Contacts of the helix formed by residues 125 - 149 (chain M) in PDB entry 2QJK
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 ARG 125 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119M GLY 5.2 0.2 + - - -
120M SER* 2.9 27.5 - - - +
121M TYR 3.8 5.9 - - - +
122M LYS 3.7 4.9 + - - +
123M ALA* 3.2 4.4 - - - +
124M PRO* 1.3 94.7 - - + +
126M GLU* 1.3 62.7 + - - +
127M VAL 3.5 1.3 - - - -
128M THR* 3.6 14.1 - - - +
129M TRP* 3.3 19.4 + - - +
219M THR* 4.1 13.2 + - - +
220M GLY 3.6 7.8 + - - -
221M ASN 3.4 8.5 + - - -
222M ASN* 3.2 38.8 - - - +
228M GLU* 3.3 31.1 + - - -
355M ARG* 3.9 19.2 - - - +
501M HEM 3.0 33.7 + - - +
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Residues in contact with GLU 126 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121M TYR 3.9 13.9 - - - +
123M ALA* 3.0 37.7 + - - +
124M PRO 3.0 2.0 + - - -
125M ARG* 1.3 73.3 - - - +
127M VAL* 1.3 68.6 + - - +
129M TRP* 3.0 7.1 + - - +
130M ILE* 2.9 26.0 + - + +
347M PRO* 4.2 16.1 - - + +
348M TRP* 4.4 17.1 + - + -
18P TRP* 3.6 26.3 + - + -
22P ARG* 2.5 36.1 + - - -
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Residues in contact with VAL 127 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124M PRO 4.5 0.2 + - - -
125M ARG 3.5 0.2 - - - -
126M GLU* 1.3 75.3 - - - +
128M THR* 1.3 70.1 + - - +
130M ILE* 3.0 12.9 + - + +
131M VAL* 2.9 34.7 + - + +
215M ALA* 4.7 5.4 - - + -
18P TRP* 4.4 11.0 - - + -
19P LEU* 4.3 20.4 - - + -
22P ARG* 3.9 32.5 - - + +
23P LEU* 4.2 26.7 - - + -
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Residues in contact with THR 128 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125M ARG* 3.6 20.7 + - - +
126M GLU 3.2 0.2 - - - -
127M VAL* 1.3 82.2 - - - +
129M TRP* 1.3 63.4 + - - +
131M VAL* 3.1 4.0 + - - +
132M GLY* 2.8 19.4 + - - -
212M HIS* 3.6 28.9 + - + +
215M ALA* 3.8 23.9 + - - +
216M PHE* 3.8 16.1 + - + +
219M THR* 4.8 2.4 + - - +
501M HEM 3.7 34.1 + - + -
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Residues in contact with TRP 129 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112M ILE* 3.8 28.3 - - + -
115M GLY* 4.6 3.6 - - - -
116M LEU* 3.8 21.8 - - + -
121M TYR* 3.4 31.2 - + + -
125M ARG 3.3 8.8 + - - +
126M GLU* 3.0 11.1 + - - +
128M THR* 1.3 79.3 - - - +
130M ILE* 1.3 66.9 + - + +
132M GLY 3.2 0.5 + - - -
133M MET* 2.9 30.6 + - + +
343M MET* 3.2 36.8 + - + -
344M ALA* 3.6 20.9 + - - +
346M VAL* 3.4 12.0 - - + +
347M PRO* 3.7 11.4 - - + -
501M HEM 3.0 58.0 - - + +
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Residues in contact with ILE 130 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126M GLU* 2.9 23.9 + - + +
127M VAL* 3.6 11.7 - - + +
129M TRP* 1.3 75.9 - - + +
131M VAL* 1.3 69.2 + - + +
133M MET* 2.9 21.6 + - + +
134M LEU* 3.0 24.8 + - + +
344M ALA* 5.2 2.2 - - + +
348M TRP* 3.8 32.1 - - + -
18P TRP* 5.0 7.0 - - + -
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Residues in contact with VAL 131 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127M VAL* 2.9 31.9 + - + +
128M THR* 3.5 8.1 - - - +
130M ILE* 1.3 73.2 - - + +
132M GLY* 1.3 66.7 + - - +
134M LEU* 2.8 29.6 + - + +
135M ILE* 3.0 14.1 + - + +
208M LEU* 4.0 25.1 - - + +
211M ILE* 4.2 19.7 - - + -
212M HIS* 4.0 28.9 - - + +
215M ALA* 5.7 0.9 - - + -
23P LEU* 5.7 0.2 - - + -
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Residues in contact with GLY 132 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128M THR 2.8 13.7 + - - -
129M TRP 3.2 0.2 + - - -
131M VAL* 1.3 77.4 - - - +
133M MET* 1.3 60.5 + - - +
135M ILE* 3.1 7.9 + - - +
136M TYR 2.9 9.2 + - - -
212M HIS* 3.9 6.2 + - - -
501M HEM 2.8 56.1 - - - +
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Residues in contact with MET 133 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112M ILE* 6.0 1.8 - - - -
129M TRP* 2.9 41.9 + - + +
130M ILE* 2.9 13.7 + - + +
132M GLY* 1.3 75.4 - - - +
134M LEU* 1.3 65.1 + - + +
136M TYR* 3.0 16.3 + - + +
137M LEU* 2.9 25.9 + - + +
340M ILE* 3.8 33.7 - - + +
343M MET* 4.0 17.3 - - + -
344M ALA* 3.9 28.9 - - + +
501M HEM 3.1 16.9 - - + +
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Residues in contact with LEU 134 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130M ILE* 3.0 25.1 + - + +
131M VAL* 2.8 26.2 + - + +
133M MET* 1.3 71.9 - - + +
135M ILE* 1.3 63.4 + - - +
137M LEU* 3.1 16.0 + - + +
138M ALA* 2.9 23.4 + - - +
208M LEU* 3.9 26.0 - - + +
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Residues in contact with ILE 135 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131M VAL* 3.0 12.7 + - + +
132M GLY* 3.1 12.1 - - - +
134M LEU* 1.3 75.4 - - - +
136M TYR* 1.3 54.2 + - - +
138M ALA* 3.1 8.3 + - - +
139M MET* 2.7 51.1 + - + +
205M ILE* 4.4 6.3 - - + +
208M LEU* 3.8 21.1 - - + +
209M VAL* 4.0 28.5 - - + +
212M HIS* 4.1 17.0 - - + -
501M HEM 3.3 51.4 - - + -
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Residues in contact with TYR 136 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105M PHE* 4.3 17.7 - + - -
108M VAL* 4.5 12.1 - - + -
109M TYR* 2.6 44.8 + + - -
112M ILE* 4.3 15.0 - - + -
132M GLY 2.9 6.4 + - - +
133M MET* 3.2 21.5 - - + +
135M ILE* 1.3 77.5 - - - +
137M LEU* 1.3 65.8 + - + +
139M MET* 3.4 6.4 + - - +
140M MET* 3.2 51.0 + - + +
301M PHE* 3.0 29.0 - + - -
340M ILE* 4.6 13.9 - - + -
343M MET* 4.5 10.3 - - + -
501M HEM 3.7 16.2 - - + -
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Residues in contact with LEU 137 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133M MET* 2.9 14.4 + - + +
134M LEU* 3.5 18.6 - - + +
136M TYR* 1.3 80.6 - - + +
138M ALA* 1.3 65.4 + - - +
140M MET* 3.1 15.2 + - + +
141M ALA* 2.9 22.7 + - - +
337M PHE* 5.4 7.2 - - + -
340M ILE* 5.1 17.5 - - + -
503M SMA 3.5 29.1 - - - +
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Residues in contact with ALA 138 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134M LEU 2.9 12.4 + - - +
135M ILE* 3.4 10.5 - - - +
137M LEU* 1.3 75.5 - - - +
139M MET* 1.3 64.4 + - - +
141M ALA* 3.1 9.0 + - - +
142M THR* 2.8 28.9 + - - -
201M LEU* 3.8 13.4 - - + +
204M VAL* 5.8 2.7 - - + -
205M ILE* 3.9 21.8 - - + +
208M LEU* 5.2 6.7 - - + -
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Residues in contact with MET 139 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104M PHE* 3.5 61.5 - - + +
105M PHE* 4.1 18.8 - - + -
108M VAL* 3.8 28.7 - - + -
135M ILE* 2.7 47.2 + - + +
136M TYR* 3.5 9.9 - - - +
138M ALA* 1.3 74.3 - - - +
140M MET* 1.3 65.8 + - - +
142M THR* 3.0 3.8 + - - -
143M ALA* 2.8 22.2 + - - +
205M ILE* 3.9 18.6 - - + +
501M HEM 4.4 1.1 - - - -
502M HEM 5.0 3.9 - - + +
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Residues in contact with MET 140 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105M PHE* 3.9 22.4 - - + -
109M TYR* 5.0 0.2 - - - -
136M TYR* 3.2 54.7 + - + +
137M LEU* 3.1 12.6 + - + +
139M MET* 1.3 74.6 - - - +
141M ALA* 1.3 71.4 + - - +
142M THR 3.1 0.2 + - - -
143M ALA* 3.1 2.8 + - - +
144M PHE* 2.9 21.3 + - - +
298M PHE* 3.7 31.3 - - + -
301M PHE* 4.8 4.5 - - - -
340M ILE* 3.9 20.0 - - + -
503M SMA 3.9 35.9 - - - +
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Residues in contact with ALA 141 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137M LEU 2.9 16.3 + - - +
138M ALA* 3.3 11.4 - - - +
140M MET* 1.3 74.2 - - - +
142M THR* 1.3 68.1 + - - +
144M PHE* 3.1 15.0 + - - +
145M MET* 3.2 15.6 + - + +
201M LEU* 3.7 15.7 - - + -
503M SMA 3.8 32.1 + - + +
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Residues in contact with THR 142 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138M ALA 2.8 20.0 + - - -
139M MET 3.0 8.9 + - - -
141M ALA* 1.3 71.1 - - - +
143M ALA* 1.3 54.9 + - - +
144M PHE 2.6 13.0 + - - -
145M MET* 2.7 28.6 + - - +
146M GLY 3.0 8.8 + - - -
198M HIS* 3.4 28.6 + - + +
201M LEU* 3.3 21.3 - - + +
202M PRO* 4.0 10.8 - - + -
205M ILE* 3.9 6.9 - - - +
502M HEM 3.5 26.7 - - + -
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Residues in contact with ALA 143 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101M ALA* 5.5 0.7 - - + -
105M PHE* 3.7 28.9 - - + -
139M MET 2.8 10.8 + - - +
140M MET* 3.5 7.4 - - - +
142M THR* 1.3 79.3 - - - +
144M PHE* 1.3 60.4 + - - +
146M GLY* 3.9 1.4 - - - -
147M TYR* 3.2 21.5 + - - +
295M GLU* 5.0 0.3 - - - +
297M TYR* 3.9 19.7 + - + +
298M PHE* 4.6 1.6 - - + -
502M HEM 4.1 24.6 - - + +
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Residues in contact with PHE 144 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140M MET 2.9 10.3 + - - +
141M ALA 3.1 9.9 - - - +
142M THR 2.6 5.5 + - - -
143M ALA* 1.3 71.2 - - - +
145M MET* 1.3 73.0 + - + +
147M TYR* 3.0 16.7 + - + +
148M VAL* 3.2 21.7 + - + +
158M GLY 4.4 0.9 - - - -
159M ALA* 3.8 23.1 - - - -
162M ILE* 3.6 42.2 - - + -
163M THR* 5.0 2.5 - - + -
194M PHE* 3.6 32.8 - + - -
295M GLU* 5.2 2.7 - - - -
298M PHE* 4.5 10.8 - + + -
503M SMA 3.5 53.6 - - + -
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Residues in contact with MET 145 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141M ALA* 3.2 31.6 - - + +
142M THR* 2.7 16.7 + - - +
144M PHE* 1.3 85.6 - - + +
146M GLY* 1.3 64.3 + - - +
148M VAL* 2.9 25.2 + - - +
149M LEU* 3.2 11.0 + - - +
194M PHE* 3.7 34.9 - - + +
197M LEU* 3.6 30.1 - - + -
198M HIS* 4.2 10.8 - - + +
201M LEU* 3.7 16.6 - - + -
503M SMA 3.6 24.0 - - + -
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Residues in contact with GLY 146 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142M THR 3.0 10.3 + - - -
143M ALA 4.1 0.7 - - - -
145M MET* 1.3 76.4 - - - +
147M TYR* 1.3 63.5 + - - +
148M VAL 3.0 1.4 + - - -
149M LEU* 3.0 17.1 + - - +
150M PRO* 3.2 10.0 - - - +
198M HIS* 3.5 29.7 + - - -
502M HEM 3.5 22.7 - - - +
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Residues in contact with TYR 147 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143M ALA 3.2 12.9 + - - +
144M PHE* 3.0 11.0 + - + +
146M GLY* 1.3 74.6 - - - +
148M VAL* 1.3 53.5 + - - +
150M PRO* 3.3 6.1 - - - +
154M MET* 3.4 40.4 - - + +
155M SER* 2.7 29.4 + - - -
158M GLY* 6.2 0.4 - - - -
275M GLY* 6.4 0.7 - - - -
276M HIS* 3.6 24.4 + - - +
279M ASN* 3.4 23.8 + - + +
293M VAL 5.6 0.2 + - - -
295M GLU* 3.0 48.4 + - + +
297M TYR* 5.1 0.7 - - - +
502M HEM 3.8 36.5 - - + -
503M SMA 4.5 2.7 - - - -
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Residues in contact with VAL 148 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144M PHE* 3.3 33.9 - - + +
145M MET* 2.9 9.7 + - - +
147M TYR* 1.3 79.6 - - + +
149M LEU* 1.3 52.4 + - - +
151M TRP* 2.8 54.9 + - + -
155M SER* 3.3 20.9 - - - +
159M ALA* 4.0 11.9 - - + -
191M LEU* 4.3 8.3 - - + -
194M PHE* 3.7 31.6 - - + -
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Residues in contact with LEU 149 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69M TYR* 2.6 36.2 + - + +
76M ALA* 3.9 1.7 - - - +
145M MET 3.5 8.7 - - - +
146M GLY 3.0 7.9 + - - +
148M VAL* 1.3 74.2 - - - +
150M PRO* 1.3 60.4 - - + +
151M TRP* 2.6 18.9 + - - +
191M LEU* 3.7 18.8 - - + +
194M PHE* 4.6 3.1 - - + -
195M PHE* 4.0 30.1 - - + +
198M HIS* 3.6 28.7 - - + -
502M HEM 3.4 42.4 - - + -
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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