Contacts of the helix formed by residues 125 - 149 (chain P) 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 P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119P GLY 5.1 0.2 - - - -
120P SER* 3.0 30.4 - - - +
121P TYR 3.8 6.1 - - - +
122P LYS 3.3 4.5 + - - +
123P ALA 3.2 4.2 + - - -
124P PRO* 1.3 96.5 - - + +
126P GLU* 1.3 63.6 + - - +
127P VAL 3.5 1.3 - - - -
128P THR* 3.5 14.9 - - - +
129P TRP* 3.3 18.9 + - - +
219P THR* 4.1 13.9 + - - +
220P GLY 3.3 9.0 + - - -
221P ASN 3.1 27.3 + - - -
222P ASN* 3.1 27.9 + - - +
228P GLU* 3.5 31.9 + - - -
355P ARG* 4.1 10.5 - - - +
501P HEM 3.0 30.4 + - - +
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Residues in contact with GLU 126 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18M TRP* 3.9 25.0 + - + -
22M ARG* 2.6 36.4 + - - +
121P TYR 3.9 14.1 - - - +
123P ALA* 3.0 38.4 + - - +
124P PRO 3.0 2.3 + - - -
125P ARG* 1.3 73.7 - - - +
127P VAL* 1.3 68.7 + - - +
129P TRP* 3.0 7.4 + - - +
130P ILE* 3.0 25.9 + - + +
347P PRO* 4.2 16.3 - - + +
348P TRP* 4.4 17.8 + - + -
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Residues in contact with VAL 127 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18M TRP* 4.5 15.3 - - + -
19M LEU* 4.5 13.9 - - + -
22M ARG* 3.8 34.7 - - + +
23M LEU* 4.2 26.7 - - + -
124P PRO 4.5 0.2 + - - -
125P ARG 3.5 0.2 - - - -
126P GLU* 1.3 74.0 - - - +
128P THR* 1.3 68.9 + - - +
130P ILE* 3.1 13.3 + - + +
131P VAL* 2.9 35.3 + - + +
215P ALA* 4.7 5.4 - - + -
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Residues in contact with THR 128 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125P ARG* 3.5 20.0 + - - +
127P VAL* 1.3 80.5 - - - +
129P TRP* 1.3 63.7 + - - +
131P VAL* 3.2 4.0 + - - +
132P GLY* 2.9 19.4 + - - -
212P HIS* 3.6 26.9 + - + +
215P ALA* 3.8 23.8 + - - +
216P PHE* 3.9 16.3 + - + +
219P THR* 4.9 2.9 + - - +
501P HEM 3.6 34.8 + - + -
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Residues in contact with TRP 129 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112P ILE* 4.0 27.4 - - + -
115P GLY* 4.5 6.5 - - - -
116P LEU* 3.8 21.8 - - + -
121P TYR* 3.4 32.5 - + + -
125P ARG 3.3 8.8 + - - +
126P GLU* 3.0 11.3 + - - +
128P THR* 1.3 78.3 - - - +
130P ILE* 1.3 66.3 + - + +
132P GLY 3.2 1.6 + - - -
133P MET* 3.0 31.4 + - + +
343P MET* 3.2 37.4 + - + -
344P ALA* 3.6 21.4 + - - +
346P VAL* 3.4 12.5 - - + +
347P PRO* 3.7 10.8 - - + -
501P HEM 3.2 53.0 - - + +
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Residues in contact with ILE 130 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18M TRP* 5.0 8.1 - - + -
126P GLU* 3.0 22.8 + - + +
127P VAL* 3.6 11.9 - - + +
129P TRP* 1.3 78.8 - - + +
131P VAL* 1.3 65.6 + - + +
133P MET* 2.9 21.7 + - + +
134P LEU* 3.0 25.3 + - + +
344P ALA* 5.2 2.9 - - + +
348P TRP* 3.8 32.5 - - + -
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Residues in contact with VAL 131 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23M LEU* 5.7 0.4 - - + -
127P VAL* 2.9 33.7 + - + +
128P THR* 3.5 7.6 - - - +
130P ILE* 1.3 72.9 - - + +
132P GLY* 1.3 66.6 + - - +
134P LEU* 2.8 29.5 + - + +
135P ILE* 3.0 15.0 + - + +
208P LEU* 3.9 32.3 - - + +
211P ILE* 4.2 18.8 - - + -
212P HIS* 3.9 20.6 - - + +
215P ALA* 5.7 0.7 - - + -
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Residues in contact with GLY 132 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128P THR 2.9 14.2 + - - -
129P TRP 3.6 0.7 - - - -
131P VAL* 1.3 78.3 - - - +
133P MET* 1.3 55.8 + - - +
135P ILE* 3.0 7.8 + - - +
136P TYR 2.9 23.9 + - - -
212P HIS* 3.9 6.7 + - - -
501P HEM 3.1 43.9 - - - +
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Residues in contact with MET 133 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112P ILE* 5.7 1.6 - - - -
129P TRP* 3.0 43.5 + - + +
130P ILE* 2.9 12.9 + - + +
132P GLY* 1.3 74.4 - - - +
134P LEU* 1.3 64.7 + - + +
136P TYR* 3.1 15.6 + - + +
137P LEU* 2.9 29.6 + - + +
340P ILE* 3.8 33.2 - - + +
343P MET* 4.0 16.8 - - + -
344P ALA* 3.9 30.5 - - + +
501P HEM 3.0 16.5 - - + +
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Residues in contact with LEU 134 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130P ILE* 3.0 25.6 + - + +
131P VAL* 2.8 27.4 + - + +
133P MET* 1.3 71.8 - - + +
135P ILE* 1.3 63.1 + - - +
137P LEU* 3.1 20.4 + - + +
138P ALA* 2.9 22.7 + - - +
208P LEU* 3.9 25.1 - - + +
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Residues in contact with ILE 135 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131P VAL* 3.0 12.1 + - + +
132P GLY* 3.0 18.4 + - - +
134P LEU* 1.3 76.5 - - - +
136P TYR* 1.3 53.3 + - - +
138P ALA* 3.1 7.8 + - - +
139P MET* 2.7 53.2 + - + +
205P ILE* 4.4 7.4 - - + +
208P LEU* 3.8 21.1 - - + -
209P VAL* 3.9 25.6 - - + +
212P HIS* 4.2 17.7 - - + -
501P HEM 3.3 45.1 - - + -
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Residues in contact with TYR 136 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105P PHE* 4.3 16.2 - + - -
108P VAL* 4.5 9.2 - - + -
109P TYR* 2.7 44.2 + + - -
112P ILE* 4.4 13.7 - - + -
132P GLY 2.9 6.8 + - - +
133P MET* 3.3 20.4 - - + +
135P ILE* 1.3 75.1 - - - +
137P LEU* 1.3 67.4 + - + +
139P MET* 3.5 5.6 + - - +
140P MET* 3.2 49.3 + - + +
301P PHE* 3.0 30.4 - + - -
340P ILE* 4.6 13.9 - - + -
343P MET* 4.4 11.7 - - + -
501P HEM 3.7 20.4 - - + +
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Residues in contact with LEU 137 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133P MET* 2.9 18.1 + - + +
134P LEU* 3.2 24.9 - - + +
136P TYR* 1.3 80.2 - - + +
138P ALA* 1.3 65.3 + - - +
140P MET* 3.1 14.7 + - + +
141P ALA* 2.9 22.4 + - - +
337P PHE* 5.8 4.9 - - + -
340P ILE* 5.0 16.2 - - + -
503P SMA 4.2 22.2 - - - +
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Residues in contact with ALA 138 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134P LEU 2.9 9.5 + - - +
135P ILE* 3.3 10.8 - - - +
137P LEU* 1.3 79.1 - - - +
139P MET* 1.3 65.4 + - - +
141P ALA* 3.2 8.4 + - - +
142P THR* 2.8 28.6 + - - -
201P LEU* 3.8 13.8 - - + +
204P VAL* 5.8 2.9 - - + -
205P ILE* 3.9 20.4 - - + +
208P LEU* 5.2 7.0 - - + -
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Residues in contact with MET 139 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104P PHE* 3.5 60.1 - - + +
105P PHE* 4.0 24.7 - - + -
108P VAL* 3.7 24.9 - - + -
135P ILE* 2.7 42.8 + - + +
136P TYR* 3.5 10.3 - - - +
138P ALA* 1.3 74.7 - - - +
140P MET* 1.3 53.4 + - - +
142P THR* 3.0 3.0 + - - -
143P ALA* 2.8 34.5 + - - +
205P ILE* 3.9 19.0 - - + +
501P HEM 4.4 1.1 - - - -
502P HEM 5.0 4.0 - - + +
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Residues in contact with MET 140 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105P PHE* 4.0 21.0 - - + -
109P TYR* 5.0 0.4 - - - -
136P TYR* 3.3 53.2 - - + +
137P LEU* 3.1 12.0 + - + +
139P MET* 1.3 79.2 - - - +
141P ALA* 1.3 69.2 + - - +
143P ALA* 3.0 2.0 + - - +
144P PHE* 2.9 21.4 + - - +
298P PHE* 3.7 33.6 - - + -
301P PHE* 4.8 4.5 - - - -
340P ILE* 4.0 20.6 - - + -
503P SMA 4.1 32.3 - - - +
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Residues in contact with ALA 141 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137P LEU 2.9 16.1 + - - +
138P ALA* 3.4 10.1 - - - +
140P MET* 1.3 73.4 - - - +
142P THR* 1.3 68.6 + - - +
144P PHE* 3.1 14.4 + - - +
145P MET* 3.1 15.5 - - + +
201P LEU* 3.7 14.6 - - + -
503P SMA 4.0 33.9 + - + +
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Residues in contact with THR 142 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138P ALA 2.8 21.4 + - - -
139P MET 3.0 9.2 - - - -
141P ALA* 1.3 71.9 - - - +
143P ALA* 1.3 55.4 + - - +
144P PHE 2.6 13.5 + - - -
145P MET* 2.6 29.0 + - - +
146P GLY 3.0 8.7 + - - -
198P HIS* 3.4 27.8 + - + +
201P LEU* 3.3 21.2 - - + +
202P PRO* 4.0 10.5 - - + +
205P ILE* 3.9 6.2 - - - +
502P HEM 3.6 28.3 - - + -
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Residues in contact with ALA 143 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101P ALA* 5.5 0.2 - - + -
105P PHE* 3.7 29.4 - - + -
139P MET 2.8 17.7 + - - +
140P MET* 3.5 4.7 - - - +
142P THR* 1.3 75.3 - - - +
144P PHE* 1.3 60.7 + - - +
146P GLY* 3.9 1.5 - - - -
147P TYR* 3.3 21.0 + - - +
295P GLU* 4.8 0.7 - - - +
297P TYR* 3.8 20.3 + - + +
298P PHE* 4.6 2.0 - - + -
502P HEM 4.3 23.0 - - + +
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Residues in contact with PHE 144 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140P MET 2.9 9.7 + - - +
141P ALA 3.2 12.6 - - - +
142P THR 2.6 5.3 + - - -
143P ALA* 1.3 72.4 - - - +
145P MET* 1.3 76.1 + - + +
147P TYR* 3.1 16.4 + - + +
148P VAL* 3.2 17.3 + - + +
158P GLY 4.1 1.3 - - - -
159P ALA* 3.8 23.1 - - - -
162P ILE* 3.5 46.7 - - + -
163P THR 5.0 0.7 - - - -
194P PHE* 3.6 27.4 - + - -
295P GLU* 5.2 2.7 - - - -
298P PHE* 4.5 8.7 - + + -
503P SMA 3.5 56.1 - - + -
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Residues in contact with MET 145 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141P ALA* 3.1 34.3 + - + +
142P THR* 2.6 16.0 + - - +
144P PHE* 1.3 87.2 - - + +
146P GLY* 1.3 63.0 + - - +
148P VAL* 2.9 24.7 + - - +
149P LEU* 3.3 11.1 + - - +
194P PHE* 3.7 36.4 - - + +
197P LEU* 3.7 29.4 - - + -
198P HIS* 4.2 9.4 - - + +
201P LEU* 3.7 17.5 - - + -
503P SMA 3.8 23.3 - - + -
----------------------------------------------------------
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Residues in contact with GLY 146 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142P THR 3.0 10.5 + - - -
143P ALA 4.2 0.4 - - - -
145P MET* 1.3 76.0 - - - +
147P TYR* 1.3 62.9 + - - +
148P VAL 3.0 1.2 + - - -
149P LEU* 3.1 16.2 + - - +
150P PRO* 3.2 10.7 - - - +
198P HIS* 3.5 30.3 + - - -
502P HEM 3.4 22.4 - - - +
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Residues in contact with TYR 147 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143P ALA 3.3 14.0 + - - +
144P PHE* 3.1 10.1 + - + +
146P GLY* 1.3 75.7 - - - +
148P VAL* 1.3 54.2 + - + +
150P PRO* 3.3 5.9 - - - +
154P MET* 3.4 41.2 - - + +
155P SER* 2.6 29.5 + - - -
158P GLY* 6.2 0.4 - - - -
275P GLY* 6.4 0.7 - - - -
276P HIS* 3.6 24.2 + - - +
279P ASN* 3.4 24.6 + - + +
293P VAL 5.7 0.4 + - - -
295P GLU* 3.2 45.8 - - + +
297P TYR* 5.1 0.9 - - - +
502P HEM 3.5 31.6 - - + +
503P SMA 4.8 2.9 - - - -
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Residues in contact with VAL 148 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144P PHE* 3.2 33.8 + - + +
145P MET 2.9 10.1 + - - +
147P TYR* 1.3 78.5 - - + +
149P LEU* 1.3 52.6 + - - +
151P TRP* 2.7 55.9 + - + -
155P SER* 3.3 20.7 - - - +
159P ALA* 4.0 11.7 - - + +
191P LEU* 4.3 8.3 - - + -
194P PHE* 3.7 31.0 - - + -
----------------------------------------------------------
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Residues in contact with LEU 149 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69P TYR* 2.7 37.4 + - + +
76P ALA* 3.9 1.2 - - - +
145P MET 3.5 10.8 - - - +
146P GLY 3.1 2.8 + - - +
148P VAL* 1.3 70.0 - - - +
150P PRO* 1.3 60.7 - - + +
151P TRP* 2.5 24.9 + - - +
191P LEU* 3.7 17.4 - - + +
194P PHE* 4.6 4.0 - - + -
195P PHE* 4.0 30.3 - - + +
198P HIS* 3.5 30.5 - - + -
502P HEM 3.4 41.7 - - + -
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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