Contacts of the helix formed by residues 187 - 210 (chain A) in PDB entry 3RFU
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 TYR 187 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A ALA* 4.8 12.1 - - + +
162A TYR* 3.1 51.2 + + - -
163A SER* 3.8 7.2 - - - -
177A PHE* 6.1 0.2 - - - -
185A ALA* 4.6 5.0 - - + +
186A VAL* 1.3 73.0 - - - +
188A PHE* 1.3 64.7 + - - +
189A GLU* 3.1 3.4 - - - +
190A ALA* 2.8 23.1 + - + +
191A ALA* 3.0 11.9 + - - +
375A VAL* 6.2 0.4 - - + -
376A SER* 4.5 4.6 + - - -
379A ILE* 4.4 31.4 - - + -
708A LEU* 2.7 44.4 + - + +
709A SER 3.7 2.0 - - - -
710A PRO* 3.2 46.1 - - + +
713A ALA* 4.8 5.2 - - + -
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Residues in contact with PHE 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A VAL* 4.5 1.3 - - + -
115A SER 3.9 1.6 - - - -
118A GLN* 3.8 13.5 - - + +
119A LEU* 3.3 40.6 - - + -
122A ALA* 3.7 26.1 - - + +
160A TRP* 3.7 31.2 - + + -
163A SER* 2.8 30.3 - - - -
164A MET* 3.2 31.6 - - + -
167A VAL* 3.8 9.2 - - + -
186A VAL* 3.2 22.4 - - + +
187A TYR* 1.3 76.5 - - - +
189A GLU* 1.3 64.3 + - - +
191A ALA* 3.1 8.5 + - + +
192A ALA* 2.9 24.1 + - - +
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Residues in contact with GLU 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A VAL* 3.9 15.1 - - + +
96A VAL* 4.0 37.3 - - + +
99A GLU* 3.9 35.6 - - + +
100A MET* 3.8 22.7 - - - +
118A GLN* 4.6 2.2 - - - +
186A VAL 4.8 1.7 + - - +
187A TYR* 3.1 1.7 - - - -
188A PHE* 1.3 79.1 - - - +
190A ALA* 1.3 62.7 + - - +
192A ALA* 3.9 0.7 - - - +
193A VAL* 3.0 27.7 + - + +
710A PRO* 4.6 8.9 - - + +
714A ALA* 3.9 18.2 - - - +
717A MET* 4.4 12.4 - - - +
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Residues in contact with ALA 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A TYR* 2.8 23.3 + - + +
189A GLU* 1.3 81.4 + - - +
191A ALA* 1.3 63.0 + - - +
194A ILE* 3.0 37.2 + - + +
379A ILE* 4.0 22.9 - - + -
710A PRO* 6.2 1.1 - - + -
713A ALA* 5.0 10.3 - - + -
717A MET* 4.2 16.6 - - + -
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Residues in contact with ALA 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ALA* 5.4 0.7 - - + -
126A VAL* 3.5 23.6 - - + -
156A ILE* 3.6 17.2 - - + +
159A ALA* 4.4 18.0 - - + +
160A TRP* 4.9 7.2 - - + +
187A TYR 3.0 10.2 + - - +
188A PHE* 3.1 13.9 + - + +
190A ALA* 1.3 76.7 - - - +
192A ALA* 1.3 64.3 + - - +
195A THR* 3.0 27.7 + - - +
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Residues in contact with ALA 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A THR* 3.3 27.6 - - + +
95A VAL* 4.6 7.0 - - + -
122A ALA* 4.4 6.5 - - + -
125A VAL* 3.5 25.5 - - + +
126A VAL* 4.2 0.6 - - - +
188A PHE 2.9 15.4 + - - +
189A GLU 3.9 3.1 - - - +
191A ALA* 1.3 75.8 - - - +
193A VAL* 1.3 63.0 + - - +
195A THR* 2.8 18.7 + - - -
196A THR* 2.9 14.5 + - - +
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Residues in contact with VAL 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A THR* 4.0 7.0 - - + -
96A VAL* 3.9 28.7 - - + -
189A GLU* 3.0 17.2 + - + +
192A ALA* 1.3 78.9 - - - +
194A ILE* 1.3 65.5 + - - +
196A THR* 3.4 4.7 + - - -
197A LEU* 3.0 48.3 + - + +
384A CYS* 4.5 1.1 - - + -
717A MET* 3.3 36.3 - - + -
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Residues in contact with ILE 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A ILE* 4.7 5.4 - - + -
156A ILE* 3.4 27.4 - - + -
190A ALA* 3.0 37.8 + - + +
193A VAL* 1.3 77.5 - - - +
195A THR* 1.3 58.8 + - - +
197A LEU* 3.8 1.4 - - - +
198A VAL* 2.9 33.2 + - + +
379A ILE* 4.7 9.0 - - + +
382A CYS* 3.7 38.6 - - + +
383A PRO 4.7 2.0 - - - +
384A CYS* 3.8 32.7 - - + +
717A MET* 4.2 11.4 - - + -
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Residues in contact with THR 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ALA* 5.1 0.3 - - - +
125A VAL* 3.2 26.0 + - - +
126A VAL* 4.0 9.2 - - + -
130A GLY* 4.7 10.1 - - - -
133A PHE* 3.6 8.0 - - + -
156A ILE* 3.6 35.2 - - + -
191A ALA 3.0 15.9 + - - +
192A ALA* 2.8 17.7 + - - -
194A ILE* 1.3 76.2 - - - +
196A THR* 1.3 56.5 + - - +
198A VAL* 3.0 11.0 - - - +
199A LEU* 3.0 34.3 + - - +
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Residues in contact with THR 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A PHE* 3.4 20.5 - - - -
88A ALA* 3.3 25.6 - - + -
89A LEU* 4.3 15.8 - - - +
92A THR* 3.1 29.5 - - - +
125A VAL* 3.7 3.4 - - + -
192A ALA 2.9 17.1 + - - +
193A VAL* 3.5 8.7 + - - +
195A THR* 1.3 75.1 - - - +
197A LEU* 1.3 68.7 + - - +
199A LEU* 4.2 8.3 - - - -
200A LEU 3.0 19.8 + - - -
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Residues in contact with LEU 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A LEU* 6.6 0.2 - - + -
193A VAL* 3.0 40.2 + - + +
194A ILE 3.8 3.4 - - - +
196A THR* 1.3 86.9 + - - +
198A VAL* 1.3 59.6 + - - +
200A LEU* 3.2 15.2 - - + +
201A GLY 3.0 19.8 + - - -
384A CYS* 3.4 43.3 - - + +
385A ALA* 4.8 0.7 - - - +
388A LEU* 3.5 26.5 - - + +
721A SER* 3.8 14.1 - - - +
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Residues in contact with VAL 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A PHE* 3.1 35.4 - - + -
148A MET* 5.1 2.0 - - - -
149A PHE* 5.0 4.7 - - + -
152A ILE* 3.3 34.8 - - + -
194A ILE 2.9 21.8 + - - +
195A THR* 3.0 20.9 - - - +
197A LEU* 1.3 74.7 - - - +
199A LEU* 1.3 63.5 + - - +
201A GLY* 3.0 3.7 + - - +
202A GLN* 3.0 27.7 + - - +
384A CYS 4.3 6.9 + - - +
387A GLY* 4.6 11.6 - - - -
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Residues in contact with LEU 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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81A MET* 3.9 19.8 - - + +
84A ARG* 3.9 36.8 - - + -
85A PHE* 4.0 22.7 - - + -
88A ALA* 4.2 16.4 - - + -
129A GLY 4.0 11.9 - - - +
130A GLY 4.2 6.7 - - - +
132A PRO* 5.4 1.1 - - + -
133A PHE* 3.5 23.1 - - + -
195A THR* 3.0 24.8 + - - +
196A THR* 3.6 6.5 - - - +
198A VAL* 1.3 73.3 - - - +
200A LEU* 1.3 65.7 + - - +
202A GLN* 3.1 6.4 + - - +
203A VAL* 3.0 24.9 + - - +
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Residues in contact with LEU 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A PHE* 3.4 41.7 - - + -
196A THR 3.0 9.1 + - - +
197A LEU* 3.2 18.8 - - + +
198A VAL 3.2 0.2 - - - -
199A LEU* 1.3 75.8 - - - +
201A GLY* 1.3 60.8 + - - +
203A VAL* 3.3 10.0 + - + +
204A LEU* 3.0 47.9 + - + +
388A LEU* 3.8 27.1 - - + -
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Residues in contact with GLY 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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197A LEU 3.0 9.3 + - - -
198A VAL 3.0 6.8 + - - -
200A LEU* 1.3 78.2 - - - +
202A GLN* 1.3 59.5 + - - +
204A LEU* 3.4 2.2 + - - +
205A GLU* 3.0 30.4 + - - +
387A GLY* 2.9 32.6 - - - +
388A LEU* 3.8 5.2 - - - -
391A PRO* 4.2 4.1 - - - +
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Residues in contact with GLN 202 (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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81A MET* 4.0 27.0 - - + +
133A PHE* 4.0 18.5 - - + -
136A ARG* 4.4 13.5 + - - -
148A MET* 4.4 8.3 - - - +
149A PHE* 3.8 34.2 - - - -
198A VAL* 3.0 22.6 + - - +
199A LEU* 3.1 7.6 + - - +
201A GLY* 1.3 76.1 - - - +
203A VAL* 1.3 65.3 + - - +
205A GLU* 3.4 23.1 + - - +
206A LEU* 3.0 36.3 + - + +
387A GLY* 5.6 2.2 + - - -
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Residues in contact with VAL 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A TYR* 3.5 26.3 - - + +
81A MET* 4.0 8.7 - - + +
82A ARG* 3.9 36.1 - - + +
85A PHE* 4.3 14.4 - - + -
199A LEU 3.0 17.1 + - - +
200A LEU* 3.3 14.1 + - + +
202A GLN* 1.3 77.2 - - - +
204A LEU* 1.3 70.1 + - + +
207A LYS* 3.0 30.7 + - + +
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Residues in contact with LEU 204 (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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200A LEU* 3.0 32.3 + - + +
201A GLY 3.9 1.1 - - - +
202A GLN 3.3 0.2 - - - -
203A VAL* 1.3 85.9 - - + +
205A GLU* 1.3 65.6 + - - +
207A LYS* 3.4 24.8 + - - +
208A ALA* 3.0 24.9 + - - +
388A LEU* 4.5 13.9 - - + -
391A PRO* 3.9 17.4 - - + +
392A MET* 4.5 18.8 - - + -
395A MET* 4.4 26.1 - - - +
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Residues in contact with GLU 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A MET* 5.4 4.3 - - - +
201A GLY 3.0 17.3 + - - +
202A GLN* 3.8 25.3 + - - +
204A LEU* 1.3 75.5 - - - +
206A LEU* 1.3 76.1 + - + +
208A ALA* 3.2 2.9 + - - +
209A ARG* 3.0 55.6 + - - +
334A ARG* 3.6 32.5 + - - -
391A PRO* 4.0 12.0 - - + +
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Residues in contact with LEU 206 (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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75A SER* 5.2 0.7 - - - +
77A GLU* 4.2 24.2 - - + +
78A TYR* 3.2 52.5 - - + +
81A MET* 4.3 14.1 - - + -
202A GLN* 3.0 28.8 + - + +
205A GLU* 1.3 92.1 - - + +
207A LYS* 1.3 55.3 + - - +
209A ARG* 3.0 4.3 + - + -
210A GLU* 2.6 40.7 + - + +
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Residues in contact with LYS 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A TYR* 3.8 22.1 - - + +
203A VAL* 3.0 20.3 + - - +
204A LEU* 3.4 25.5 + - - +
206A LEU* 1.3 75.6 - - - +
208A ALA* 1.3 58.9 + - - +
210A GLU* 3.9 22.2 + - - +
211A GLN* 4.3 6.6 + - - +
395A MET* 6.0 6.0 - - - +
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Residues in contact with ALA 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A LEU 3.0 16.9 + - - +
205A GLU* 3.5 7.0 - - - +
206A LEU 3.0 1.0 - - - -
207A LYS* 1.3 79.8 - - - +
209A ARG* 1.3 66.5 + - + +
210A GLU 3.5 0.4 - - - -
211A GLN* 5.6 0.7 - - - -
391A PRO* 5.3 4.5 - - + +
394A ILE* 4.5 21.8 - - + +
395A MET* 5.3 10.5 - - + -
398A VAL* 6.5 0.2 - - + -
409A LYS 5.6 0.5 - - - +
410A ASN* 4.9 5.0 - - - -
411A ALA 4.8 6.9 + - - -
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Residues in contact with ARG 209 (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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205A GLU* 3.0 44.9 + - - +
206A LEU* 3.0 6.0 + - + +
208A ALA* 1.3 84.2 - - + +
210A GLU* 1.3 65.4 + - - +
211A GLN 3.8 4.5 - - - +
212A THR* 5.0 4.2 - - - +
334A ARG* 3.0 34.9 - - - +
390A THR* 4.1 15.0 - - - +
391A PRO* 4.9 5.5 - - - +
394A ILE* 4.2 9.1 - - - +
410A ASN* 5.5 5.6 - - + +
411A ALA* 3.5 32.3 - - + +
412A GLU* 4.1 17.9 + - - +
415A GLU* 3.3 23.8 + - - -
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Residues in contact with GLU 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A VAL* 4.2 8.1 - - - +
75A SER* 3.6 38.6 + - - +
78A TYR* 4.3 23.1 - - + -
79A LEU* 5.3 1.0 - - - +
206A LEU* 2.6 20.4 + - + +
207A LYS* 3.9 19.8 - - - +
208A ALA 3.5 2.4 - - - -
209A ARG* 1.3 75.7 - - - +
211A GLN* 1.3 89.7 + - + +
212A THR* 3.1 14.9 + - - +
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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