Contacts of the helix formed by residues 135 - 157 (chain D) in PDB entry 1OHV
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 CYS 135 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134C ALA* 5.7 1.3 - - + -
138C CYS* 5.5 1.3 - - - -
352C ASN* 6.1 4.5 - - - -
354C TRP* 4.2 9.0 - - + -
800C FES 2.3 44.2 - - - -
133D MET* 3.4 1.0 - - - +
134D ALA* 1.3 80.7 - - - +
136D GLY* 1.3 60.0 + - - +
137D SER* 3.6 6.7 - - - -
138D CYS* 3.5 15.2 - - - -
139D SER* 2.6 32.8 + - - -
328D SER* 3.4 13.0 - - - -
334D GLY* 4.1 0.6 - - - -
600D PLP 3.5 17.3 - - - +
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Residues in contact with GLY 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135D CYS* 1.3 73.1 - - - +
137D SER* 1.3 63.3 - - - +
139D SER* 3.2 5.3 + - - -
140D ASN* 3.0 27.4 + - - +
300D VAL* 3.9 12.4 - - - +
328D SER* 3.2 19.2 + - - -
600D PLP 3.0 25.9 + - - -
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Residues in contact with SER 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352C ASN* 5.2 2.8 - - - +
800C FES 4.8 0.7 - - - -
135D CYS* 3.4 7.3 - - - -
136D GLY* 1.3 76.6 - - - +
138D CYS* 1.3 57.2 + - - +
140D ASN 3.2 0.9 + - - -
141D GLU* 2.9 33.7 + - - +
190D HIS 4.4 1.6 - - - -
191D GLY* 3.4 18.5 - - - -
192D ARG 3.6 5.4 + - - -
193D THR* 3.8 27.6 + - - +
196D CYS* 3.2 11.1 - - - -
600D PLP 2.6 25.0 + - - -
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Residues in contact with CYS 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135C CYS* 5.4 1.8 - - - -
193C THR* 4.5 6.1 - - + -
800C FES 2.3 43.7 - - - -
133D MET* 3.8 10.6 - - - +
134D ALA* 3.7 12.8 - - - -
135D CYS* 3.5 22.5 - - - -
137D SER* 1.3 75.7 - - - +
139D SER* 1.3 58.7 + - - +
141D GLU* 3.8 8.7 - - - -
142D ASN* 2.8 46.5 + - - +
352D ASN* 4.9 6.3 - - - +
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Residues in contact with SER 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133D MET* 3.5 10.6 - - - +
135D CYS 2.6 19.3 + - - -
136D GLY* 3.2 11.8 + - - -
137D SER 3.1 0.6 - - - -
138D CYS* 1.3 78.0 - - - +
140D ASN* 1.3 56.7 + - - +
143D ALA* 2.9 29.3 + - - +
326D THR* 3.8 10.8 - - - -
327D PHE 3.5 5.7 + - - -
335D GLY* 2.8 41.9 + - - -
336D PHE* 3.6 7.9 - - - -
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Residues in contact with ASN 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136D GLY 3.0 10.7 + - - +
139D SER* 1.3 74.3 - - - +
141D GLU* 1.3 58.7 + - - +
143D ALA* 3.3 4.3 + - - +
144D PHE* 2.9 47.5 + - + -
190D HIS* 2.8 25.4 + - + +
196D CYS* 3.7 16.4 - - - -
263D ILE* 4.0 13.7 - - - +
296D LEU* 4.4 0.9 - - - +
298D ASP* 2.8 27.1 + - - +
300D VAL* 4.7 0.6 - - - +
326D THR* 2.7 30.5 + - - +
600D PLP 3.8 5.3 - - - -
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Residues in contact with GLU 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193C THR* 3.9 26.9 - - + -
194C MET* 3.0 41.0 + - - +
137D SER 2.9 21.3 + - - +
138D CYS 4.0 3.8 - - - +
140D ASN* 1.3 76.5 - - - +
142D ASN* 1.3 58.3 + - - +
144D PHE* 3.2 11.0 + - - +
145D LYS* 3.1 30.7 + - - +
193D THR* 2.4 30.6 + - - +
194D MET 3.7 0.3 + - - -
195D GLY* 2.9 28.0 + - - -
196D CYS* 3.1 6.3 + - - -
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Residues in contact with ASN 142 (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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192C ARG* 5.6 2.3 + - - +
193C THR* 5.0 5.8 - - - +
133D MET* 3.3 34.8 - - + +
138D CYS* 2.8 35.3 + - - +
141D GLU* 1.3 78.1 - - - +
143D ALA* 1.3 55.3 + - - +
145D LYS* 3.4 28.0 + - - -
146D THR* 2.7 37.4 + - - -
336D PHE* 3.7 10.3 - - + -
350D ILE* 3.5 18.7 - - + +
351D PHE 4.3 5.3 + - - +
352D ASN* 4.3 5.1 - - - +
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Residues in contact with ALA 143 (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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139D SER 2.9 20.3 + - - +
140D ASN 3.5 5.2 - - - +
142D ASN* 1.3 74.5 - - - +
144D PHE* 1.3 64.8 + - - +
146D THR* 3.2 6.3 + - - -
147D ILE* 2.9 29.8 + - - +
296D LEU* 3.9 14.8 - - + -
324D VAL* 4.0 13.9 - - + -
326D THR* 3.7 19.7 - - + -
336D PHE* 3.9 7.1 - - + -
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Residues in contact with PHE 144 (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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194C MET* 3.5 22.9 - - + -
140D ASN* 2.9 25.9 + - + -
141D GLU* 3.2 11.0 + - - +
143D ALA* 1.3 76.7 - - - +
145D LYS* 1.3 57.0 + - - +
147D ILE* 3.2 7.8 + - - +
148D PHE* 2.9 48.1 + - + -
182D ILE* 3.9 26.9 - - + -
195D GLY 3.7 24.2 - - - -
196D CYS* 3.9 6.3 - - - -
199D THR* 3.5 29.2 - - + -
215D TRP* 4.6 0.7 - + - -
263D ILE* 3.8 13.7 - - + -
296D LEU* 3.5 27.4 - - + -
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Residues in contact with LYS 145 (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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192C ARG* 2.7 47.1 + - - +
193C THR* 5.4 0.7 - - - +
194C MET* 4.5 9.6 - - + +
197C LEU* 4.3 6.4 - - + +
206C HIS 4.8 4.0 + - - -
210C ILE* 3.6 44.1 - - + +
141D GLU 3.1 12.4 + - - +
142D ASN* 3.4 26.4 + - - +
143D ALA 3.3 0.2 - - - -
144D PHE* 1.3 72.5 - - - +
146D THR* 1.3 66.7 - - - +
148D PHE* 3.1 4.2 + - - +
149D MET* 2.9 30.2 + - - +
349D ARG 3.5 21.6 + - - -
350D ILE* 3.7 9.4 - - + +
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Residues in contact with THR 146 (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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131D ILE* 5.2 0.2 - - - +
142D ASN 2.7 22.3 + - - -
143D ALA* 3.4 6.3 - - - -
145D LYS* 1.3 76.5 - - - +
147D ILE* 1.3 58.3 + - - +
149D MET* 3.5 8.8 + - + +
150D TRP* 3.0 27.4 + - - +
324D VAL* 5.3 3.6 - - + -
336D PHE* 3.3 26.0 - - + -
338D HIS* 4.6 5.4 - - + +
342D PHE* 3.2 41.9 - - + +
344D PRO* 5.0 5.1 - - + +
350D ILE* 3.5 15.6 - - - +
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Residues in contact with ILE 147 (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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143D ALA 2.9 18.9 + - - +
144D PHE* 3.4 9.4 - - - +
145D LYS 3.1 0.2 - - - -
146D THR* 1.3 74.7 - - - +
148D PHE* 1.3 59.7 - - - +
150D TRP* 3.3 7.4 + - + +
151D TYR* 2.9 27.4 + - - +
182D ILE* 4.2 8.3 - - + -
260D ALA* 3.4 36.6 - - + +
261D GLY* 3.9 7.6 - - - +
294D ALA* 3.6 25.6 - - + -
296D LEU* 3.9 35.2 - - + -
324D VAL* 4.2 12.8 - - + -
342D PHE* 4.2 7.6 - - + -
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Residues in contact with PHE 148 (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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194C MET* 3.9 18.8 - - - -
209C ASP 3.4 19.1 - - - +
210C ILE* 4.4 4.9 - - + -
211C PRO* 3.3 31.4 - - + -
144D PHE* 2.9 35.7 + - + +
145D LYS* 3.7 9.0 - - - +
147D ILE* 1.3 71.9 - - - +
149D MET* 1.3 57.5 + - - +
151D TYR* 3.3 4.5 + - - +
152D ARG* 3.0 33.3 + - - +
180D TYR* 3.9 30.1 - - + -
181D SER 3.9 8.5 - - - -
182D ILE* 3.5 33.0 - - + -
215D TRP* 4.1 11.2 - + - -
260D ALA* 3.8 11.4 - - + -
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Residues in contact with MET 149 (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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208C ILE 5.6 0.2 - - - +
209C ASP* 4.3 11.2 - - + +
210C ILE* 4.3 13.9 - - + -
145D LYS 2.9 20.2 + - - +
146D THR* 3.6 7.4 - - + +
148D PHE* 1.3 74.6 - - - +
150D TRP* 1.3 59.7 + - - +
152D ARG* 3.7 1.9 + - - +
153D SER* 3.0 28.6 + - - -
156D ARG* 5.2 0.2 + - - -
342D PHE 5.6 0.2 - - - +
344D PRO* 3.5 43.5 - - + -
345D ASN 4.8 0.2 - - - +
349D ARG* 3.2 60.0 + - + +
350D ILE* 3.9 16.4 - - + -
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Residues in contact with TRP 150 (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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146D THR 3.0 18.2 + - - +
147D ILE 3.5 8.5 - - - +
149D MET* 1.3 75.5 - - - +
151D TYR* 1.3 80.3 + + - +
153D SER* 3.2 8.8 + - - -
154D LYS* 3.0 67.6 + - + +
260D ALA 3.7 1.3 - - - -
292D GLY* 3.3 19.5 - - - -
293D CYS 4.3 1.1 - - - -
294D ALA* 3.7 22.9 - - + -
323D ASP* 5.7 1.1 - - - -
341D GLU* 3.0 53.0 + - + +
342D PHE* 3.1 43.7 - + + +
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Residues in contact with TYR 151 (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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147D ILE 2.9 16.1 + - - +
148D PHE 3.6 4.3 - - - +
150D TRP* 1.3 92.1 - + - +
152D ARG* 1.3 63.8 + - - +
154D LYS* 3.1 28.1 + - - +
155D GLU* 3.2 38.0 + - + +
180D TYR* 3.7 12.3 - + + -
258D THR* 3.3 30.1 - - + +
259D VAL 3.9 4.0 + - - -
260D ALA* 3.5 34.5 - - + -
291D HIS 4.3 10.4 + - - -
292D GLY* 3.2 21.5 - - - -
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Residues in contact with ARG 152 (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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209C ASP* 3.2 36.9 + - + +
148D PHE 3.0 18.7 + - - +
149D MET 4.1 0.9 - - - +
151D TYR* 1.3 76.1 - - - +
153D SER* 1.3 57.9 + - - +
155D GLU* 3.2 15.6 + - - +
156D ARG* 2.9 74.3 + - - +
165D GLU* 3.0 24.0 + - - +
175D PRO* 3.6 23.9 + - - +
178D PRO* 3.6 16.8 - - + +
180D TYR* 3.3 31.1 + - + -
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Residues in contact with SER 153 (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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149D MET 3.0 21.7 + - - -
150D TRP* 3.4 11.9 - - - -
151D TYR 3.1 0.4 - - - -
152D ARG* 1.3 74.5 - - - +
154D LYS* 1.3 58.5 + - - +
156D ARG* 4.3 11.4 - - - +
157D GLY* 2.9 31.6 + - - +
345D ASN* 6.0 5.1 - - - +
349D ARG* 6.4 0.2 - - - -
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Residues in contact with LYS 154 (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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150D TRP* 3.0 58.3 + - + +
151D TYR* 3.1 22.7 + - - +
153D SER* 1.3 79.2 + - - +
155D GLU* 1.3 62.4 + - + +
157D GLY* 3.8 6.4 + - - -
292D GLY* 2.8 37.4 + - - -
341D GLU* 5.2 2.7 - - - +
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Residues in contact with GLU 155 (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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151D TYR* 3.2 30.5 + - + +
152D ARG* 3.2 20.9 + - - +
154D LYS* 1.3 83.7 - - + +
156D ARG* 1.3 60.4 + - + +
157D GLY 3.7 0.2 + - - -
180D TYR* 2.6 43.1 + - - -
258D THR* 5.2 2.4 + - - +
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Residues in contact with ARG 156 (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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208C ILE* 4.5 1.0 - - - +
209C ASP* 2.7 44.2 + - - -
149D MET 5.2 0.2 + - - -
152D ARG* 2.9 54.5 + - - +
153D SER* 4.3 7.4 - - - +
155D GLU* 1.3 76.7 - - - +
157D GLY* 1.3 67.4 + - - +
158D GLN 3.2 0.9 + - - -
159D SER* 3.0 47.9 + - - +
160D ALA 4.1 11.8 + - - +
161D PHE* 3.7 20.8 - - - +
165D GLU* 3.1 25.6 + - - +
349D ARG* 5.4 0.6 - - - +
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Residues in contact with GLY 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153D SER* 2.9 23.6 + - - +
154D LYS* 3.8 5.1 + - - -
155D GLU 3.4 2.6 - - - -
156D ARG* 1.3 77.9 - - - +
158D GLN* 1.3 62.7 + - - -
159D SER 3.4 6.6 + - - +
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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