Contacts of the helix formed by residues 125 - 149 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119G GLY 4.5 1.1 - - - -
120G SER* 3.0 29.2 - - - +
121G TYR 3.8 5.7 - - - +
122G LYS 3.5 11.9 - - - +
123G ALA 3.2 3.6 - - - -
124G PRO* 1.3 85.5 - - + +
126G GLU* 1.3 63.3 + - - +
127G VAL 3.5 1.6 - - - -
128G THR* 3.5 14.4 - - - +
129G TRP* 3.3 19.1 + - - +
219G THR* 4.5 9.6 + - - +
220G GLY 3.1 11.8 + - - -
221G ASN 2.7 38.2 + - - -
222G ASN* 2.8 28.7 + - - +
228G GLU* 3.0 34.8 + - - -
355G ARG* 3.9 11.3 - - - +
501G HEM 3.2 22.4 + - - +
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Residues in contact with GLU 126 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121G TYR 3.9 13.9 - - - +
123G ALA* 2.9 39.7 + - - +
124G PRO 3.0 2.5 + - - -
125G ARG* 1.3 74.3 - - - +
127G VAL* 1.3 69.1 + - - +
129G TRP* 3.0 7.9 + - - +
130G ILE* 3.0 25.8 + - + +
347G PRO* 4.1 15.9 - - + -
348G TRP* 4.4 15.9 + - + -
18J TRP* 3.8 26.3 + - + -
22J ARG* 2.5 40.1 + - - +
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Residues in contact with VAL 127 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124G PRO 4.5 0.4 + - - +
125G ARG 3.5 0.4 - - - -
126G GLU* 1.3 74.0 - - - +
128G THR* 1.3 69.1 + - - +
130G ILE* 3.1 12.6 + - + +
131G VAL* 2.9 34.3 + - + +
215G ALA* 4.7 5.6 - - + -
18J TRP* 4.5 10.1 - - + -
19J LEU* 4.4 20.4 - - + -
22J ARG* 3.6 36.3 - - + +
23J LEU* 4.2 26.2 - - + -
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Residues in contact with THR 128 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125G ARG* 3.5 21.6 + - - +
127G VAL* 1.3 80.2 - - - +
129G TRP* 1.3 63.6 + - - +
131G VAL* 3.1 3.9 + - - +
132G GLY* 2.8 21.1 + - - -
212G HIS* 3.6 30.6 + - + +
215G ALA* 3.9 12.9 + - - +
216G PHE* 3.9 27.1 + - + +
219G THR* 4.8 3.3 + - - +
501G HEM 3.8 33.6 + - + -
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Residues in contact with TRP 129 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112G ILE* 4.2 22.0 - - + -
115G GLY* 4.6 4.5 - - - -
116G LEU* 3.8 26.2 - - + -
121G TYR* 3.4 31.6 - + + -
125G ARG 3.3 8.6 + - - +
126G GLU* 3.0 10.7 + - - +
128G THR* 1.3 80.8 - - - +
130G ILE* 1.3 66.7 + - + +
132G GLY 3.2 1.9 + - - -
133G MET* 3.0 27.5 + - + +
343G MET* 3.2 35.2 + - + -
344G ALA* 3.6 20.5 + - - +
346G VAL* 3.4 12.5 - - + +
347G PRO* 3.7 11.9 - - + -
501G HEM 3.2 59.3 - - + +
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Residues in contact with ILE 130 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126G GLU* 3.0 22.1 + - + +
127G VAL* 3.6 10.3 - - + +
129G TRP* 1.3 80.4 - - + +
131G VAL* 1.3 67.8 + - + +
133G MET* 2.9 21.4 + - + +
134G LEU* 3.0 24.4 + - + +
344G ALA* 5.2 2.9 - - + +
348G TRP* 3.9 32.3 - - + -
18J TRP* 4.7 9.4 - - + -
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Residues in contact with VAL 131 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127G VAL* 2.9 33.0 + - + +
128G THR* 3.5 8.3 - - - +
130G ILE* 1.3 72.1 - - + +
132G GLY* 1.3 66.1 + - - +
134G LEU* 2.8 29.1 + - + +
135G ILE* 2.9 14.9 + - + +
208G LEU* 4.0 20.4 - - + +
211G ILE* 4.2 19.1 - - + +
212G HIS* 3.9 34.3 - - + +
215G ALA* 5.7 0.4 - - + -
23J LEU* 5.5 0.4 - - + -
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Residues in contact with GLY 132 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128G THR 2.8 13.4 + - - -
129G TRP 3.2 0.4 + - - -
131G VAL* 1.3 77.0 - - - +
133G MET* 1.3 56.2 + - - +
135G ILE* 3.0 7.8 + - - +
136G TYR 2.9 13.9 + - - -
212G HIS* 4.0 6.4 + - - -
501G HEM 2.8 56.0 - - - +
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Residues in contact with MET 133 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112G ILE* 5.6 1.3 - - - -
129G TRP* 3.0 37.5 + - + +
130G ILE* 2.9 13.0 + - + +
132G GLY* 1.3 70.9 - - - +
134G LEU* 1.3 68.2 + - + +
136G TYR* 3.0 15.2 + - + +
137G LEU* 2.9 26.8 + - + +
340G ILE* 3.8 31.2 - - + +
343G MET* 3.9 20.0 - - + -
344G ALA* 3.9 33.9 - - + +
501G HEM 3.2 17.2 - - + +
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Residues in contact with LEU 134 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130G ILE* 3.0 18.7 + - + +
131G VAL* 2.8 31.6 + - + +
133G MET* 1.3 72.4 - - + +
135G ILE* 1.3 64.8 + - - +
137G LEU* 3.1 17.1 + - + +
138G ALA* 3.0 22.7 + - - +
208G LEU* 3.9 24.9 - - + +
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Residues in contact with ILE 135 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131G VAL* 2.9 12.3 + - + +
132G GLY* 3.1 13.5 - - - +
134G LEU* 1.3 75.4 - - - +
136G TYR* 1.3 55.2 + - - +
138G ALA* 3.1 7.9 + - - +
139G MET* 2.7 51.4 + - + +
205G ILE* 4.4 6.5 - - + +
208G LEU* 3.8 21.1 - - + +
209G VAL* 4.0 23.8 - - + +
212G HIS* 4.1 16.2 - - + -
501G HEM 3.2 56.3 - - + -
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Residues in contact with TYR 136 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105G PHE* 4.3 17.3 - + - -
108G VAL* 4.6 9.9 - - + -
109G TYR* 2.6 47.1 + + - -
112G ILE* 4.3 14.4 - - + -
132G GLY 2.9 6.8 + - - +
133G MET* 3.2 29.2 - - + +
135G ILE* 1.3 76.5 - - - +
137G LEU* 1.3 66.9 + - + +
139G MET* 3.5 6.5 - - - +
140G MET* 3.2 47.4 + - + +
301G PHE* 3.1 26.0 - + - -
340G ILE* 4.5 5.8 - - + -
343G MET* 4.4 11.9 - - + -
501G HEM 3.6 19.3 - - + -
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Residues in contact with LEU 137 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133G MET* 2.9 15.1 + - + +
134G LEU* 3.3 20.6 - - + +
136G TYR* 1.3 75.4 - - + +
138G ALA* 1.3 65.4 + - - +
140G MET* 3.0 25.3 + - + +
141G ALA* 2.8 23.5 + - - +
337G PHE* 5.8 5.2 - - + -
340G ILE* 4.9 17.3 - - + -
503G SMA 4.5 17.6 - - - +
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Residues in contact with ALA 138 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134G LEU 3.0 9.2 + - - +
135G ILE* 3.4 9.9 - - - +
137G LEU* 1.3 77.4 - - - +
139G MET* 1.3 66.0 + - - +
141G ALA* 3.1 9.2 + - - +
142G THR* 2.8 27.5 + - - -
201G LEU* 3.9 13.5 - - + +
204G VAL* 5.9 2.7 - - + -
205G ILE* 3.9 22.7 - - + +
208G LEU* 5.2 5.4 - - + -
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Residues in contact with MET 139 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104G PHE* 3.5 52.9 - - + +
105G PHE* 4.0 19.7 - - + -
108G VAL* 3.8 37.9 - - + -
135G ILE* 2.7 42.2 + - + +
136G TYR* 3.5 9.4 - - - +
138G ALA* 1.3 74.2 - - - +
140G MET* 1.3 66.0 + - - +
142G THR* 3.0 3.5 + - - -
143G ALA* 2.8 23.4 + - - +
205G ILE* 3.9 18.8 - - + +
501G HEM 4.5 0.7 - - - -
502G HEM 5.4 3.6 - - + +
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Residues in contact with MET 140 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105G PHE* 3.9 21.1 - - + -
109G TYR* 5.0 0.4 - - - -
136G TYR* 3.3 53.8 - - + +
137G LEU* 3.0 19.1 + - + +
139G MET* 1.3 77.5 - - - +
141G ALA* 1.3 67.1 + - - +
142G THR 3.0 0.3 + - - -
143G ALA* 3.1 2.3 + - - +
144G PHE* 2.9 24.3 + - - +
298G PHE* 3.7 26.2 - - + -
301G PHE* 4.8 4.3 - - - -
340G ILE* 3.9 20.6 - - + -
503G SMA 3.9 33.1 - - + +
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Residues in contact with ALA 141 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137G LEU 2.8 14.8 + - - +
138G ALA* 3.3 11.9 - - - +
140G MET* 1.3 73.1 - - - +
142G THR* 1.3 62.8 + - - +
144G PHE* 3.4 14.6 - - - +
145G MET* 2.9 18.6 - - + +
201G LEU* 3.8 13.2 - - + -
503G SMA 4.1 33.6 + - + +
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Residues in contact with THR 142 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138G ALA 2.8 20.1 + - - -
139G MET* 3.0 10.3 - - - -
141G ALA* 1.3 67.5 - - - +
143G ALA* 1.3 54.7 + - - +
144G PHE 2.7 16.6 + - - -
145G MET* 2.7 26.7 + - - +
146G GLY 3.0 9.5 + - - -
198G HIS* 3.4 30.2 + - + +
201G LEU* 3.3 20.7 - - + +
202G PRO* 4.0 10.0 - - + +
205G ILE* 3.9 6.8 - - - +
502G HEM 3.8 24.9 - - + -
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Residues in contact with ALA 143 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101G ALA* 5.5 0.7 - - + -
105G PHE* 3.7 28.9 - - + -
139G MET 2.8 13.9 + - - +
140G MET* 3.5 4.9 - - - +
142G THR* 1.3 79.6 - - - +
144G PHE* 1.3 60.2 + - - +
146G GLY 3.9 0.9 - - - -
147G TYR* 3.2 22.3 + - - +
295G GLU* 4.6 0.6 - - - +
297G TYR* 4.0 16.9 + - + +
298G PHE* 4.6 1.3 - - + -
502G HEM 3.9 27.9 - - + +
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Residues in contact with PHE 144 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140G MET 2.9 9.9 + - - +
141G ALA 3.4 7.0 - - - +
142G THR 2.7 5.1 + - - -
143G ALA* 1.3 72.8 - - - +
145G MET* 1.3 70.3 + - - +
147G TYR* 3.1 17.3 + - + +
148G VAL* 3.2 22.6 + - + +
158G GLY 4.1 0.4 - - - -
159G ALA* 3.8 21.8 - - - -
162G ILE* 3.3 47.6 - - + -
163G THR* 5.0 2.5 - - + -
194G PHE* 3.6 27.1 - + - -
295G GLU* 4.9 1.3 - - - -
298G PHE* 4.5 8.5 - + + -
503G SMA 3.3 66.2 - - + -
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Residues in contact with MET 145 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141G ALA* 2.9 32.3 + - + +
142G THR* 2.7 17.5 + - - +
144G PHE* 1.3 76.6 - - + +
146G GLY* 1.3 63.0 + - - +
148G VAL* 2.9 25.4 + - - +
149G LEU* 3.2 11.3 + - - +
194G PHE* 3.7 34.4 - - + +
197G LEU* 3.6 34.3 - - + -
198G HIS* 4.2 9.4 - - + +
201G LEU* 3.7 17.5 - - + -
503G SMA 3.4 30.5 - - + -
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Residues in contact with GLY 146 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142G THR 3.0 10.5 + - - -
143G ALA 3.7 0.9 + - - -
145G MET* 1.3 74.3 - - - +
147G TYR* 1.3 61.8 + - - +
148G VAL 2.9 1.4 + - - -
149G LEU* 3.0 16.8 + - - +
150G PRO* 3.2 10.4 - - - +
198G HIS* 3.5 30.3 + - - -
502G HEM 3.5 22.0 - - - +
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Residues in contact with TYR 147 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143G ALA 3.2 13.7 + - - +
144G PHE* 3.1 10.6 + - + +
146G GLY* 1.3 74.9 - - - +
148G VAL* 1.3 53.2 + - + +
150G PRO* 3.3 6.2 - - - +
154G MET* 3.5 41.0 - - + +
155G SER* 2.7 29.7 + - - -
158G GLY* 6.2 0.2 - - - -
275G GLY* 6.4 0.9 - - - -
276G HIS* 3.6 24.4 + - - +
279G ASN* 3.5 24.1 + - + +
293G VAL 5.6 0.6 + - - -
295G GLU* 3.6 45.4 - - + +
297G TYR* 5.4 0.4 - - - -
502G HEM 3.8 35.2 - - + -
503G SMA 4.6 5.4 - - - -
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Residues in contact with VAL 148 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144G PHE* 3.2 34.1 + - + +
145G MET* 2.9 9.3 + - - +
147G TYR* 1.3 79.5 - - - +
149G LEU* 1.3 52.7 + - - +
151G TRP* 2.8 55.9 + - + -
155G SER* 3.3 20.6 - - - +
159G ALA* 4.1 11.7 - - + -
190G THR* 6.6 0.2 - - - -
191G LEU* 4.3 8.1 - - + -
194G PHE* 3.7 32.3 - - + -
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Residues in contact with LEU 149 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69G TYR* 2.6 41.7 + - + +
76G ALA* 3.9 2.4 - - - +
145G MET 3.5 8.5 - - - +
146G GLY 3.0 7.2 + - - +
148G VAL* 1.3 75.6 - - - +
150G PRO* 1.3 59.7 - - + +
151G TRP* 2.6 18.4 + - - +
191G LEU* 3.8 17.1 - - + +
194G PHE* 4.6 3.6 - - + -
195G PHE* 4.0 33.9 - - + +
198G HIS* 3.6 35.4 - - + -
502G HEM 3.6 28.3 - - + -
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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