Contacts of the helix formed by residues 154 - 179 (chain D) in PDB entry 2VT4
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 154 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75D LEU* 3.4 14.9 - - - +
150D GLN 5.7 1.1 - - - +
151D SER 5.0 5.4 - - - +
152D LEU 3.4 11.9 + - - +
153D MET* 1.3 79.9 - - - +
155D ARG* 1.3 60.1 + - - +
156D ALA* 3.6 8.1 + - - +
157D ARG* 3.2 32.2 + - - +
158D ALA* 3.0 21.3 + - - +
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Residues in contact with ARG 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73D GLN* 2.9 37.8 + - - +
74D THR* 3.9 14.5 - - - +
75D LEU* 4.1 12.8 - - + +
78D LEU* 4.0 23.8 - - + +
154D THR* 1.3 72.9 - - - +
156D ALA* 1.3 64.7 + - - +
157D ARG 3.2 0.2 - - - -
158D ALA* 3.8 1.2 - - - +
159D LYS* 3.1 37.7 + - - +
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Residues in contact with ALA 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154D THR* 3.6 7.0 + - - +
155D ARG* 1.3 78.0 - - - +
157D ARG* 1.3 62.0 + - - +
159D LYS* 3.4 10.1 + - - +
160D VAL* 3.2 24.9 + - - +
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Residues in contact with ARG 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205C ARG* 5.1 10.3 - - - +
151D SER 4.3 4.4 + - - -
152D LEU* 2.7 57.8 + - - +
153D MET* 4.7 7.4 - - - +
154D THR* 3.2 26.6 + - - +
155D ARG 3.2 0.4 - - - -
156D ALA* 1.3 78.3 - - - +
158D ALA* 1.3 65.6 + - - +
160D VAL* 3.0 13.1 + - + +
161D ILE* 3.0 28.4 + - + +
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Residues in contact with ALA 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75D LEU* 4.2 9.2 - - + +
78D LEU* 4.1 18.8 - - + -
79D PHE* 4.0 22.1 - - + -
153D MET* 4.5 4.2 - - - -
154D THR 3.0 17.4 + - - +
155D ARG 3.8 4.5 - - - +
157D ARG* 1.3 76.2 - - - +
159D LYS* 1.3 57.6 + - - +
161D ILE* 3.1 15.9 + - - +
162D ILE* 2.8 32.7 + - - +
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Residues in contact with LYS 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78D LEU* 4.5 24.9 - - + -
155D ARG* 3.1 27.3 + - - +
156D ALA* 3.6 9.2 - - - +
158D ALA* 1.3 73.6 - - - +
160D VAL* 1.3 65.8 + - + +
162D ILE* 3.2 15.1 + - + +
163D CYS* 3.0 32.4 + - - -
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Residues in contact with VAL 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206C ALA* 4.0 27.1 - - + +
402C SOG 4.8 20.5 - - - +
156D ALA 3.2 11.6 + - - +
157D ARG* 3.0 15.5 + - + +
159D LYS* 1.3 79.2 - - - +
161D ILE* 1.3 61.0 + - + +
163D CYS* 3.2 5.5 + - - +
164D THR* 2.9 31.6 + - - +
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Residues in contact with ILE 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D PHE* 4.6 6.7 - - + -
134D VAL* 4.0 34.8 - - + -
153D MET* 4.0 27.6 - - + -
157D ARG* 3.0 24.3 + - + +
158D ALA* 3.1 15.7 + - - +
160D VAL* 1.3 78.9 - - + +
162D ILE* 1.3 61.7 + - - +
164D THR* 3.5 7.2 + - - -
165D VAL* 3.1 24.0 + - + +
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Residues in contact with ILE 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78D LEU* 3.6 38.6 - - + +
79D PHE* 4.0 17.7 - - + -
82D SER* 3.6 27.6 - - - +
131D THR* 6.2 0.2 - - + -
158D ALA 2.8 20.7 + - - +
159D LYS* 3.5 20.0 - - + +
161D ILE* 1.3 71.4 - - - +
163D CYS* 1.3 64.9 + - - +
165D VAL* 3.2 8.3 + - - +
166D TRP* 3.0 40.6 + - + +
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Residues in contact with CYS 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402C SOG 3.0 43.2 + - - +
159D LYS* 3.0 24.0 + - - +
160D VAL* 3.7 4.0 - - - +
162D ILE* 1.3 80.1 - - - +
164D THR* 1.3 58.1 + - - +
166D TRP* 3.7 7.1 - - - +
167D ALA* 2.7 36.6 + - - +
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Residues in contact with THR 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206C ALA* 3.4 27.1 - - + +
210C ALA* 3.9 28.7 - - + -
402C SOG 4.1 17.3 - - + -
160D VAL* 2.9 18.6 + - - +
161D ILE* 3.7 8.7 - - - -
163D CYS* 1.3 75.5 - - - +
165D VAL* 1.3 58.3 + - + +
167D ALA* 3.4 5.5 + - - +
168D ILE* 2.9 40.6 + - + +
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Residues in contact with VAL 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406C D10 6.3 2.7 - - + -
82D SER* 5.7 0.2 - - - +
127D ALA* 4.2 4.9 - - + +
130D GLU* 3.4 33.1 - - + +
131D THR* 3.8 22.0 - - - +
134D VAL* 3.8 28.0 - - + -
161D ILE* 3.1 17.9 + - + +
162D ILE* 3.3 12.1 - - - +
164D THR* 1.3 78.1 - - + +
166D TRP* 1.3 61.0 + - + +
168D ILE* 4.7 4.9 - - + -
169D SER* 2.8 34.9 + - - +
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Residues in contact with TRP 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82D SER* 3.0 32.3 + - - +
85D CYS* 4.5 8.3 - - + -
86D ALA* 3.8 35.9 - - + -
89D VAL* 5.4 6.3 - - + -
123D LEU* 3.9 36.7 - - + +
124D CYS* 5.1 5.8 - - - -
127D ALA* 4.0 27.7 - - + +
131D THR* 5.0 1.0 + - - -
162D ILE* 3.0 37.3 + - + +
163D CYS* 3.2 7.1 + - - +
165D VAL* 1.3 75.7 - - + +
167D ALA* 1.3 59.9 + - - +
169D SER* 3.2 5.3 + - - -
170D ALA* 2.9 29.5 + - - +
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Residues in contact with ALA 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181C TRP* 3.9 26.1 - - + -
402C SOG 4.3 20.2 - - + +
163D CYS 2.7 21.7 + - - +
164D THR* 3.5 5.4 - - - +
166D TRP* 1.3 69.4 - - - +
168D ILE* 1.3 66.6 + - - +
169D SER 3.1 0.2 + - - -
170D ALA* 3.2 6.7 + - - +
171D LEU* 3.0 22.5 + - - +
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Residues in contact with ILE 168 (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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181C TRP* 5.2 0.9 - - - -
210C ALA* 3.8 20.6 - - + -
214C ILE* 3.7 33.7 - - + -
402C SOG 4.1 18.6 - - + -
406C D10 5.3 10.1 - - + -
130D GLU* 3.8 21.3 - - - +
164D THR* 2.9 31.3 + - + +
165D VAL* 3.8 8.1 - - + +
167D ALA* 1.3 71.3 - - - +
169D SER* 1.3 62.4 + - - +
171D LEU* 3.2 13.4 - - + +
172D VAL* 3.2 31.6 + - + +
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Residues in contact with SER 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123D LEU* 3.8 13.0 - - - -
126D THR* 3.7 18.0 - - - +
127D ALA* 3.4 26.0 + - - -
130D GLU* 3.3 11.7 + - - -
165D VAL 2.8 22.1 + - - -
166D TRP* 3.4 8.5 - - - -
167D ALA 3.0 0.2 - - - -
168D ILE* 1.3 79.3 - - - +
170D ALA* 1.3 55.8 + - - +
172D VAL* 3.5 2.9 + - - +
173D SER* 2.6 34.2 + - - -
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Residues in contact with ALA 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181C TRP* 5.7 2.7 - - + -
123D LEU* 3.5 6.1 - - + +
166D TRP 2.9 18.7 + - - +
167D ALA* 3.8 4.9 - - - +
169D SER* 1.3 69.3 - - - +
171D LEU* 1.3 63.1 + - - +
173D SER* 3.5 7.0 - - - -
174D PHE* 2.8 59.5 + - + +
175D LEU* 3.4 2.5 + - - +
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Residues in contact with LEU 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171C LEU* 3.5 36.5 - - + +
172C VAL* 4.3 11.0 - - + -
175C LEU* 4.8 4.3 - - + -
176C PRO* 3.9 19.7 - - + -
179C MET* 5.0 1.8 - - - -
181C TRP* 4.4 17.1 - - + -
214C ILE* 6.4 0.2 - - + -
402C SOG 4.3 16.8 - - + -
167D ALA 3.0 11.7 + - - +
168D ILE* 3.2 16.6 - - + +
170D ALA* 1.3 79.0 - - - +
172D VAL* 1.3 64.6 + - + +
175D LEU* 3.2 48.9 - - + +
176D PRO* 3.3 6.2 - - - +
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Residues in contact with VAL 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171C LEU* 4.3 14.4 - - + -
172C VAL* 5.1 9.0 - - + -
406C D10 6.0 2.2 - - + -
122D VAL* 4.9 1.9 - - - +
126D THR* 3.9 22.0 - - + -
130D GLU* 4.9 2.7 - - - +
168D ILE* 3.2 24.6 + - + +
169D SER 3.7 9.4 - - - +
171D LEU* 1.3 82.8 - - + +
173D SER* 1.3 60.2 + - - +
176D PRO* 3.9 12.4 - - - +
207D TYR* 5.4 2.9 + - - -
211D SER* 5.4 4.3 - - - -
214D ILE* 3.9 26.0 - - + -
215D SER* 3.9 16.7 + - - +
402D SOG 4.3 9.4 - - + +
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Residues in contact with SER 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119D SER* 4.5 4.1 + - - -
122D VAL* 3.5 32.4 - - - +
123D LEU* 3.5 27.2 - - - +
126D THR* 4.6 1.6 - - - -
169D SER 2.6 23.9 + - - -
171D LEU 3.3 0.4 - - - -
172D VAL* 1.3 83.6 - - - +
174D PHE* 1.3 75.2 + - - +
175D LEU 3.5 0.4 - - - -
176D PRO* 4.0 3.6 - - - +
177D ILE* 3.4 22.2 - - - +
207D TYR* 5.3 1.9 + - - -
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Residues in contact with PHE 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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116D LEU* 5.0 1.8 - - + -
119D SER* 3.5 45.0 + - - -
120D LEU* 3.9 15.5 - - + -
123D LEU* 3.6 28.0 - - + -
170D ALA* 2.8 43.1 + - + +
173D SER* 1.3 78.2 + - - +
175D LEU* 1.3 59.6 + - + +
177D ILE* 3.1 7.3 + - - +
178D MET* 2.9 40.8 + - - +
403D SOG 3.9 20.8 - - + +
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Residues in contact with LEU 175 (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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171C LEU* 4.1 8.1 - - + -
175C LEU* 4.0 17.3 - - + -
179C MET* 4.0 26.5 - - + -
181C TRP* 5.4 0.9 - - + -
170D ALA 3.4 3.2 + - - +
171D LEU* 3.2 47.1 - - + +
174D PHE* 1.3 79.7 - - + +
176D PRO* 1.3 63.5 - - + +
178D MET* 3.3 27.0 + - + +
179D MET* 3.1 35.9 + - + +
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Residues in contact with PRO 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171C LEU* 3.8 26.0 - - + -
171D LEU 3.3 13.5 - - - +
172D VAL 3.9 14.4 - - - +
173D SER 4.0 3.1 - - - +
174D PHE 3.8 0.9 - - - -
175D LEU* 1.3 90.1 - - + +
177D ILE* 1.3 60.2 + - - +
179D MET* 5.3 0.2 - - - -
180D HIS 3.1 2.3 + - - -
181D TRP* 2.8 58.6 + - + +
182D TRP* 3.8 3.1 - - - -
207D TYR* 4.1 18.8 - - + +
402D SOG 3.9 12.6 - - + -
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Residues in contact with ILE 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115D GLU* 4.0 13.1 - - + +
118D THR* 3.8 30.5 - - + +
119D SER* 3.5 22.9 - - - +
122D VAL* 5.2 3.1 - - + -
173D SER 3.4 17.0 - - - +
174D PHE 3.1 9.2 + - - +
176D PRO* 1.3 79.2 - - - +
178D MET* 1.3 61.4 + - - +
180D HIS* 3.1 11.8 + - - -
182D TRP* 3.7 25.2 + - + +
201D PHE* 4.0 16.8 - - + -
207D TYR* 4.6 10.3 - - - +
403D SOG 3.5 22.8 - - + +
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Residues in contact with MET 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B ASP* 4.6 3.3 - - - +
197B GLY* 5.3 0.3 - - - -
174D PHE* 2.9 31.4 + - - +
175D LEU* 3.5 32.3 - - + +
177D ILE* 1.3 76.9 - - - +
179D MET* 1.3 59.6 + - + +
180D HIS* 3.2 17.1 + - - -
403D SOG 2.6 92.6 + - + +
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Residues in contact with MET 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B GLN 4.5 15.3 - - - +
195B ASP* 4.0 18.4 - - + +
196B PRO* 3.7 16.0 - - + +
171C LEU* 5.8 0.4 - - - -
175C LEU* 4.4 26.9 - - + -
175D LEU* 3.1 28.1 + - + +
176D PRO* 5.3 0.2 - - - -
177D ILE 3.2 0.4 - - - -
178D MET* 1.3 76.5 - - + +
180D HIS* 1.3 75.0 + - - +
181D TRP* 3.1 55.1 + - + +
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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) + - + + + + + -
------------------------------------------------------------
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