.9 - - + +
175A ALA* 1.4 61.7 + - - +
177A PHE* 3.1 7.1 + - - +
178A TYR* 3.0 45.7 + + + -
354A PRO* 3.5 42.0 + - + +
355A VAL* 3.5 24.9 - - + -
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Residues in contact with ALA 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A VAL* 3.7 8.7 - - + +
171A PRO 3.1 5.1 + - - +
172A GLU 3.1 8.2 + - - +
174A TRP* 1.4 77.0 - - - +
176A ARG* 1.4 55.7 + - - +
178A TYR 3.4 0.2 + - - -
179A THR* 2.8 40.2 + - - -
268A LEU* 3.9 8.1 - - + -
271A MET* 3.7 25.5 - - + +
272A LEU* 3.6 28.0 - - + -
337A PHE* 4.4 2.2 - - + -
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Residues in contact with ARG 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A GLU* 2.8 20.9 + - - +
173A LYS* 3.5 32.2 + - - +
174A TRP 3.2 0.2 - - - -
175A ALA* 1.4 74.9 - - - +
177A PHE* 1.4 55.8 + - - +
179A THR* 3.8 1.4 - - - -
180A ALA* 3.0 33.0 + - - +
337A PHE* 3.0 46.1 + - + +
338A PHE* 3.4 29.5 + - + -
339A LYS 3.9 6.3 + - - -
340A ASN* 3.9 19.9 - - - +
342A GLN* 5.7 5.1 - - - +
343A TRP* 3.7 19.6 - - + +
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Residues in contact with PHE 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A LYS 3.5 8.9 + - - +
174A TRP 3.1 9.1 + - - +
176A ARG* 1.4 78.7 - - - +
178A TYR* 1.4 81.0 + + - +
180A ALA* 3.3 5.4 + - - +
181A GLU* 2.9 67.3 + - - +
210A GLY 4.2 4.7 - - - -
211A HIS* 3.5 23.8 - + - -
343A TRP* 4.5 14.7 - + - +
348A LEU* 3.7 21.2 - - + +
351A THR* 4.4 8.3 - - - -
352A VAL 4.9 1.6 - - - -
353A ALA* 3.8 8.3 - - + -
354A PRO* 3.3 38.1 - - + -
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Residues in contact with TYR 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A LEU* 4.2 20.6 - - + -
164A LEU* 3.4 28.7 - - + +
170A VAL* 5.0 0.7 - - + -
174A TRP* 3.0 39.4 + + + +
175A ALA 4.0 2.5 - - - +
177A PHE* 1.4 92.8 - + - +
179A THR* 1.4 64.6 + - - +
181A GLU* 3.2 7.0 + - - +
182A VAL* 2.9 26.0 + - - +
206A LEU* 4.1 24.2 - - + +
210A GLY 4.3 4.5 + - - -
212A LEU* 4.7 6.5 - - + +
267A PHE* 3.9 21.3 - - + -
271A MET* 4.1 7.0 - - - -
354A PRO* 3.3 28.0 - - + +
355A VAL* 3.4 22.7 + - - +
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Residues in contact with THR 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A ALA 2.8 23.8 + - - -
176A ARG 3.8 3.1 - - - -
178A TYR* 1.4 70.2 - - - +
180A ALA* 1.4 49.9 + - - +
182A VAL* 3.0 7.9 + - - +
183A VAL* 2.9 35.4 + - + +
264A VAL* 3.8 25.5 - - + +
267A PHE* 3.9 10.4 - - - -
268A LEU* 3.5 23.4 - - + +
271A MET* 3.4 15.9 - - - +
312A LEU* 4.5 3.8 - - + -
337A PHE* 4.5 2.0 - - + -
338A PHE* 3.7 25.1 - - + -
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Residues in contact with ALA 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A ARG 3.0 18.9 + - - +
177A PHE 3.4 4.9 - - - +
179A THR* 1.4 72.9 - - - +
181A GLU* 1.4 56.1 + - - +
183A VAL* 3.1 3.3 + - - +
184A LEU* 3.0 24.8 + - - +
338A PHE* 3.6 5.0 - - + -
343A TRP* 3.6 30.1 - - + -
345A TRP* 3.3 28.2 - - + -
348A LEU* 3.7 12.1 - - + -
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Residues in contact with GLU 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A TRP* 3.5 28.4 - - + -
177A PHE* 2.9 38.2 + - + +
178A TYR* 3.6 7.6 - - - +
180A ALA* 1.4 73.0 - - - +
182A VAL* 1.4 51.8 + - - +
184A LEU* 3.2 5.0 + - - +
185A ALA* 2.8 34.3 + - - +
211A HIS* 2.8 31.3 + - - -
212A LEU* 2.8 45.0 + - + +
348A LEU* 3.6 22.5 - - + +
349A ARG* 3.8 1.7 - - - +
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Residues in contact with VAL 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A TYR 2.9 18.9 + - - +
179A THR* 3.0 9.4 + - - +
181A GLU* 1.4 71.6 - - - +
183A VAL* 1.3 55.1 + - - +
185A ALA* 3.6 1.2 - - - +
186A LEU* 2.8 54.3 + - + +
199A VAL* 4.2 3.6 - - + -
204A MET* 3.7 42.4 - - + -
212A LEU* 3.8 22.9 - - + -
214A LEU* 5.1 4.7 - - + -
264A VAL* 4.1 11.0 - - + -
267A PHE* 3.9 10.3 - - + -
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Residues in contact with VAL 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A THR* 2.9 27.4 + - + +
180A ALA* 3.1 10.1 + - - +
182A VAL* 1.3 75.7 - - - +
184A LEU* 1.3 56.9 + - - +
186A LEU* 3.4 0.3 + - - -
187A ASP* 2.9 31.2 + - - +
261A TRP* 4.0 20.0 - - + -
264A VAL* 4.5 8.7 - - + -
329A VAL* 3.9 22.4 - - + -
332A ILE* 4.1 29.8 - - + -
333A LYS* 4.8 6.5 - - + -
338A PHE* 4.4 8.7 - - + -
345A TRP* 4.2 14.1 - - + -
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Residues in contact with LEU 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A TRP* 3.7 33.6 - - + +
180A ALA 3.0 13.5 + - - +
181A GLU 3.5 6.5 - - - +
183A VAL* 1.3 74.0 - - - +
185A ALA* 1.3 64.0 + - - +
187A ASP* 3.4 7.8 + - + +
188A ALA* 3.1 22.9 + - - +
333A LYS* 3.9 24.0 - - - +
345A TRP* 3.7 40.2 - - + +
348A LEU* 3.7 29.2 - - + -
349A ARG 5.6 0.2 - - - +
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Residues in contact with ALA 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A TRP* 3.6 28.3 - - + +
136A VAL* 5.5 0.3 - - - +
181A GLU 2.8 16.2 + - - +
182A VAL 3.3 4.9 + - - +
184A LEU* 1.3 76.3 - - - +
186A LEU* 1.4 61.5 + - - +
188A ALA* 3.2 18.5 + - - +
189A ILE* 3.4 11.4 + - - +
212A LEU* 3.9 13.7 - - + -
214A LEU* 3.7 26.0 - - + +
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Residues in contact with LEU 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A VAL* 2.8 30.1 + - + +
185A ALA* 1.4 68.2 - - - +
187A ASP* 1.4 61.3 + - - +
189A ILE* 3.1 7.8 + - + +
190A HIS* 2.9 42.6 + - + +
196A HIS* 3.8 18.2 - - + -
199A VAL* 3.5 29.2 - - + -
214A LEU* 4.1 15.0 - - + -
260A ASP* 3.8 17.7 - - + +
261A TRP* 3.7 15.9 - - + -
264A VAL* 3.5 32.8 - - + -
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Residues in contact with ASP 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A VAL 2.9 18.0 + - - +
184A LEU* 3.5 9.9 - - + +
186A LEU* 1.4 75.2 - - - +
188A ALA* 1.4 49.8 + - - +
190A HIS* 3.2 14.3 + - - +
191A SER* 2.7 44.9 + - - -
257A ARG* 5.4 3.3 + - - -
261A TRP* 4.5 0.8 - - - -
329A VAL* 3.4 41.4 - - + +
333A LYS* 4.1 13.2 + - - -
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Residues in contact with ALA 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A SER* 4.0 24.9 - - - +
135A TRP* 4.3 8.7 - - + -
136A VAL* 5.2 2.7 - - + -
184A LEU 3.1 12.4 + - - +
185A ALA* 3.3 12.3 - - - +
187A ASP* 1.4 74.6 - - - +
189A ILE* 1.4 57.1 + - + +
191A SER* 3.3 10.1 - - - -
192A MET* 3.1 32.5 + - - +
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Residues in contact with ILE 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A ILE* 3.8 13.5 - - + -
136A VAL* 3.7 21.1 - - + -
185A ALA 3.6 12.6 - - - +
186A LEU* 3.1 10.2 + - + +
188A ALA* 1.4 70.5 - - - +
190A HIS* 1.3 66.4 + - + +
192A MET* 3.0 21.9 + - - +
193A GLY 3.3 0.2 + - - -
194A PHE* 3.0 42.4 + - + +
196A HIS* 4.5 21.5 - - + +
214A LEU* 4.0 16.6 - - + -
217A PHE* 3.5 30.5 - - + -
220A CYS* 4.8 2.9 - - - -
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Residues in contact with HIS 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A LEU* 2.9 33.1 + - + +
187A ASP* 3.4 11.7 + - - +
189A ILE* 1.3 75.7 - - + +
191A SER* 1.4 53.7 + - - +
193A GLY* 2.8 25.3 + - - -
194A PHE 3.2 20.2 - - - -
195A ILE* 4.3 1.1 - - - -
196A HIS 4.8 0.9 - - - -
223A MET* 3.5 8.2 - - + +
257A ARG* 3.6 55.5 + - + +
260A ASP* 2.9 33.8 + - + -
261A TRP* 3.7 29.7 - + - -
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Residues in contact with SER 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A ASP* 2.7 30.2 + - - -
188A ALA* 3.3 13.3 - - - -
189A ILE 3.2 0.2 - - - -
190A HIS* 1.4 70.8 - - - +
192A MET* 1.4 55.0 - - - +
193A GLY* 3.0 8.9 + - - -
257A ARG* 5.0 1.5 - - - +
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Residues in contact with MET 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A ASP 4.7 2.5 - - - +
127A ILE* 3.9 35.4 - - + +
130A PHE* 4.6 4.5 - - + +
131A ALA* 3.6 46.7 - - - +
133A SER* 6.1 0.9 - - - -
136A VAL* 5.0 1.8 - - - -
188A ALA* 3.1 18.1 + - - +
189A ILE* 3.0 19.1 + - - +
191A SER* 1.4 74.1 - - - +
193A GLY* 1.3 58.1 + - - +
194A PHE* 3.5 17.2 - - + -
222A LYS* 3.1 23.4 + - - -
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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
------------------------------------------------------------
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