Contacts of the helix formed by residues 148 - 177 (chain D) in PDB entry 3RT0
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 148 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143D VAL* 3.9 2.9 - - - -
146D GLY 5.6 0.4 - - - +
147D ASN* 1.3 79.7 - - - +
149D LYS* 1.3 66.2 + - - +
150D GLU* 3.8 8.5 + - - +
151D GLU* 2.9 48.2 + - - +
152D THR* 2.9 13.9 + - - -
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Residues in contact with LYS 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D GLN 5.7 0.4 - - - +
27D CYS* 3.3 22.0 - - + +
28D SER 5.3 3.8 - - - +
143D VAL* 3.8 25.5 - - + +
148D THR* 1.3 71.1 - - - +
150D GLU* 1.3 65.8 + - + +
152D THR* 3.3 2.2 + - - -
153D CYS* 2.9 45.7 + - - -
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Residues in contact with GLU 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148D THR* 3.1 7.9 - - - +
149D LYS* 1.3 89.8 - - + +
151D GLU* 1.3 63.4 + - + +
153D CYS* 3.6 4.8 + - - +
154D PHE* 3.1 43.9 + - + +
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Residues in contact with GLU 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B ILE* 4.1 22.7 - - + +
384B GLN* 5.2 7.8 + - - +
385B TRP* 4.7 1.8 - - + -
146D GLY 4.5 1.2 - - - +
147D ASN* 2.7 38.3 + - + +
148D THR* 2.9 41.8 + - - +
150D GLU* 1.3 78.7 - - + +
152D THR* 1.3 57.0 + - - +
154D PHE* 3.2 9.1 + - - +
155D PHE* 2.9 30.1 + - - +
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Residues in contact with THR 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B TRP* 3.9 25.2 - - + -
27D CYS* 3.7 21.5 - - - -
113D LEU* 4.9 2.2 - - + -
141D VAL* 4.0 16.6 - - + -
142D ASP 4.6 0.9 - - - +
143D VAL* 3.5 7.0 - - - +
144D PRO* 3.5 26.3 - - + +
147D ASN* 4.1 1.4 - - - +
148D THR 2.9 12.8 + - - -
149D LYS* 3.7 7.4 - - - -
151D GLU* 1.3 73.5 - - - +
153D CYS* 1.3 64.9 + - - +
155D PHE* 3.1 1.4 + - - +
156D VAL* 2.9 33.5 + - + +
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Residues in contact with CYS 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D CYS* 3.7 25.1 - - - -
28D SER 3.9 21.8 - - - -
29D SER* 4.3 3.6 - - - -
139D PHE* 4.3 7.6 - - - -
149D LYS* 2.9 32.6 + - - +
150D GLU* 4.0 4.7 - - - +
152D THR* 1.3 75.7 - - - +
154D PHE* 1.3 55.0 + - - +
157D GLU* 2.7 55.0 + - + +
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Residues in contact with PHE 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B LYS* 3.8 46.7 - - + -
383B ILE* 3.8 15.4 - - + +
391B PHE* 5.1 11.4 - + - -
150D GLU* 3.1 36.3 + - + +
151D GLU* 3.2 11.4 + - - +
153D CYS* 1.3 79.1 - - - +
155D PHE* 1.3 56.9 + - - +
157D GLU* 3.8 14.7 + - + +
158D ALA* 3.0 30.7 + - + +
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Residues in contact with PHE 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B ILE* 4.0 8.7 - - + +
385B TRP* 3.6 61.7 - + + -
391B PHE 4.4 2.0 - - - +
392B GLY* 3.1 40.6 - - - -
84D PRO* 3.9 11.9 - - + -
113D LEU* 4.2 15.7 - - + -
151D GLU 2.9 15.6 + - - +
152D THR 3.1 3.8 + - - +
154D PHE* 1.3 72.7 - - - +
156D VAL* 1.3 75.8 + - + +
158D ALA* 3.3 7.1 + - - +
159D LEU* 3.1 51.1 + - + +
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Residues in contact with VAL 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113D LEU* 4.2 27.1 - - + -
116D TYR* 3.8 16.6 - - + +
139D PHE* 3.4 49.6 - - + -
141D VAL* 4.6 1.6 - - + -
152D THR* 2.9 27.1 + - + +
155D PHE* 1.3 74.3 - - + +
157D GLU* 1.3 62.5 + - - +
159D LEU* 2.9 9.4 + - + +
160D ILE* 2.8 38.5 + - + +
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Residues in contact with GLU 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D SER* 2.6 37.5 + - - +
31D LEU* 3.4 27.5 - - + +
139D PHE* 4.5 0.7 - - + -
153D CYS* 2.7 40.5 + - - +
154D PHE* 3.8 16.2 - - + +
156D VAL* 1.3 72.9 - - - +
158D ALA* 1.3 57.7 + - - +
160D ILE 3.3 0.2 + - - -
161D GLN* 2.8 33.9 + - + +
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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
----------------------------------------------------------
391B PHE* 4.0 35.4 - - + +
393B VAL* 5.5 2.2 - - + -
154D PHE* 3.0 20.7 + - + +
155D PHE 3.4 5.4 - - - +
156D VAL 3.1 0.2 - - - -
157D GLU* 1.3 76.2 - - - +
159D LEU* 1.3 59.7 + - + +
161D GLN* 3.5 4.9 + - - +
162D SER* 2.6 34.7 + - - -
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Residues in contact with LEU 159 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B PHE 5.8 0.4 - - - +
393B VAL* 4.1 19.7 - - + -
58D PHE* 3.9 31.5 - - + -
83D LEU* 6.0 3.1 - - + -
113D LEU* 5.6 6.5 - - + -
155D PHE* 3.1 39.8 + - + +
156D VAL* 2.9 10.1 + - + +
158D ALA* 1.3 81.2 - - + +
160D ILE* 1.3 63.2 + - + +
162D SER* 3.3 5.4 + - - +
163D ASN* 3.0 32.8 + - - +
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Residues in contact with ILE 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D LEU* 3.9 20.0 - - + -
116D TYR* 3.6 13.2 - - - +
137D GLU* 3.8 43.3 - - + +
139D PHE* 3.4 35.7 - - + -
156D VAL* 2.8 27.9 + - + +
157D GLU 4.0 2.7 - - - +
159D LEU* 1.3 70.1 - - + +
161D GLN* 1.3 66.6 + - - +
163D ASN* 3.0 12.6 + - - +
164D LEU* 2.8 34.7 + - + +
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Residues in contact with GLN 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D LEU* 3.5 26.9 - - + +
32D VAL 4.0 16.6 + - - +
33D LYS* 5.1 2.5 - - - +
157D GLU 2.8 18.2 + - - +
158D ALA* 3.8 6.3 - - - +
160D ILE* 1.3 72.9 - - - +
162D SER* 1.3 63.8 + - - +
163D ASN 3.1 0.2 + - - -
164D LEU* 3.1 9.1 + - - +
165D ASN* 2.8 65.7 + - - +
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Residues in contact with SER 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B TYR* 6.0 5.6 - - - -
57D PRO* 4.8 8.7 - - - +
58D PHE* 4.8 18.0 - - - -
158D ALA 2.6 23.8 + - - -
159D LEU* 3.6 8.2 + - - +
160D ILE 3.3 0.2 - - - -
161D GLN* 1.3 77.6 - - - +
163D ASN* 1.3 59.9 + - - +
165D ASN* 3.8 7.9 - - - +
166D SER* 2.9 31.0 + - - -
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Residues in contact with ASN 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55D TYR* 3.6 13.7 - - + -
56D LYS* 3.6 41.8 - - + +
57D PRO* 3.7 14.5 - - - +
58D PHE* 5.4 5.2 + - - +
137D GLU* 5.3 7.2 + - - +
159D LEU* 3.0 26.3 + - - +
160D ILE* 3.0 15.2 + - - +
162D SER* 1.3 77.6 - - - +
164D LEU* 1.3 59.0 + - + +
166D SER* 3.3 5.2 + - - -
167D LEU* 2.9 27.7 + - - +
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Residues in contact with LEU 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D LEU* 4.0 37.0 - - + +
32D VAL 4.4 1.6 - - - +
33D LYS* 3.7 30.3 - - + +
55D TYR* 5.9 2.2 - - + -
120D ILE* 4.4 11.2 - - + -
135D ALA* 4.2 24.7 - - + +
137D GLU* 4.2 18.4 - - + +
160D ILE* 2.8 28.5 + - + +
161D GLN* 3.7 9.9 - - - +
163D ASN* 1.3 72.7 - - + +
165D ASN* 1.3 59.0 + - - +
167D LEU* 3.1 12.5 + - + +
168D ALA* 2.9 29.6 + - - +
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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
----------------------------------------------------------
33D LYS* 3.5 29.1 + - - +
161D GLN* 2.8 50.6 + - - +
162D SER* 3.8 7.1 - - - +
164D LEU* 1.3 72.7 - - - +
166D SER* 1.3 62.1 + - - +
168D ALA* 3.5 2.3 + - - +
169D ASP* 3.0 23.0 + - - +
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Residues in contact with SER 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55D TYR* 2.5 32.2 + - - -
57D PRO* 4.1 16.1 - - - +
162D SER 2.9 17.8 + - - -
163D ASN 3.7 1.3 - - - -
165D ASN* 1.3 74.2 - - - +
167D LEU* 1.3 60.6 + - - +
169D ASP* 3.3 6.8 + - - +
170D VAL* 2.8 36.7 + - - +
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Residues in contact with LEU 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D ILE* 3.8 22.4 - - + -
42D VAL* 4.1 3.8 - - + -
45D ILE* 3.8 21.5 - - + -
46D VAL* 3.6 27.8 - - + -
55D TYR* 3.5 41.0 - - + -
120D ILE* 4.8 2.2 - - + -
135D ALA* 4.8 5.4 - - + -
163D ASN 2.9 9.1 + - - +
164D LEU* 3.1 24.4 + - + +
166D SER* 1.3 74.1 - - - +
168D ALA* 1.3 65.3 + - - +
170D VAL* 3.2 1.2 + - - -
171D THR* 2.9 37.5 + - + +
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Residues in contact with ALA 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D LYS* 3.5 32.3 - - - +
35D ILE* 3.8 21.7 - - + +
164D LEU 2.9 7.3 + - - +
165D ASN 3.5 6.7 - - - +
167D LEU* 1.3 76.4 - - - +
169D ASP* 1.3 62.7 + - - +
171D THR* 3.3 0.9 + - - -
172D GLU* 2.9 45.4 + - - +
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Residues in contact with ASP 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B GLU* 5.7 0.7 - - - +
165D ASN 3.0 14.7 + - - +
166D SER* 3.4 11.7 - - - +
168D ALA* 1.3 75.2 - - - +
170D VAL* 1.3 67.2 + - + +
172D GLU* 4.1 6.4 - - - +
173D ARG* 3.1 34.7 + - - +
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Residues in contact with VAL 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D ILE* 3.7 24.9 - - + -
54D LYS* 3.8 25.4 - - + +
55D TYR* 4.3 6.7 - - + -
166D SER* 2.8 33.6 + - - +
167D LEU 3.9 2.5 - - - +
169D ASP* 1.3 76.5 - - + +
171D THR* 1.3 59.7 + - + +
173D ARG* 3.4 32.6 + - - +
174D LEU* 3.1 29.0 + - + +
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Residues in contact with THR 171 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D ILE* 3.1 23.7 - - - +
37D ALA* 3.9 14.3 - - - +
41D LEU* 4.3 6.9 - - + +
42D VAL* 4.0 24.2 - - + -
45D ILE* 3.9 23.1 - - + -
167D LEU* 2.9 36.3 + - + +
170D VAL* 1.3 73.0 - - + +
172D GLU* 1.3 62.8 + - - +
174D LEU* 3.3 8.1 + - - +
175D GLN* 2.9 28.9 + - - +
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Residues in contact with GLU 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D HIS 4.5 1.9 - - - +
35D ILE* 3.6 10.6 - - + +
36D LYS* 2.7 75.1 + - + +
168D ALA* 2.9 29.5 + - - +
169D ASP* 4.1 5.1 + - - +
171D THR* 1.3 77.8 + - - +
173D ARG* 1.3 62.9 + - - +
175D GLN* 3.3 8.1 + - - +
176D ALA* 3.1 22.3 + - - +
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Residues in contact with ARG 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169D ASP* 3.1 29.2 + - - +
170D VAL* 3.6 37.3 - - - +
171D THR 3.2 0.2 - - - -
172D GLU* 1.3 78.7 - - - +
174D LEU* 1.3 77.3 + - - +
176D ALA* 3.4 6.0 + - - +
177D GLU* 2.9 58.9 + - + +
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Residues in contact with LEU 174 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D LEU* 4.2 23.3 - - + +
45D ILE* 3.3 36.8 - - + -
170D VAL* 3.1 21.6 + - + +
171D THR* 3.3 5.6 + - - +
173D ARG* 1.3 89.1 - - - +
175D GLN* 1.3 57.3 + - - +
177D GLU* 3.4 22.3 + - + +
178D SER* 3.2 25.3 + - - -
----------------------------------------------------------
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Residues in contact with GLN 175 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D LYS 4.2 11.4 - - - +
37D ALA* 4.4 4.8 - - + -
38D PRO* 3.4 34.6 - - - +
40D HIS* 5.9 0.2 - - - -
41D LEU* 3.6 12.3 - - + +
171D THR 2.9 17.8 + - - +
172D GLU* 3.3 9.4 - - - +
173D ARG 3.1 0.2 - - - -
174D LEU* 1.3 74.8 - - - +
176D ALA* 1.3 65.4 + - - +
178D SER* 2.5 32.1 + - - -
179D MET* 3.3 28.0 + - + +
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Residues in contact with ALA 176 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172D GLU 3.1 9.5 + - - +
173D ARG* 3.8 7.9 - - - +
175D GLN* 1.3 75.1 - - - +
177D GLU* 1.3 59.4 + - + +
178D SER 2.9 10.3 + - - -
179D MET* 3.0 26.1 + - - +
180D GLU* 4.0 6.2 + - - +
----------------------------------------------------------
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Residues in contact with GLU 177 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173D ARG* 2.9 54.5 + - + +
174D LEU* 3.4 28.1 - - + +
175D GLN 3.2 0.2 - - - -
176D ALA* 1.3 75.5 - - + +
178D SER* 1.3 58.0 + - - +
180D GLU* 4.1 13.7 - - - +
----------------------------------------------------------
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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
------------------------------------------------------------
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