Contacts of the helix formed by residues 180 - 202 (chain A) in PDB entry 2R4V
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 THR 180 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A LEU* 5.5 0.4 - - - -
102A LEU* 3.2 20.4 - - - +
103A SER 4.6 1.8 - - - +
104A PRO* 4.2 9.4 - - + +
175A ASP* 4.0 29.0 - - + +
178A GLN* 3.5 14.1 - - + +
179A LEU* 1.3 77.7 - - - +
181A LEU* 1.3 63.7 + - - +
182A ALA* 3.2 19.6 + - - +
183A ASP* 2.9 19.7 + - - +
184A CYS* 3.0 26.8 + - - -
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Residues in contact with LEU 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ARG* 5.1 2.4 + - - -
39A ILE* 3.6 37.7 - - + -
87A GLU* 3.8 21.0 - - + +
91A GLU* 4.0 23.1 - - + +
102A LEU* 2.9 36.3 + - + +
103A SER* 3.8 23.1 - - - +
104A PRO* 4.3 1.3 - - + -
110A PHE* 3.8 21.6 - - + -
180A THR* 1.3 71.8 - - - +
182A ALA* 1.3 61.8 + - - +
184A CYS* 3.2 5.0 + - - +
185A SER* 3.0 24.3 + - - -
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Residues in contact with ALA 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A PRO* 4.5 4.4 - - + +
109A SER* 3.6 40.1 - - - +
110A PHE* 3.7 19.3 - - + +
174A LEU* 3.7 11.6 - - + +
180A THR* 3.0 13.7 + - - +
181A LEU* 1.3 78.5 - - - +
183A ASP* 1.3 56.5 + - - +
185A SER* 3.5 3.0 + - - -
186A LEU* 3.0 31.4 + - - +
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Residues in contact with ASP 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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38A MET* 4.9 0.7 - - + -
173A PHE* 3.9 6.1 - - - +
174A LEU* 3.2 16.9 + - - +
175A ASP 4.8 0.5 + - - -
178A GLN 3.9 1.4 - - - +
179A LEU* 3.5 31.2 - - + -
180A THR* 2.9 35.7 + - - +
182A ALA* 1.3 76.1 - - - +
184A CYS* 1.3 59.7 + - - +
187A LEU* 2.9 38.5 + - + +
215A TYR* 2.6 42.1 + - - +
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Residues in contact with CYS 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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35A ARG* 3.4 29.0 - - + +
38A MET* 3.7 25.4 - - + -
39A ILE* 3.9 22.2 - - + -
42A LEU* 3.5 29.4 - - - -
102A LEU* 5.3 1.1 - - - -
180A THR 3.0 20.3 + - - -
181A LEU* 3.2 9.4 + - - +
183A ASP* 1.3 77.5 - - - +
185A SER* 1.3 55.3 + - - +
188A PRO* 3.1 24.1 - - - +
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Residues in contact with SER 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A PRO 5.5 0.9 - - - +
35A ARG* 3.7 36.3 + - - +
110A PHE* 5.2 6.5 - - - -
181A LEU 3.0 15.0 + - - -
182A ALA* 3.7 6.1 - - - -
184A CYS* 1.3 77.4 - - - +
186A LEU* 1.3 63.2 + - - +
188A PRO* 3.5 9.2 - - - +
189A LYS* 3.0 42.7 + - - +
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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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112A VAL 4.6 9.6 - - - +
113A GLY* 4.2 17.7 - - - +
116A LEU* 4.1 18.2 - - + -
146A LEU* 3.9 28.7 - - + -
174A LEU* 3.9 20.9 - - + -
182A ALA 3.0 19.1 + - - +
183A ASP 4.5 0.2 - - - +
185A SER* 1.3 77.1 - - - +
187A LEU* 1.3 61.8 + - - +
189A LYS* 2.9 19.9 + - + +
190A LEU* 2.8 50.9 + - + +
215A TYR* 4.4 3.6 - - + +
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Residues in contact with LEU 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A MET* 4.2 8.3 - - + -
179A LEU* 4.1 11.2 - - + -
183A ASP* 2.9 33.5 + - + +
186A LEU* 1.3 71.2 - - - +
188A PRO* 1.4 65.9 - - + +
190A LEU* 3.6 9.4 - - + +
191A ASN 2.9 20.4 + - - -
215A TYR* 3.4 36.3 - - + +
216A LEU* 4.5 6.1 - - + -
219A ALA* 3.5 35.2 - - + -
225A PHE* 3.5 40.1 - - + -
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Residues in contact with PRO 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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31A PRO* 3.9 24.9 - - + +
34A GLN* 3.3 46.6 - - + +
35A ARG 4.1 1.8 - - - +
38A MET* 4.2 6.5 - - - -
184A CYS 3.1 29.6 - - - +
185A SER 3.5 7.4 - - - +
187A LEU* 1.4 91.4 - - + +
189A LYS* 1.3 59.0 - - - +
191A ASN* 3.4 3.6 + - + +
192A ILE* 3.2 30.5 + - + +
225A PHE* 4.0 2.2 - - + -
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Residues in contact with LYS 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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31A PRO* 4.6 14.4 - - + -
35A ARG* 4.8 7.4 - - - +
113A GLY 5.4 7.7 + - - +
114A CYS* 5.8 4.8 + - - +
117A PHE* 3.8 40.9 - - + +
185A SER* 3.0 39.3 + - - +
186A LEU* 2.9 19.5 + - + +
188A PRO* 1.3 73.5 - - - +
190A LEU* 1.3 58.7 + - - +
192A ILE* 3.3 6.0 + - - +
193A ILE* 3.0 37.1 + - + +
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Residues in contact with LEU 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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116A LEU* 3.4 28.7 - - + -
143A PHE* 3.7 23.1 - - + -
146A LEU* 4.2 8.7 - - + -
186A LEU* 2.8 33.8 + - + +
187A LEU* 3.6 11.7 - - + +
189A LYS* 1.3 72.3 - - - +
191A ASN* 1.3 56.4 + - - +
193A ILE* 3.4 4.6 + - + +
194A LYS* 2.9 30.8 + - - +
205A ILE* 5.2 4.4 - - + +
212A VAL* 5.4 1.8 - - + -
215A TYR* 3.7 31.9 - - + -
216A LEU* 3.9 26.0 - - + -
220A TYR* 4.7 1.1 - - - -
225A PHE* 5.8 0.2 - - + -
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Residues in contact with ASN 191 (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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34A GLN* 5.1 1.2 - - - +
187A LEU 2.9 12.5 + - - +
188A PRO* 3.6 10.3 - - + +
189A LYS 3.4 0.2 - - - -
190A LEU* 1.3 71.2 - - - +
192A ILE* 1.3 60.3 + - - +
194A LYS* 3.3 2.6 + - - +
195A VAL* 2.9 46.5 + - - +
220A TYR* 2.7 39.4 + - - +
225A PHE* 4.0 8.5 - - + -
229A CYS* 3.7 24.7 - - - +
230A PRO* 4.4 4.9 - - - +
232A ASP* 4.9 4.4 + - - +
235A ILE* 3.4 22.5 - - - +
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Residues in contact with ILE 192 (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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29A ASN* 3.3 28.3 - - - +
31A PRO* 3.6 32.8 - - + -
34A GLN* 6.1 0.4 - - - +
117A PHE* 3.9 18.8 - - + -
120A PHE* 4.1 3.8 - - + -
188A PRO 3.2 16.0 + - - +
189A LYS* 3.3 6.0 + - - +
191A ASN* 1.3 76.4 - - + +
193A ILE* 1.3 58.3 + - - +
196A ALA* 2.8 35.9 + - - +
230A PRO* 6.4 0.4 - - + -
235A ILE* 3.9 19.9 - - + +
239A TYR* 3.8 34.5 - - + +
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Residues in contact with ILE 193 (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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116A LEU* 3.7 39.9 - - + +
117A PHE* 4.3 10.3 - - + -
120A PHE* 3.6 46.0 - - + -
139A LEU* 4.5 7.9 - - + -
143A PHE* 3.9 26.7 - - + -
189A LYS* 3.0 25.9 + - + +
190A LEU* 3.7 5.6 - - - +
192A ILE* 1.3 75.4 - - - +
194A LYS* 1.3 64.6 + - - +
197A ALA* 2.9 34.2 + - + +
203A PHE* 5.2 2.7 - - + -
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Residues in contact with LYS 194 (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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190A LEU 2.9 18.3 + - - +
191A ASN* 3.6 4.9 - - - +
193A ILE* 1.3 78.9 - - - +
195A VAL* 1.3 65.0 + - + +
197A ALA* 4.6 0.8 - - - +
198A LYS* 3.3 23.3 + - + +
203A PHE* 4.7 3.1 - - - +
205A ILE* 4.4 20.4 - - + +
213A TRP* 3.3 41.2 - - - -
216A LEU* 4.3 10.1 - - + -
220A TYR* 3.6 30.5 - - + +
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Residues in contact with VAL 195 (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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191A ASN* 2.9 31.3 + - - +
192A ILE 4.0 1.8 - - - +
194A LYS* 1.3 79.5 - - + +
196A ALA* 1.3 65.8 + - - +
198A LYS* 3.9 2.6 - - - +
199A LYS* 3.2 22.0 + - - +
232A ASP* 3.4 56.3 - - + +
235A ILE* 3.8 18.8 - - + -
236A GLU* 3.7 18.3 - - + +
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Residues in contact with ALA 196 (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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120A PHE* 3.7 21.5 - - + -
124A ILE* 3.7 4.6 - - + +
192A ILE 2.8 22.4 + - - +
195A VAL* 1.3 77.6 - - - +
197A ALA* 1.3 57.1 + - - +
199A LYS* 3.4 1.4 + - - -
200A TYR* 3.1 42.1 + - + +
235A ILE* 4.0 6.3 - - + +
236A GLU* 5.5 0.9 - - - -
239A TYR* 3.8 24.5 - - + -
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Residues in contact with ALA 197 (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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120A PHE* 4.3 4.2 - - + -
123A TYR* 3.8 27.4 - - + +
124A ILE* 4.1 9.9 - - - -
193A ILE* 2.9 23.6 + - + +
194A LYS 4.6 0.4 - - - +
196A ALA* 1.3 73.5 - - - +
198A LYS* 1.3 66.0 + - - +
201A ARG* 3.0 20.4 + - - +
203A PHE* 3.1 30.9 + - + -
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Residues in contact with LYS 198 (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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194A LYS 3.3 19.3 + - - +
195A VAL* 3.9 4.3 - - - +
196A ALA 3.3 0.4 - - - -
197A ALA* 1.3 79.1 - - - +
199A LYS* 1.3 59.8 + - - +
202A ASP* 3.0 39.8 + - - +
203A PHE 3.2 14.3 + - - +
204A ASP* 3.1 37.7 + - - +
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Residues in contact with LYS 199 (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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195A VAL 3.2 15.4 + - - +
196A ALA 3.8 3.8 - - - +
198A LYS* 1.3 81.2 - - - +
200A TYR* 1.3 90.1 + - + +
202A ASP* 4.7 6.9 + - - +
233A LYS* 6.1 0.4 - - - +
236A GLU* 3.7 40.9 + - + +
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Residues in contact with TYR 200 (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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124A ILE* 4.0 6.5 - - + -
196A ALA* 3.1 26.2 + - - +
199A LYS* 1.3 102.7 - - + +
201A ARG* 1.3 78.8 + - - +
202A ASP* 3.7 3.8 - - - +
236A GLU* 2.7 38.5 + - - +
239A TYR* 3.6 16.2 - - + -
240A ALA* 3.3 19.4 - - - +
243A ALA* 3.5 37.4 - - + +
244A LYS* 3.7 29.4 + - + -
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Residues in contact with ARG 201 (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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123A TYR* 3.2 57.5 + - + +
124A ILE* 3.1 30.7 + - + -
126A ASN 2.9 26.9 + - - -
132A ASN* 4.0 17.6 - - - +
136A GLU* 5.7 0.5 - - - +
197A ALA 3.0 7.2 + - - +
200A TYR* 1.3 92.9 + - - +
202A ASP* 1.3 74.9 + - - +
203A PHE* 3.0 5.7 + - - +
243A ALA 2.9 25.1 + - - -
245A GLN* 3.3 24.6 + - - +
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Residues in contact with ASP 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A LYS* 3.0 32.7 + - - +
199A LYS 4.7 6.4 - - - +
200A TYR 4.8 2.6 - - - +
201A ARG* 1.3 84.0 + - - +
203A PHE* 1.3 59.7 + - - +
204A ASP* 3.8 10.7 + - - +
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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