Contacts of the helix formed by residues 125 - 149 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D SER 3.0 28.5 - - - +
121D TYR 3.8 4.8 - - - +
122D LYS 3.3 5.1 + - - +
123D ALA 3.2 3.8 - - - -
124D PRO* 1.3 88.5 - - + +
126D GLU* 1.3 63.8 + - - +
127D VAL 3.5 1.8 - - - -
128D THR* 3.5 15.7 - - - +
129D TRP* 3.3 19.2 + - - +
219D THR* 4.1 11.9 + - - +
220D GLY 3.6 17.6 + - - -
221D ASN 3.6 10.9 + - - -
222D ASN* 3.5 20.3 + - - +
228D GLU* 3.0 39.4 + - - -
355D ARG* 3.7 22.4 - - - +
501D HEM 3.1 31.2 + - - +
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Residues in contact with GLU 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A TRP* 4.0 24.6 + - + -
22A ARG* 2.7 35.1 + - - +
121D TYR 3.9 14.4 - - - +
123D ALA* 2.9 38.7 + - - +
124D PRO 2.9 7.6 + - - -
125D ARG* 1.3 75.7 - - - +
127D VAL* 1.3 63.6 + - - +
129D TRP* 3.0 7.8 + - - +
130D ILE* 3.0 24.2 + - - +
347D PRO* 4.1 15.7 - - + +
348D TRP* 4.4 18.7 + - + +
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Residues in contact with VAL 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A TRP* 4.6 14.6 - - + -
19A LEU* 4.6 13.0 - - + -
22A ARG* 3.8 34.5 - - + -
23A LEU* 4.2 26.5 - - + -
124D PRO 4.4 0.8 + - - +
125D ARG 3.5 0.4 - - - -
126D GLU* 1.3 75.3 - - - +
128D THR* 1.3 68.7 + - - +
130D ILE* 3.1 12.2 + - + +
131D VAL* 2.9 34.5 + - + +
215D ALA* 4.7 7.4 - - + -
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Residues in contact with THR 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125D ARG* 3.5 22.1 + - - +
127D VAL* 1.3 82.1 - - - +
129D TRP* 1.3 53.6 + - - +
131D VAL* 3.1 4.7 + - - +
132D GLY* 2.8 30.1 + - - -
212D HIS* 3.6 31.0 + - + +
215D ALA* 3.9 21.3 + - - +
216D PHE* 3.9 15.7 + - + +
219D THR* 4.9 2.8 + - - +
501D HEM 3.7 33.3 + - + -
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Residues in contact with TRP 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111D HIS 5.8 0.2 - - - -
112D ILE* 4.3 22.4 - - + -
115D GLY* 4.5 6.1 - - - -
116D LEU* 3.8 25.6 - - + -
121D TYR* 3.4 31.0 - + + -
125D ARG 3.3 8.4 + - - +
126D GLU* 3.0 10.4 + - - +
128D THR* 1.3 79.3 - - - +
130D ILE* 1.3 67.9 + - + +
132D GLY* 3.1 3.4 + - - +
133D MET* 2.9 35.6 + - + +
343D MET* 3.2 37.0 + - + -
344D ALA* 3.6 19.7 + - - +
346D VAL* 3.4 12.5 - - + +
347D PRO* 3.8 11.4 - - + -
501D HEM 3.5 46.2 - - + +
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Residues in contact with ILE 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A TRP* 5.0 8.1 - - + -
126D GLU* 3.0 22.3 + - + +
127D VAL* 3.6 11.7 - - + +
129D TRP* 1.3 78.5 - - + +
131D VAL* 1.3 67.2 + - + +
133D MET* 2.8 21.7 + - + +
134D LEU* 3.0 25.5 + - + +
344D ALA* 5.2 3.4 - - + +
348D TRP* 3.8 31.9 - - + -
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Residues in contact with VAL 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 5.7 0.2 - - + -
127D VAL* 2.9 32.1 + - + +
128D THR* 3.4 8.7 - - - +
130D ILE* 1.3 74.0 - - + +
132D GLY* 1.3 65.6 + - - +
134D LEU* 2.7 29.7 + - + +
135D ILE* 2.9 15.7 + - + +
208D LEU* 4.0 19.1 - - + +
211D ILE* 4.3 17.9 - - + -
212D HIS* 3.9 33.4 - - + +
215D ALA* 5.7 0.9 - - + -
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Residues in contact with GLY 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128D THR 2.8 13.6 + - - -
129D TRP 3.1 1.1 + - - -
131D VAL* 1.3 75.1 - - - +
133D MET* 1.3 62.3 + - - +
135D ILE* 3.1 10.2 + - - +
136D TYR 2.9 18.0 + - - -
212D HIS* 4.0 6.5 + - - -
501D HEM 3.1 43.0 - - - +
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Residues in contact with MET 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112D ILE* 5.5 1.8 - - - -
129D TRP* 2.9 43.0 + - + +
130D ILE* 2.8 16.4 + - + +
132D GLY* 1.3 68.7 - - - +
134D LEU* 1.3 67.9 + - + +
136D TYR* 3.0 14.8 + - + +
137D LEU* 2.9 28.4 + - + +
340D ILE* 3.8 30.7 - - + +
343D MET* 3.9 20.0 - - + -
344D ALA* 3.9 30.5 - - + +
501D HEM 3.0 16.7 - - + +
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Residues in contact with LEU 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130D ILE* 3.0 19.4 + - + +
131D VAL* 2.7 33.1 + - + +
133D MET* 1.3 71.3 - - + +
135D ILE* 1.3 63.9 + - - +
137D LEU* 3.1 18.4 + - + +
138D ALA* 2.9 22.7 + - - +
208D LEU* 3.9 25.1 - - + +
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Residues in contact with ILE 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131D VAL* 2.9 15.9 + - + +
132D GLY* 3.2 11.2 - - - +
134D LEU* 1.3 76.2 - - - +
136D TYR* 1.3 55.9 + - - +
138D ALA* 3.0 8.0 + - - +
139D MET* 2.7 49.3 + - + +
205D ILE* 4.4 7.0 - - + +
208D LEU* 3.8 22.0 - - + -
209D VAL* 4.0 32.3 - - + +
212D HIS* 4.1 20.9 - - + -
501D HEM 3.5 40.2 - - + -
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Residues in contact with TYR 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105D PHE* 4.3 16.6 - + - -
108D VAL* 4.6 8.3 - - + -
109D TYR* 2.7 44.5 + + - -
112D ILE* 4.2 15.5 - - + -
132D GLY 2.9 12.4 + - - +
133D MET* 3.2 30.5 - - + +
135D ILE* 1.3 76.7 - - - +
137D LEU* 1.3 67.2 + - + +
139D MET* 3.5 7.3 + - - +
140D MET* 3.2 47.0 + - + +
301D PHE* 3.1 28.1 - + - -
340D ILE* 4.5 7.0 - - + -
343D MET* 4.4 10.8 - - + -
501D HEM 3.8 13.7 - - + -
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Residues in contact with LEU 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D SMA 3.5 28.7 - - - +
133D MET* 2.9 16.8 + - + +
134D LEU* 3.3 21.5 - - + +
136D TYR* 1.3 77.0 - - + +
138D ALA* 1.3 65.0 + - - +
140D MET* 3.1 17.4 + - + +
141D ALA* 2.9 23.7 + - - +
337D PHE* 5.6 6.7 - - + -
340D ILE* 5.4 15.5 - - + -
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Residues in contact with ALA 138 (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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134D LEU 2.9 9.4 + - - +
135D ILE* 3.3 10.8 - - - +
137D LEU* 1.3 78.9 - - - +
139D MET* 1.3 64.2 + - - +
141D ALA* 3.0 9.0 + - - +
142D THR* 2.8 27.6 + - - -
201D LEU* 3.9 13.3 - - + +
204D VAL* 5.9 2.5 - - + -
205D ILE* 3.9 21.3 - - + +
208D LEU* 5.1 7.6 - - + -
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Residues in contact with MET 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104D PHE* 3.5 54.3 - - + +
105D PHE* 4.0 25.4 - - + -
108D VAL* 3.6 27.8 - - + -
135D ILE* 2.7 42.7 + - + +
136D TYR* 3.5 9.9 - - - +
138D ALA* 1.3 75.4 - - - +
140D MET* 1.3 66.0 + - - +
142D THR* 3.0 3.6 + - - -
143D ALA* 2.8 23.2 + - - +
205D ILE* 3.9 19.3 - - + +
501D HEM 4.3 0.4 - - - -
502D HEM 5.0 3.8 - - + +
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Residues in contact with MET 140 (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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2D SMA 3.8 31.4 - - - +
105D PHE* 3.9 20.4 - - + -
109D TYR* 5.0 0.2 - - - -
136D TYR* 3.2 54.0 + - + +
137D LEU* 3.1 14.4 + - + +
139D MET* 1.3 78.2 - - - +
141D ALA* 1.3 69.6 + - - +
143D ALA* 3.2 2.0 + - - +
144D PHE* 2.9 22.4 + - - +
298D PHE* 3.7 34.0 - - + -
301D PHE* 4.8 4.3 - - - -
340D ILE* 3.9 20.4 - - + -
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Residues in contact with ALA 141 (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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2D SMA 4.1 38.0 + - + -
137D LEU 2.9 15.1 + - - +
138D ALA* 3.3 11.2 - - - +
140D MET* 1.3 73.3 - - - +
142D THR* 1.3 67.4 + - - +
144D PHE* 3.2 15.1 + - - +
145D MET* 3.0 15.7 - - + +
201D LEU* 3.8 13.9 - - + -
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Residues in contact with THR 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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138D ALA 2.8 20.7 + - - -
139D MET* 3.0 10.7 + - - -
141D ALA* 1.3 71.5 - - - +
143D ALA* 1.3 54.6 + - - +
144D PHE 2.7 1.2 + - - -
145D MET* 2.7 41.0 + - - +
146D GLY 3.0 9.4 + - - -
198D HIS* 3.4 28.2 + - + +
201D LEU* 3.3 20.5 - - + +
202D PRO* 4.0 9.9 - - + -
205D ILE* 4.0 8.0 - - - +
502D HEM 3.7 24.7 - - + -
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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
----------------------------------------------------------
101D ALA* 5.5 0.4 - - + -
105D PHE* 3.7 29.4 - - + -
139D MET 2.8 14.1 + - - +
140D MET* 3.5 4.7 - - - +
142D THR* 1.3 77.0 - - - +
144D PHE* 1.3 60.8 + - - +
146D GLY 3.9 0.4 - - - -
147D TYR* 3.2 22.3 + - - +
295D GLU* 5.0 0.3 - - - +
297D TYR* 4.0 19.9 + - + +
298D PHE* 4.7 2.0 - - + -
502D HEM 4.0 26.3 - - + +
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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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2D SMA 3.7 49.4 - - + -
140D MET 2.9 11.5 + - - +
141D ALA 3.2 13.0 - - - +
142D THR 2.7 4.6 + - - -
143D ALA* 1.3 71.0 - - - +
145D MET* 1.3 73.3 + - + +
147D TYR* 3.1 15.8 + - + +
148D VAL* 3.1 23.5 + - + +
158D GLY 4.2 2.0 - - - -
159D ALA* 3.8 16.6 - - - -
162D ILE* 3.6 44.4 - - + -
163D THR* 5.0 1.8 - - + -
194D PHE* 3.6 32.5 - + - -
295D GLU* 5.0 4.0 - - - -
298D PHE* 4.5 9.6 - - + -
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Residues in contact with MET 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D SMA 4.0 23.3 - - + -
141D ALA* 3.0 34.1 - - + +
142D THR* 2.7 16.6 + - - +
144D PHE* 1.3 85.2 - - + +
146D GLY* 1.3 63.6 + - - +
148D VAL* 2.9 25.0 + - - +
149D LEU* 3.2 12.0 + - - +
194D PHE* 3.7 37.6 - - + +
197D LEU* 3.8 26.2 - - + -
198D HIS* 4.2 13.2 - - + +
201D LEU* 3.7 17.5 - - + -
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Residues in contact with GLY 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142D THR 3.0 10.5 + - - -
143D ALA 3.7 0.6 + - - -
145D MET* 1.3 76.0 - - - +
147D TYR* 1.3 62.3 - - - +
148D VAL 3.0 1.0 + - - -
149D LEU* 3.0 17.3 + - - +
150D PRO* 3.2 10.2 - - - +
198D HIS* 3.5 33.2 + - - -
502D HEM 3.5 18.9 - - - +
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Residues in contact with TYR 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D SMA 4.5 3.1 - - - -
143D ALA 3.2 13.9 + - - +
144D PHE* 3.1 10.4 + - + +
146D GLY* 1.3 74.4 - - - +
148D VAL* 1.3 59.5 + - + +
150D PRO* 3.3 6.8 - - - +
154D MET* 3.5 40.5 - - + +
155D SER* 2.8 22.7 + - - -
158D GLY* 6.2 0.7 - - - -
275D GLY* 6.4 0.7 - - - -
276D HIS* 3.6 25.1 + - - +
279D ASN* 3.5 23.4 + - + +
293D VAL 5.6 0.8 + - - -
295D GLU* 3.6 46.0 - - + +
297D TYR* 5.1 0.7 - - - +
502D HEM 3.8 33.4 - - + +
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Residues in contact with VAL 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144D PHE* 3.1 34.0 + - + +
145D MET* 2.9 10.9 + - - +
147D TYR* 1.3 78.7 - - - +
149D LEU* 1.3 53.6 + - - +
151D TRP* 2.8 54.3 + - + -
155D SER* 3.2 21.7 - - - +
159D ALA* 4.1 11.7 - - + -
191D LEU* 4.3 7.4 - - + -
194D PHE* 3.7 32.1 - - + -
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Residues in contact with LEU 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D TYR* 2.7 34.3 + - + +
76D ALA* 3.9 1.7 - - - +
145D MET 3.5 9.2 - - - +
146D GLY 3.0 7.7 + - - +
148D VAL* 1.3 70.3 - - - +
150D PRO* 1.3 60.5 - - + +
151D TRP* 2.5 24.0 + - - +
191D LEU* 3.8 17.3 - - + +
194D PHE* 4.5 4.0 - - + -
195D PHE* 4.0 33.0 - - + +
198D HIS* 3.4 36.3 - - + -
502D HEM 3.5 35.2 - - + -
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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