Contacts of the helix formed by residues 128 - 155 (chain B) in PDB entry 3MYV
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 ASP 128 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B VAL* 3.9 22.1 - - + +
125B GLU 5.0 0.2 + - - -
126B SER 3.8 2.2 - - - -
127B GLY* 1.3 79.4 - - - +
129B GLU* 1.3 59.3 + - - +
130B LYS* 4.1 5.7 + - - +
131B LYS* 3.4 33.9 + - + +
132B LEU* 2.9 30.5 + - - +
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Residues in contact with GLU 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B GLY 3.9 1.8 - - - +
128B ASP* 1.3 72.5 + - - +
130B LYS* 1.3 59.6 + - - +
132B LEU* 3.7 16.1 - - - +
133B ASN* 2.8 52.7 + - - +
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Residues in contact with LYS 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B ASP* 3.3 6.4 + - - +
129B GLU* 1.3 79.9 - - - +
131B LYS* 1.3 56.3 + - - +
133B ASN* 3.3 6.8 + - - +
134B ALA* 2.9 26.4 + - + +
203B LEU 4.8 0.9 - - - +
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Residues in contact with LYS 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B VAL* 3.7 18.7 + - + +
40B THR* 5.5 5.5 + - - +
43B ASP* 3.8 25.9 + - - +
128B ASP* 3.4 29.1 + - - +
129B GLU 3.4 0.2 - - - -
130B LYS* 1.3 76.7 - - - +
132B LEU* 1.3 62.0 + - - +
134B ALA* 3.0 9.6 + - + +
135B LEU* 2.8 46.6 + - + +
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Residues in contact with LEU 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B VAL* 4.1 14.1 - - + +
42B VAL* 4.1 24.5 - - + -
119B ILE* 3.9 39.7 - - + -
124B ILE* 4.0 29.8 - - + +
125B GLU 5.2 2.0 - - - +
128B ASP 2.9 19.2 + - - +
129B GLU* 3.7 16.6 - - - +
131B LYS* 1.3 75.7 - - - +
133B ASN* 1.3 59.1 + - - +
135B LEU* 3.3 5.0 + - - +
136B LYS* 2.9 27.4 + - - +
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Residues in contact with ASN 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B GLU* 2.8 42.2 + - - +
130B LYS* 3.6 6.0 - - - +
132B LEU* 1.3 77.5 - - - +
134B ALA* 1.3 56.8 + - - +
136B LYS* 3.2 18.7 + - - +
137B GLY 3.0 25.1 + - - -
203B LEU* 3.4 39.1 - - + +
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Residues in contact with ALA 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B LYS* 2.9 14.5 + - + +
131B LYS* 3.0 14.8 + - + +
133B ASN* 1.3 75.4 - - - +
135B LEU* 1.3 60.7 + - + +
137B GLY* 3.5 1.4 + - - -
138B GLU* 3.0 28.4 + - - +
203B LEU 3.3 16.7 + - - +
204B MSE 3.9 5.9 - - - +
205B SER* 4.2 25.1 - - - +
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Residues in contact with LEU 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B VAL* 3.8 35.0 - - + +
42B VAL* 4.0 17.7 - - + -
43B ASP* 3.7 26.2 - - + +
46B VAL* 4.2 6.9 - - + +
119B ILE* 5.0 1.6 - - - -
131B LYS* 2.8 29.0 + - + +
132B LEU* 3.7 6.5 - - - +
134B ALA* 1.3 76.2 - - + +
136B LYS* 1.3 59.9 + - - +
138B GLU* 3.8 9.2 - - - +
139B THR* 2.7 35.0 + - - -
212B ARG* 3.3 29.4 - - - +
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Residues in contact with LYS 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B LEU* 3.8 19.0 - - + +
119B ILE* 4.1 32.7 - - + +
132B LEU 2.9 13.8 + - - +
133B ASN* 3.2 20.1 + - - +
135B LEU* 1.3 74.3 - - - +
137B GLY* 1.3 59.4 + - - +
139B THR* 3.3 4.5 + - - -
140B MSE 2.9 44.2 + - - +
199B GLU* 4.2 11.9 + - - -
203B LEU* 3.9 22.0 - - + +
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Residues in contact with GLY 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B ASN 3.0 13.6 + - - -
134B ALA 3.8 3.4 - - - -
136B LYS* 1.3 79.2 - - - +
138B GLU* 1.3 55.1 + - - +
140B MSE 3.2 2.4 + - - -
141B ALA* 2.9 24.1 + - - +
200B ALA* 3.1 24.1 - - - +
203B LEU* 3.8 11.8 - - - +
204B MSE 3.6 15.9 - - - -
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Residues in contact with GLU 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B VAL* 3.6 9.0 - - + +
50B TYR* 2.8 31.9 + - + +
134B ALA 3.0 16.8 + - - +
135B LEU* 3.8 12.2 - - - +
136B LYS 3.3 0.4 - - - -
137B GLY* 1.3 72.5 - - - +
139B THR* 1.3 65.2 - - - +
141B ALA* 3.1 3.5 + - - +
142B VAL* 3.0 23.3 + - - +
204B MSE 3.7 17.0 - - + +
209B ASN* 4.8 3.3 + - - -
212B ARG* 2.8 48.6 + - - +
213B MSE 3.7 16.8 - - + +
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Residues in contact with THR 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B VAL* 3.2 22.3 - - - +
49B LEU* 4.1 9.0 - - + -
112B ALA* 3.4 39.9 - - + +
115B ILE* 3.9 11.7 - - + +
116B LEU* 4.0 15.9 - - + -
135B LEU 2.7 22.4 + - - -
136B LYS* 3.5 5.2 - - - -
138B GLU* 1.3 77.0 - - - +
140B MSE 1.3 56.1 + - - +
142B VAL* 3.3 7.9 + - - +
143B ILE* 3.0 27.4 + - - +
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Residues in contact with MSE 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B LEU* 3.9 23.1 - - + -
136B LYS* 2.9 29.5 + - - +
137B GLY* 3.5 8.1 - - - +
139B THR* 1.3 73.8 - - - +
141B ALA* 1.3 58.3 + - - +
143B ILE* 3.2 9.5 + - - +
144B ALA* 2.8 24.8 + - - +
196B THR* 3.5 48.5 - - + +
199B GLU* 3.5 28.9 - - + +
200B ALA* 3.9 7.4 - - + -
203B LEU* 4.0 26.5 - - - -
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Residues in contact with ALA 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B GLY 2.9 12.7 + - - +
138B GLU* 3.1 9.6 + - - +
140B MSE 1.3 74.5 - - - +
142B VAL* 1.3 59.5 + - - +
144B ALA* 3.3 2.9 + - - +
145B LEU* 3.0 28.2 + - - +
197B LEU* 3.8 25.6 - - + -
200B ALA* 3.9 0.6 - - - +
204B MSE 4.1 16.6 - - + -
213B MSE 3.7 18.0 - - + +
218B ALA* 4.4 5.4 - - + -
221B LEU* 4.2 2.8 - - + +
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Residues in contact with VAL 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B VAL* 5.5 0.2 - - + -
49B LEU* 4.2 24.0 - - + -
50B TYR* 3.8 32.3 - - + +
53B MSE 4.3 12.8 - - + -
108B ILE* 3.6 29.8 - - + -
112B ALA* 4.9 2.0 - - + -
138B GLU 3.0 19.1 + - - +
139B THR 3.3 7.8 + - - +
141B ALA* 1.3 72.4 - - - +
143B ILE* 1.3 66.5 + - - +
145B LEU* 3.3 2.9 + - - +
146B CYS* 3.0 26.0 + - - -
213B MSE 3.8 12.3 - - + -
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Residues in contact with ILE 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B LEU* 3.5 26.6 - - + +
112B ALA* 3.4 28.0 - - + -
113B TRP* 4.0 20.4 - - + +
116B LEU* 3.4 35.7 - - + -
139B THR 3.0 20.7 + - - +
140B MSE 3.2 9.4 + - + +
142B VAL* 1.3 74.9 - - - +
144B ALA* 1.3 63.2 + - - +
146B CYS* 3.3 1.0 + - - -
147B GLN* 3.0 22.3 + - - +
192B PHE* 3.8 30.1 - - + -
196B THR* 4.6 4.9 - - + -
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Residues in contact with ALA 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B MSE 2.8 16.1 + - - +
141B ALA 3.3 6.0 + - - +
143B ILE* 1.3 79.1 - - - +
145B LEU* 1.3 56.2 + - - +
147B GLN* 3.6 0.7 + - - -
148B PHE* 3.0 31.1 + - - +
192B PHE* 5.8 0.4 - - - -
193B ILE* 3.8 27.6 - - + +
196B THR* 4.6 3.4 - - + -
197B LEU* 4.1 36.3 - - + +
221B LEU* 5.0 1.1 - - - -
225B ILE* 5.1 0.4 - - - -
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Residues in contact with LEU 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B MSE 4.1 15.3 - - - -
58B TYR* 4.3 3.6 - - - +
59B TYR* 3.7 23.8 - - + +
141B ALA 3.0 16.5 + - - +
142B VAL* 3.7 5.8 - - - +
144B ALA* 1.3 76.9 - - - +
146B CYS* 1.3 63.6 + - - +
148B PHE* 3.3 7.8 + - + +
149B ASP* 3.0 48.5 + - - +
213B MSE 4.0 22.0 - - + -
221B LEU* 4.0 30.9 - - + +
224B ARG* 4.8 0.7 - - - +
276B PHE* 4.2 11.0 - - + -
357B VAL* 4.6 5.6 - - + -
358B LEU* 5.8 0.4 - - + -
513B EDO 4.6 5.4 - - - +
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Residues in contact with CYS 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B MSE 6.0 2.0 - - - -
58B TYR* 3.5 25.4 - - - -
105B PRO* 3.9 10.0 - - + +
108B ILE* 3.5 37.0 - - - -
109B LEU* 3.6 22.0 - - + -
142B VAL* 3.0 26.7 + - - +
143B ILE 3.8 0.9 - - - +
145B LEU* 1.3 77.7 - - - +
147B GLN* 1.3 59.6 + - - +
149B ASP* 3.4 2.9 + - - +
150B LEU* 3.0 32.3 + - - +
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Residues in contact with GLN 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B LEU* 3.6 17.2 - - + +
143B ILE 3.0 16.1 + - - +
146B CYS* 1.3 75.0 - - - +
148B PHE* 1.3 55.8 + - - +
150B LEU* 3.3 16.0 + - - +
151B THR* 2.6 43.4 + - - +
168B ALA* 4.3 6.9 + - - +
169B PRO 3.1 21.6 + - - +
170B LEU* 3.5 27.4 - - + +
171B ILE* 2.9 28.8 + - - +
189B ALA* 5.1 1.0 - - - +
192B PHE* 4.4 7.9 - - + -
193B ILE* 3.9 19.7 - - + -
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Residues in contact with PHE 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B ALA 3.0 20.6 + - - +
145B LEU* 3.6 13.5 - - + +
147B GLN* 1.3 76.5 - - - +
149B ASP* 1.3 61.7 + - - +
151B THR* 3.1 5.1 + - - -
152B ARG* 3.0 58.5 + - + +
190B TYR* 3.4 36.1 - + - -
193B ILE* 3.6 14.3 - - + +
221B LEU* 4.6 0.9 - - + -
224B ARG* 3.9 16.2 - - - -
225B ILE* 3.8 34.1 - - + -
228B TYR* 3.5 38.1 - + - -
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Residues in contact with ASP 149 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B TYR* 2.7 32.8 + - + +
59B TYR* 2.6 24.8 + - - -
63B MSE 3.6 13.9 - - - +
101B LEU 5.9 0.7 - - - -
105B PRO* 5.3 2.5 - - + -
145B LEU* 3.0 19.1 + - - +
146B CYS 3.7 2.0 - - - +
148B PHE* 1.3 75.0 - - - +
150B LEU* 1.3 65.3 + - - +
151B THR 3.2 0.2 + - - -
152B ARG* 2.8 37.6 + - - +
153B CYS* 3.0 31.3 + - - +
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Residues in contact with LEU 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B LEU 3.5 24.7 - - - +
102B TRP 3.8 8.7 - - - +
105B PRO* 3.8 10.5 - - + -
106B PHE* 3.6 40.8 - - + -
109B LEU* 3.6 31.4 - - + -
146B CYS 3.0 15.3 + - - +
147B GLN* 3.3 12.5 + - - +
149B ASP* 1.3 75.4 - - - +
151B THR* 1.3 56.5 + - - +
153B CYS* 4.6 0.2 - - - -
154B PHE* 2.9 50.8 + - + +
168B ALA* 4.0 13.8 - - + +
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Residues in contact with THR 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B GLN* 2.6 26.5 + - - +
148B PHE* 3.1 9.2 + - - -
150B LEU* 1.3 78.0 - - - +
152B ARG* 1.3 57.3 + - - +
155B GLY* 2.9 31.0 + - - +
156B TYR 5.0 0.3 - - - +
167B GLY* 5.1 1.8 - - - -
168B ALA 5.0 6.9 + - - +
186B VAL* 3.7 34.5 - - + -
189B ALA* 3.4 28.8 - - + +
190B TYR* 3.9 15.7 - - + -
193B ILE* 3.9 3.4 - - - +
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Residues in contact with ARG 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B TYR* 3.7 0.2 + - - -
63B MSE 3.5 14.0 - - - +
66B TYR* 4.8 2.3 + - - -
145B LEU* 5.1 0.2 - - - +
148B PHE* 3.0 44.9 + - + +
149B ASP* 2.8 33.4 + - - +
151B THR* 1.3 76.8 - - - +
153B CYS* 1.3 58.5 + - - +
155B GLY 4.0 8.6 - - - +
156B TYR 6.3 0.2 - - - -
157B PRO* 6.4 1.6 - - - -
190B TYR* 5.2 3.4 - - - +
224B ARG* 3.7 9.1 - - - +
228B TYR* 3.0 36.0 + - + -
422B HIS* 5.5 1.4 + - - -
424B PHE* 5.2 1.2 - - - -
425B PHE* 3.6 48.0 - - + -
428B LEU* 5.9 2.3 - - - +
456B CYS 4.8 6.2 - - - +
513B EDO 3.1 38.7 + - - -
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Residues in contact with CYS 153 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B MSE 4.2 24.7 - - - -
66B TYR* 3.5 30.7 + - - +
101B LEU* 4.5 14.1 - - + +
149B ASP* 3.0 20.8 + - - +
152B ARG* 1.3 80.8 - - - +
154B PHE* 1.3 77.3 + - + +
155B GLY 3.8 0.4 - - - -
425B PHE* 4.4 4.9 - - - -
457B VAL* 3.5 5.1 - - - -
458B LEU* 2.9 34.0 + - + +
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Residues in contact with PHE 154 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B LEU* 3.8 5.4 - - + -
101B LEU 3.7 19.5 - - - -
102B TRP* 3.7 45.1 - + + -
150B LEU* 2.9 31.5 + - + +
153B CYS* 1.3 86.7 - - + +
155B GLY* 1.3 58.6 + - - +
166B LEU 4.3 0.7 - - - -
167B GLY* 4.5 1.3 - - - -
168B ALA* 4.5 13.7 - - + +
183B ARG* 3.4 11.5 + - - -
457B VAL* 3.9 4.7 - - - +
458B LEU* 3.5 39.0 - - + -
459B PRO 3.4 24.0 - - - -
460B ILE* 4.3 11.0 - - + -
474B ASN* 3.0 23.6 + - - +
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Residues in contact with GLY 155 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B LEU 4.2 0.2 + - - -
151B THR 2.9 20.7 + - - +
152B ARG* 4.0 9.5 - - - +
154B PHE* 1.3 76.6 - - - +
156B TYR* 1.3 68.9 + - - +
157B PRO* 3.7 1.7 - - - +
166B LEU 3.3 16.8 - - - -
167B GLY* 4.0 2.5 - - - -
186B VAL* 3.8 8.5 - - - -
457B VAL* 3.3 13.0 - - - +
----------------------------------------------------------
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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