Contacts of the helix formed by residues 135 - 157 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A MET 3.4 0.8 + - - -
134A ALA* 1.3 80.3 - - - +
136A GLY* 1.3 59.3 + - - +
137A SER* 3.4 18.8 - - - -
138A CYS* 3.5 7.1 - - - -
139A SER* 2.7 33.5 + - - -
328A SER* 3.4 12.6 - - - -
334A GLY* 4.5 0.7 - - - -
600A PLP 3.6 16.6 - - - +
800A FES 2.3 43.5 - - - -
134B ALA* 5.6 1.1 - - + -
138B CYS* 5.4 1.3 - - - -
352B ASN* 6.2 3.6 - - - -
354B TRP* 4.2 8.3 - - + -
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Residues in contact with GLY 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A CYS* 1.3 75.3 - - - +
137A SER* 1.3 61.0 + - - +
139A SER* 3.2 5.6 + - - -
140A ASN* 3.0 26.5 + - - -
300A VAL* 3.9 12.6 - - - +
328A SER* 3.2 19.3 + - - -
600A PLP 3.1 27.6 + - - -
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Residues in contact with SER 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A CYS* 3.3 7.1 - - - -
136A GLY* 1.3 76.4 - - - +
138A CYS* 1.3 57.8 + - - +
140A ASN 3.2 1.6 + - - -
141A GLU* 2.8 33.7 + - - +
190A HIS 4.5 1.6 - - - -
191A GLY* 3.4 20.4 - - - -
192A ARG 3.6 5.4 + - - -
193A THR* 3.8 27.5 + - - +
196A CYS* 3.2 10.9 - - - -
600A PLP 2.8 25.1 + - - -
800A FES 4.7 1.1 - - - -
352B ASN* 5.2 4.0 - - - +
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Residues in contact with CYS 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A MET* 3.8 11.5 - - - +
134A ALA* 3.7 13.0 - - - -
135A CYS* 3.5 22.5 - - - -
137A SER* 1.3 77.3 - - - +
139A SER* 1.3 56.9 + - - +
141A GLU* 4.2 8.1 - - - -
142A ASN* 2.8 45.3 + - - +
352A ASN* 4.9 6.3 - - - +
800A FES 2.2 45.4 - - - -
135B CYS* 5.4 1.3 - - - -
193B THR* 4.5 5.4 - - + -
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Residues in contact with SER 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A MET* 3.4 10.4 - - - +
135A CYS 2.7 19.6 + - - -
136A GLY* 3.2 10.7 + - - -
137A SER 3.1 0.6 - - - -
138A CYS* 1.3 79.8 - - - +
140A ASN* 1.3 58.5 + - - +
143A ALA* 2.9 28.8 + - - +
326A THR* 3.7 13.6 - - - +
327A PHE 3.5 5.1 + - - -
335A GLY 2.8 41.0 + - - -
336A PHE* 3.7 6.5 - - - -
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Residues in contact with ASN 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A GLY 3.0 11.5 + - - +
139A SER* 1.3 73.6 - - - +
141A GLU* 1.3 66.3 + - - +
143A ALA* 3.3 3.7 + - - +
144A PHE* 2.9 40.2 + - + -
190A HIS* 2.8 27.7 + - - +
196A CYS* 3.6 16.8 - - - -
263A ILE* 4.0 12.8 - - + +
296A LEU* 4.4 1.0 - - - +
298A ASP* 2.8 25.7 + - - +
300A VAL* 5.2 0.2 - - - -
326A THR* 2.6 30.2 + - - +
600A PLP 3.7 5.7 - - - -
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Residues in contact with GLU 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A SER 2.8 21.2 + - - +
138A CYS 4.0 2.7 - - - +
140A ASN* 1.3 77.2 - - - +
142A ASN* 1.3 58.7 + - - +
144A PHE* 3.2 10.6 + - - +
145A LYS* 3.1 30.4 + - - +
193A THR* 2.4 28.6 + - - +
194A MET 3.7 0.3 + - - -
195A GLY* 2.8 23.7 + - - -
196A CYS* 3.0 13.7 + - - -
141B GLU* 4.6 0.4 - - - +
193B THR* 3.9 32.5 - - + -
194B MET* 3.0 35.5 + - - +
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Residues in contact with ASN 142 (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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133A MET* 3.4 33.3 - - + +
138A CYS* 2.8 35.3 + - - +
141A GLU* 1.3 79.1 - - - +
143A ALA* 1.3 56.9 + - - +
145A LYS* 3.4 27.8 + - - +
146A THR* 2.7 37.7 + - - -
336A PHE* 3.7 10.3 - - + -
350A ILE* 3.6 19.3 - - + +
351A PHE 4.3 5.6 + - - +
352A ASN* 4.4 4.9 - - - +
192B ARG* 5.5 0.9 - - - +
193B THR* 4.9 6.7 - - - +
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Residues in contact with ALA 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A SER 2.9 18.4 + - - +
140A ASN 3.5 5.4 - - - +
142A ASN* 1.3 75.1 - - - +
144A PHE* 1.3 64.9 + - - +
146A THR* 3.3 3.4 + - - -
147A ILE* 3.0 30.5 + - - +
296A LEU* 3.9 15.3 - - + -
324A VAL* 4.0 14.1 - - + +
326A THR* 3.8 19.1 - - + -
336A PHE* 3.9 10.5 - - + -
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Residues in contact with PHE 144 (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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140A ASN* 2.9 25.9 + - + -
141A GLU* 3.2 11.0 + - - +
143A ALA* 1.3 77.0 - - - +
145A LYS* 1.3 56.5 + - - +
147A ILE* 3.2 7.6 + - - +
148A PHE* 2.8 48.7 + - + -
182A ILE* 3.9 26.5 - - + -
195A GLY 3.8 20.4 - - - -
196A CYS* 3.8 10.8 - - - -
199A THR* 3.5 29.4 - - + -
215A TRP* 4.6 0.7 - + - -
263A ILE* 3.8 13.9 - - + -
296A LEU* 3.5 26.7 - - + -
194B MET* 3.4 24.2 - - + -
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Residues in contact with LYS 145 (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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141A GLU 3.1 12.4 + - - +
142A ASN* 3.4 26.6 + - - +
143A ALA 3.3 0.2 - - - -
144A PHE* 1.3 72.3 - - - +
146A THR* 1.3 61.8 + - - +
148A PHE* 3.1 4.3 + - - +
149A MET* 2.9 36.4 + - - +
349A ARG 3.4 21.3 + - - -
350A ILE* 3.7 8.9 - - + +
192B ARG* 2.8 48.0 + - - +
193B THR* 5.3 0.7 - - - +
194B MET* 4.4 10.8 - - + -
197B LEU* 4.3 6.2 - - + +
206B HIS 4.8 4.0 + - - -
210B ILE* 3.6 43.6 - - + +
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Residues in contact with THR 146 (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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131A ILE* 5.2 0.2 - - - +
142A ASN 2.7 24.9 + - - -
143A ALA* 3.5 6.1 - - - -
145A LYS* 1.3 76.1 - - - +
147A ILE* 1.3 57.8 + - - +
149A MET* 3.5 8.6 + - + +
150A TRP* 3.0 26.9 + - - +
324A VAL* 5.3 3.8 - - + -
336A PHE* 3.2 28.3 - - + -
338A HIS* 4.6 4.9 - - + +
342A PHE* 3.2 41.2 - - + +
344A PRO* 5.0 4.4 - - + +
350A ILE* 3.5 15.5 - - - +
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Residues in contact with ILE 147 (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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143A ALA 3.0 20.5 + - - +
144A PHE* 3.4 6.3 - - - +
146A THR* 1.3 74.8 - - - +
148A PHE* 1.3 60.4 + - - +
150A TRP* 3.2 8.5 + - + +
151A TYR* 2.9 27.2 + - - +
182A ILE* 4.2 8.3 - - + -
260A ALA* 3.4 36.6 - - + +
261A GLY* 3.9 7.4 - - - +
294A ALA* 3.6 26.7 - - + -
296A LEU* 3.9 35.7 - - + -
324A VAL* 4.2 12.1 - - + -
342A PHE* 4.2 7.0 - - + -
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Residues in contact with PHE 148 (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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144A PHE* 2.8 35.7 + - + +
145A LYS* 3.1 8.0 + - - +
147A ILE* 1.3 73.2 - - - +
149A MET* 1.3 62.4 + - - +
151A TYR* 3.4 4.9 + - - +
152A ARG* 3.2 28.8 + - - +
180A TYR* 3.8 37.0 - - + -
181A SER 3.9 3.6 - - - -
182A ILE* 3.5 33.2 - - + -
215A TRP* 4.1 11.7 - + - -
260A ALA* 3.9 7.4 - - + -
194B MET* 3.8 22.4 - - - -
209B ASP 3.4 18.4 - - - +
210B ILE* 4.4 4.0 - - + -
211B PRO* 3.3 31.4 - - + -
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Residues in contact with MET 149 (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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145A LYS 2.9 21.3 + - - +
146A THR* 3.6 6.7 - - + +
148A PHE* 1.3 76.4 - - - +
150A TRP* 1.3 58.5 + - - +
152A ARG* 3.6 2.1 + - - +
153A SER* 3.1 28.6 + - - -
342A PHE 5.6 0.2 - - - +
344A PRO* 3.5 43.5 - - + -
345A ASN 4.8 0.2 - - - +
349A ARG* 3.2 58.7 + - + +
350A ILE* 3.9 17.0 - - + -
209B ASP* 4.2 10.6 - - + +
210B ILE* 4.2 13.9 - - + -
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Residues in contact with TRP 150 (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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146A THR 3.0 17.3 + - - +
147A ILE 3.2 8.5 + - - +
149A MET* 1.3 76.5 - - - +
151A TYR* 1.3 78.8 + + + +
153A SER* 3.3 8.3 + - - -
154A LYS* 3.1 63.0 + - + +
260A ALA 3.7 6.5 - - - -
292A GLY* 3.3 19.7 - - - -
293A CYS 4.3 0.9 - - - -
294A ALA* 3.6 22.9 - - + -
323A ASP* 5.7 0.9 - - - -
341A GLU* 3.0 53.6 + - + +
342A PHE* 3.1 42.6 - + + +
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Residues in contact with TYR 151 (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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147A ILE 2.9 15.9 + - - +
148A PHE 3.8 4.5 - - - +
149A MET 3.3 0.2 - - - -
150A TRP* 1.3 86.9 - + + +
152A ARG* 1.3 60.0 + - - +
154A LYS* 3.3 27.5 + - + +
155A GLU* 3.3 42.3 + - + +
180A TYR* 3.6 20.6 - + + -
258A THR* 3.2 29.7 - - + +
259A VAL 4.0 11.8 + - - -
260A ALA* 3.7 23.3 - - + -
291A HIS 4.6 6.6 + - - -
292A GLY 3.3 24.0 - - - -
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Residues in contact with ARG 152 (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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148A PHE 3.2 16.3 + - - +
149A MET 4.1 0.7 - - - +
151A TYR* 1.3 73.4 - - - +
153A SER* 1.3 59.3 + - - +
155A GLU* 3.2 27.2 + - - +
156A ARG* 3.0 65.8 + - - +
165A GLU* 3.2 21.4 + - - -
175A PRO* 3.8 19.3 + - - +
178A PRO* 3.4 19.9 - - + +
180A TYR* 3.3 27.2 + - + -
209B ASP* 3.7 34.8 + - + +
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Residues in contact with SER 153 (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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149A MET 3.1 19.0 + - - -
150A TRP* 3.6 10.5 + - - -
151A TYR 3.3 0.2 - - - -
152A ARG* 1.3 74.7 - - - +
154A LYS* 1.3 60.7 + - - +
156A ARG* 4.2 13.0 - - - +
157A GLY* 3.0 31.9 + - - +
345A ASN* 6.3 4.3 - - - -
349A ARG* 6.4 0.2 - - - -
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Residues in contact with LYS 154 (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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150A TRP* 3.1 60.2 + - + +
151A TYR* 3.4 24.4 - - - +
152A ARG 3.2 0.2 - - - -
153A SER* 1.3 79.8 + - - +
155A GLU* 1.3 65.2 + - + +
157A GLY* 3.5 8.9 + - - -
292A GLY* 2.8 36.1 + - - -
341A GLU* 5.3 2.5 - - - +
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Residues in contact with GLU 155 (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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151A TYR* 3.3 32.7 + - + +
152A ARG* 3.2 27.7 + - - +
154A LYS* 1.3 83.7 - - + +
156A ARG* 1.3 59.4 + - - +
157A GLY* 4.8 0.2 - - - -
180A TYR* 2.3 36.3 + - - -
258A THR* 5.2 2.8 + - - +
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Residues in contact with ARG 156 (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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152A ARG* 3.0 52.2 + - - +
153A SER* 4.1 10.6 - - - +
155A GLU* 1.3 75.9 - - - +
157A GLY* 1.3 65.4 + - - +
158A GLN 3.3 0.3 + - - -
159A SER* 2.6 56.2 + - - +
160A ALA 4.0 10.2 + - - +
161A PHE* 3.3 23.9 - - - +
165A GLU* 3.2 25.4 + - - +
349A ARG* 5.6 0.2 - - - +
209B ASP* 2.9 42.6 + - - -
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Residues in contact with GLY 157 (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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153A SER* 3.0 22.1 + - - +
154A LYS 3.5 6.7 + - - -
155A GLU 3.4 3.2 - - - -
156A ARG* 1.3 79.6 - - - +
158A GLN* 1.3 60.4 + - - -
159A SER 3.6 4.5 + - - +
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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
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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