Contacts of the helix formed by residues 154 - 178 (chain D) in PDB entry 1XV9
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 VAL 154 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148D LEU* 4.4 4.9 - - + -
152D ALA 3.2 1.0 + - - +
153D PRO* 1.3 72.3 - - - +
155D LEU* 1.3 53.8 + - - +
156D PRO 3.2 0.2 - - - -
157D LEU* 2.7 38.0 + - + +
158D VAL* 3.1 30.3 + - + +
231D ARG* 3.3 63.0 - - + +
232D VAL* 4.4 1.1 - - - +
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Residues in contact with LEU 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153D PRO* 4.9 5.2 - - + -
154D VAL* 1.3 78.0 - - - +
156D PRO* 1.3 66.8 - - + +
158D VAL* 4.3 7.2 - - + -
159D THR* 2.8 50.5 + - - +
339D MET* 5.0 15.3 - - + -
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Residues in contact with PRO 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136D ARG* 4.0 5.4 - - - +
138D PRO* 3.1 25.4 - - + +
153D PRO* 3.1 36.3 - - + +
154D VAL 3.4 0.4 - - - +
155D LEU* 1.3 94.3 - - + +
157D LEU* 1.3 54.6 + - - +
159D THR* 4.0 5.6 + - - +
160D HIS* 3.3 17.7 + - - +
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Residues in contact with LEU 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138D PRO* 3.3 17.2 - - + +
140D HIS* 4.1 19.7 - - + +
141D LEU* 4.5 15.7 - - + -
148D LEU* 4.5 12.6 - - + -
153D PRO 5.1 0.4 + - - +
154D VAL* 2.7 20.5 + - + +
156D PRO* 1.3 71.7 - - - +
158D VAL* 1.3 53.9 + - - +
159D THR 3.2 0.2 - - - -
160D HIS* 2.9 8.8 + - + +
161D PHE* 2.7 33.8 + - + +
224D TYR* 5.7 2.5 - - + -
228D ASP* 3.7 36.3 - - + +
231D ARG* 3.8 20.9 - - + -
232D VAL* 3.9 13.0 - - + +
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Residues in contact with VAL 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154D VAL* 3.1 32.0 + - + +
155D LEU* 3.8 11.2 - - + +
157D LEU* 1.3 77.1 - - - +
159D THR* 1.3 61.4 + - - +
161D PHE* 3.8 7.1 - - - +
162D ALA* 2.9 27.9 + - - +
232D VAL* 3.9 27.1 - - + +
333D ILE* 6.4 1.3 - - + -
336D LEU* 4.5 15.7 - - + -
339D MET* 3.8 28.7 - - + -
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Residues in contact with THR 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136D ARG* 4.7 12.3 - - + +
155D LEU* 2.8 42.0 + - - +
156D PRO* 4.1 7.1 - - - +
158D VAL* 1.3 77.8 - - - +
160D HIS* 1.3 57.0 + - - +
162D ALA* 4.5 0.2 - - - -
163D ASP* 2.6 54.5 + - - +
339D MET* 4.4 12.5 - - - -
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Residues in contact with HIS 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132D PHE 3.6 13.5 - - - -
135D PHE 2.9 24.9 + - - -
136D ARG* 4.0 3.6 - - - +
137D PRO* 3.5 25.8 - - + +
138D PRO* 3.6 8.5 - - + -
141D LEU* 3.4 22.8 - - + +
156D PRO 3.3 13.9 + - - +
157D LEU* 2.9 12.9 + - + +
159D THR* 1.3 77.4 - - - +
161D PHE* 1.3 66.8 + - - +
163D ASP* 3.2 2.1 + - - +
164D ILE* 2.9 49.5 + - + +
224D TYR* 2.7 31.1 + + - -
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Residues in contact with PHE 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157D LEU* 2.7 19.7 + - + +
158D VAL 3.8 3.8 - - - +
160D HIS* 1.3 75.7 - - - +
162D ALA* 1.3 75.4 + - - +
164D ILE* 3.9 12.5 - - + +
165D ASN* 2.9 58.0 + - + +
168D MET* 6.6 0.2 - - + -
224D TYR* 6.4 0.7 - - - -
232D VAL* 3.8 29.8 - - + -
234D PHE* 3.3 37.5 - + - -
326D TYR* 4.8 4.7 - + - -
336D LEU* 4.0 14.4 - - + -
340D MET* 3.8 21.8 - - + -
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Residues in contact with ALA 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158D VAL 2.9 22.0 + - - +
159D THR 4.0 0.4 - - - +
161D PHE* 1.3 82.4 - - + +
163D ASP* 1.3 67.9 + - - +
165D ASN* 3.6 1.6 - - - +
166D THR* 3.3 25.8 + - - -
336D LEU* 4.7 3.1 - - + -
339D MET* 3.7 40.7 - - + +
340D MET* 3.9 15.2 - - - +
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Residues in contact with ASP 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135D PHE* 4.5 13.6 - - + +
136D ARG* 2.6 33.1 + - - +
159D THR* 2.6 43.0 + - - +
160D HIS* 3.5 5.4 - - - +
161D PHE 3.1 0.2 - - - -
162D ALA* 1.3 79.2 - - - +
164D ILE* 1.3 66.0 + - - +
165D ASN 3.1 1.1 - - - -
166D THR* 3.4 7.6 + - - +
167D PHE* 3.1 19.6 + - - +
339D MET* 4.8 4.2 - - - +
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Residues in contact with ILE 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132D PHE* 3.9 30.7 - - + +
135D PHE* 3.5 26.9 - - + -
160D HIS* 2.9 53.1 + - + +
161D PHE* 3.9 13.9 - - + +
163D ASP* 1.3 69.1 - - - +
165D ASN* 1.3 73.1 + - + +
167D PHE* 3.2 9.3 - - - +
168D MET* 3.0 40.2 + - + +
224D TYR* 4.5 9.4 - - + +
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Residues in contact with ASN 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161D PHE* 2.9 53.2 + - + +
162D ALA 3.6 4.9 - - - +
164D ILE* 1.3 85.6 - - + +
166D THR* 1.3 63.7 + - - +
167D PHE 3.0 1.4 + - - -
168D MET* 3.1 23.0 + - - +
169D VAL* 3.5 11.6 + - - +
202D CYS* 6.0 1.0 - - - -
326D TYR* 3.3 17.5 + - - -
340D MET* 3.9 9.6 - - - +
343D LEU* 3.4 23.6 - - - +
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Residues in contact with THR 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162D ALA 3.3 8.7 + - - -
163D ASP* 3.7 5.8 - - - +
165D ASN* 1.3 78.2 - - - +
167D PHE* 1.3 61.1 + - - +
169D VAL* 3.8 3.6 + - - +
170D LEU* 3.2 34.8 + - + +
339D MET 4.9 0.3 + - - -
340D MET* 3.1 34.1 - - - +
341D PRO* 5.1 2.4 - - + +
342D LEU* 4.0 19.1 - - + +
343D LEU* 3.7 15.0 - - - +
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Residues in contact with PHE 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128D MET* 3.4 46.7 - - + -
131D GLN* 4.4 14.8 - - + -
132D PHE* 3.4 27.1 - + - -
135D PHE* 3.9 34.3 - + + -
163D ASP 3.1 13.9 + - - +
164D ILE* 3.2 9.6 - - - +
165D ASN 3.0 0.8 + - - -
166D THR* 1.3 76.6 - - - +
168D MET* 1.3 67.7 + - - +
170D LEU* 3.2 21.7 + - + +
171D GLN* 3.4 28.2 + - + +
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Residues in contact with MET 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128D MET* 3.6 33.0 - - + +
132D PHE* 4.0 11.4 - - + -
164D ILE* 3.0 35.5 + - + +
165D ASN* 3.1 17.7 + - - +
167D PHE* 1.3 75.4 - - - +
169D VAL* 1.3 55.7 + - - +
171D GLN* 2.8 25.8 + - - +
172D VAL* 2.8 16.2 + - + +
202D CYS* 3.8 32.1 - - + +
206D LEU* 3.6 35.2 - - + -
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Residues in contact with VAL 169 (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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165D ASN* 3.5 7.3 + - - +
166D THR 3.9 2.9 - - - +
167D PHE 3.3 0.2 - - - -
168D MET* 1.3 76.0 - - - +
170D LEU* 1.3 54.0 + - - +
172D VAL* 3.4 7.7 - - - +
173D ILE* 2.7 44.8 + - + +
198D ALA* 4.5 18.6 - - + +
199D VAL* 5.5 1.8 - - + +
202D CYS* 4.2 14.6 - - - -
342D LEU* 3.3 30.1 - - + -
343D LEU* 3.7 30.5 - - + -
346D ILE* 4.5 12.8 - - + -
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Residues in contact with LEU 170 (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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166D THR* 3.2 28.2 + - + +
167D PHE* 3.2 19.7 + - + +
168D MET 3.1 0.6 - - - -
169D VAL* 1.3 76.8 - - - +
171D GLN* 1.3 57.5 + - - +
173D ILE* 3.8 5.7 - - + +
174D LYS* 2.7 44.5 + - - +
342D LEU* 4.4 12.1 - - + -
693H LEU* 3.6 29.8 - - + +
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Residues in contact with GLN 171 (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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124D HIS* 3.2 32.9 + - - +
125D MET* 3.6 18.6 - - + +
128D MET* 3.7 21.5 - - - +
131D GLN* 5.5 2.8 + - - -
167D PHE* 3.6 31.8 - - + +
168D MET 2.8 9.9 + - - +
170D LEU* 1.3 77.7 - - - +
172D VAL* 1.3 57.7 + - - +
173D ILE 3.1 1.1 - - - -
174D LYS* 2.9 39.9 + - - +
175D PHE* 2.5 35.9 + - - +
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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
----------------------------------------------------------
125D MET* 3.6 13.0 - - - -
168D MET* 2.8 10.9 + - + +
169D VAL* 3.4 10.3 - - - +
171D GLN* 1.3 76.7 - - - +
173D ILE* 1.3 60.9 + - + +
175D PHE* 3.7 1.2 - - + +
176D THR* 3.2 32.0 + - + +
194D LEU* 4.5 9.0 - - + -
198D ALA* 3.9 20.9 - - + +
201D ILE* 3.6 48.7 - - + -
202D CYS* 3.6 28.7 - - - -
205D VAL* 5.4 0.4 - - + -
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Residues in contact with ILE 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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169D VAL* 2.7 36.2 + - + +
170D LEU* 3.8 6.1 - - - +
172D VAL* 1.3 76.1 - - + +
174D LYS* 1.3 65.2 + - + +
176D THR* 3.1 7.8 + - - -
177D LYS* 3.0 44.5 + - + +
194D LEU* 4.2 22.2 - - + -
198D ALA* 6.0 0.2 - - + -
342D LEU* 4.5 10.1 - - + -
346D ILE* 5.4 2.2 - - + -
690H LEU* 4.6 19.3 - - + -
693H LEU* 4.0 38.8 - - + -
694H LEU* 4.6 6.7 - - + -
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Residues in contact with LYS 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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124D HIS* 3.2 28.4 + - + +
170D LEU* 2.7 29.6 + - - +
171D GLN* 2.9 32.3 + - - +
173D ILE* 1.3 77.5 - - + +
175D PHE* 1.3 64.4 + - - +
177D LYS* 3.2 22.1 + - - +
178D ASP* 3.3 12.1 + - - +
693H LEU* 6.4 0.7 - - + -
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Residues in contact with PHE 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117D LEU* 3.5 19.3 - - + -
120D ALA* 3.3 24.2 - - + +
121D HIS* 3.3 34.1 - - + -
124D HIS* 3.8 12.5 - - + -
125D MET* 3.8 27.8 - - + -
171D GLN 2.5 21.7 + - - +
172D VAL* 3.7 4.0 - - + +
174D LYS* 1.3 75.4 - - - +
176D THR* 1.3 83.2 + - + +
178D ASP* 3.1 20.1 + - - +
179D LEU* 3.7 23.3 - - + +
201D ILE* 5.7 5.6 - - + -
260D VAL* 4.6 9.2 - - + -
263D ALA* 5.7 10.8 - - + -
264D ALA* 6.1 2.5 - - - -
267D LEU* 5.3 4.3 - - + -
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Residues in contact with THR 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172D VAL* 3.2 18.8 + - + +
173D ILE* 3.1 15.6 + - - -
175D PHE* 1.3 87.6 - - + +
177D LYS* 1.3 57.9 + - - +
178D ASP 3.0 5.2 - - - -
179D LEU* 3.0 37.0 + - - +
182D PHE* 3.9 26.9 - - - +
194D LEU* 4.0 12.3 - - + +
201D ILE* 5.2 2.7 - - + -
267D LEU* 3.8 29.8 - - + -
694H LEU* 6.0 0.2 - - - +
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Residues in contact with LYS 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173D ILE* 3.0 34.7 + - + +
174D LYS* 3.2 13.0 + - - +
176D THR* 1.3 77.3 + - - +
178D ASP* 1.3 54.3 + - - +
179D LEU 3.1 4.7 + - - -
182D PHE* 5.5 1.8 - - + -
183D ARG* 3.5 33.4 - - - +
693H LEU* 2.7 41.7 + - - +
694H LEU* 3.6 23.6 - - + -
696H GLU 4.1 20.7 - - - +
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Residues in contact with ASP 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116D THR* 5.0 1.9 - - - +
120D ALA* 3.3 18.3 - - + +
123D ARG* 3.4 24.3 + - - -
124D HIS* 3.6 24.6 - - + +
174D LYS 3.3 2.5 + - - +
175D PHE 3.1 10.5 + - - +
176D THR 3.0 0.6 - - - -
177D LYS* 1.3 76.2 - - - +
179D LEU* 1.3 71.8 + - - +
180D PRO* 4.3 3.8 - - - +
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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