Contacts of the helix formed by residues 129 - 156 (chain B) in PDB entry 2IAG
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 LEU 129 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A GLU* 5.9 1.6 - - - +
499A ARG* 3.5 43.1 - - + +
125B LYS* 3.3 44.2 - - + +
126B LEU* 3.4 14.2 + - + +
127B THR 3.6 0.2 - - - -
128B LEU* 1.3 87.3 - - + +
130B HIS* 1.3 94.7 + - + +
132B GLU* 3.2 6.6 + - - +
133B LEU* 3.1 18.2 + - + +
442B LEU 5.3 2.9 - - - +
445B SER* 4.1 18.6 - - - +
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Residues in contact with HIS 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A ARG* 3.1 58.8 + - - +
314A GLU* 5.7 0.9 - - - -
459A LEU 4.0 6.5 + - - -
462A LEU 4.5 2.8 + - - -
463A ASP* 3.8 24.3 + - - -
464A LEU 5.9 0.9 - - - -
465A GLU* 5.5 4.8 - - - +
499A ARG* 3.9 17.1 + - - +
126B LEU* 4.0 15.9 + - + +
129B LEU* 1.3 97.8 + - + +
131B ARG* 1.3 65.7 + - + +
133B LEU* 3.4 9.7 + - - +
134B GLN* 3.2 19.8 + - - +
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Residues in contact with ARG 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A PRO* 3.7 42.5 + - - +
306A LEU* 6.4 2.5 - - + -
307A ALA* 6.1 2.8 - - - +
130B HIS* 1.3 80.7 - - + +
132B GLU* 1.3 92.4 + - + +
134B GLN* 3.4 7.6 + - - +
135B ALA* 3.1 22.0 + - + +
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Residues in contact with GLU 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B LEU 4.2 10.1 - - - +
127B THR* 3.6 23.1 - - - +
129B LEU 3.2 6.5 + - - +
131B ARG* 1.3 110.6 + - + +
133B LEU* 1.3 55.4 + - - +
135B ALA* 3.3 13.4 + - - +
136B LEU* 3.0 30.5 + - + +
254B LYS* 3.4 45.1 + - + +
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Residues in contact with LEU 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497A ARG* 5.5 8.5 - - - +
128B LEU 3.6 13.5 - - - +
129B LEU* 3.1 33.2 + - + +
130B HIS 3.6 6.5 - - - +
131B ARG 3.3 0.2 - - - -
132B GLU* 1.3 74.3 - - - +
134B GLN* 1.3 60.8 + - - +
136B LEU* 3.2 6.7 + - + +
137B THR* 2.8 43.6 + - - +
445B SER* 3.8 20.0 - - - +
446B TYR* 3.6 39.9 - - + +
449B ASN* 4.0 10.1 - - - +
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Residues in contact with GLN 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465A GLU* 5.1 11.6 + - - +
495A ARG* 5.1 3.6 - - - +
130B HIS 3.2 11.0 + - - +
131B ARG* 3.7 10.1 - - - +
132B GLU 3.4 0.2 - - - -
133B LEU* 1.3 78.7 - - - +
135B ALA* 1.3 60.4 + - - +
137B THR* 3.3 15.8 + - - +
138B GLU* 2.8 54.8 + - - +
332B GLN* 4.1 23.3 + - - +
335B LEU* 4.8 8.3 - - - +
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Residues in contact with ALA 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B ARG* 3.1 15.1 + - + +
132B GLU* 3.5 18.2 - - - +
133B LEU 3.2 0.2 - - - -
134B GLN* 1.3 76.2 - - - +
136B LEU* 1.3 56.6 + - - +
138B GLU* 3.5 8.4 + - - +
139B ALA* 3.1 27.7 + - - +
251B HIS* 5.2 5.8 + - - +
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Residues in contact with LEU 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B THR 4.1 9.4 - - - +
128B LEU* 3.6 33.9 - - + -
132B GLU* 3.0 15.2 + - + +
133B LEU* 3.6 9.0 - - - +
135B ALA* 1.3 73.6 - - + +
137B THR* 1.3 55.4 + - - +
139B ALA* 3.3 1.9 + - + -
140B MET* 2.8 36.6 + - - +
179B THR* 3.6 18.0 - - + +
180B LEU* 3.7 17.0 - - + -
253B SER* 3.6 31.9 - - - -
254B LYS 5.5 0.9 - - - +
255B TRP* 5.2 1.3 - - + -
446B TYR* 4.1 28.7 - - + -
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Residues in contact with THR 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B LEU* 2.8 33.0 + - - +
134B GLN* 3.3 13.8 + - - +
136B LEU* 1.3 73.2 - - - +
138B GLU* 1.3 61.1 + - - +
140B MET* 3.4 4.3 + - - -
141B TYR* 3.1 18.0 + - - +
335B LEU* 3.7 30.3 - - + -
446B TYR* 4.9 3.9 - - - -
449B ASN* 3.1 24.6 + - + +
453B GLN* 3.1 32.4 + - - +
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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
----------------------------------------------------------
134B GLN* 2.8 51.0 + - - +
135B ALA* 3.9 7.4 - - - +
137B THR* 1.3 72.4 - - - +
139B ALA* 1.3 63.0 + - - +
141B TYR* 3.4 6.0 + - - +
142B THR* 2.8 31.5 + - + +
453B GLN* 5.3 0.2 - - - +
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Residues in contact with ALA 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B ALA 3.1 15.6 + - - +
136B LEU* 3.8 5.4 - - + +
138B GLU* 1.3 76.7 - - - +
140B MET* 1.3 58.4 + - - +
142B THR* 3.5 8.4 + - - +
143B ASN* 2.8 42.4 + - - +
179B THR* 4.0 16.4 - - + +
188B ARG* 5.1 0.6 + - - +
251B HIS* 3.6 32.1 - - + +
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Residues in contact with MET 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B LEU 2.8 17.6 + - - +
137B THR* 3.8 2.7 - - - +
138B GLU 3.2 0.2 - - - -
139B ALA* 1.3 74.5 - - - +
141B TYR* 1.3 60.6 + - - +
143B ASN* 3.9 0.3 - - - +
144B LEU* 2.7 46.4 + - + +
172B LEU* 3.6 17.5 - - + +
175B ALA* 3.5 21.5 - - + +
176B GLY* 3.5 19.7 - - - +
179B THR* 3.4 18.3 + - - +
288B MET* 4.5 3.1 - - + -
446B TYR* 3.5 20.2 - - + +
450B SER* 3.5 29.2 - - - +
453B GLN* 3.7 14.8 - - - +
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Residues in contact with TYR 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B THR 3.1 9.7 + - - +
138B GLU* 3.9 6.5 - - - +
139B ALA 3.3 0.2 - - - -
140B MET* 1.3 76.5 - - - +
142B THR* 1.3 67.6 + - + +
144B LEU* 3.4 3.4 + - - +
145B HIS* 3.0 34.6 + + + +
331B PRO* 4.8 24.6 - - + +
453B GLN* 3.3 36.9 + - + +
456B PHE* 4.1 25.4 - + - -
457B LEU* 4.0 36.3 - - + +
461B HIS* 4.2 9.4 + - - -
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Residues in contact with THR 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B GLU* 2.8 23.3 + - + +
139B ALA* 3.9 7.9 - - - +
141B TYR* 1.3 82.6 - - + +
143B ASN* 1.3 54.8 + - - +
145B HIS* 3.8 4.8 + - - +
146B ALA* 2.9 29.5 + - - +
188B ARG* 3.5 27.0 + - - +
251B HIS* 6.4 0.2 - - + -
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Residues in contact with ASN 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B ALA* 2.8 33.7 + - - +
140B MET 3.9 0.4 - - - +
142B THR* 1.3 71.9 - - - +
144B LEU* 1.3 65.1 + - - +
146B ALA* 3.7 3.6 - - - +
147B VAL* 2.9 29.5 + - - +
175B ALA* 3.7 23.1 - - + +
178B LEU* 3.7 20.6 + - + +
179B THR* 2.9 27.5 + - - +
183B ILE* 3.6 13.6 - - - +
188B ARG* 3.3 26.1 + - - +
196B ASP* 5.2 0.2 - - - +
251B HIS* 5.6 1.8 + - - -
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Residues in contact with LEU 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B MET* 2.7 37.7 + - + +
141B TYR* 3.9 1.3 - - - +
143B ASN* 1.3 72.4 - - - +
145B HIS* 1.3 57.6 + - - +
147B VAL* 4.0 1.6 - - - +
148B LEU* 3.0 35.7 + - + +
171B PHE* 3.9 13.7 - - + +
172B LEU* 4.0 20.0 - - + -
175B ALA* 3.6 20.9 - - + -
450B SER 3.7 10.5 - - - +
453B GLN* 3.8 13.9 - - + -
454B PHE* 3.7 41.1 - - + +
457B LEU* 3.7 15.0 - - + -
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Residues in contact with HIS 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B TYR* 3.0 30.4 + + + +
142B THR* 3.8 5.8 + - - +
144B LEU* 1.3 77.4 - - - +
146B ALA* 1.3 59.2 + - - +
148B LEU* 4.9 0.9 - - - -
149B LEU* 2.9 67.3 + - + +
457B LEU* 3.8 30.2 - - + +
461B HIS* 4.3 14.9 + - - -
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Residues in contact with ALA 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B THR* 2.9 22.6 + - - +
143B ASN* 3.7 7.9 - - - +
145B HIS* 1.3 77.7 + - - +
147B VAL* 1.3 59.0 + - + +
150B GLY* 2.9 28.3 + - - +
178B LEU* 6.4 0.7 - - + -
188B ARG* 4.3 13.7 - - - +
193B GLN* 4.3 25.6 + - + +
197B ARG* 3.6 7.7 - - + -
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Residues in contact with VAL 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B ASN 2.9 21.9 + - - +
144B LEU* 4.1 3.1 - - - +
146B ALA* 1.3 75.3 - - + +
148B LEU* 1.3 61.3 + - - +
151B ASP* 2.9 34.7 + - - +
171B PHE* 3.6 16.6 - - + +
174B ARG* 3.4 46.7 - - + +
175B ALA 4.4 10.5 - - - +
178B LEU* 3.9 25.6 - - + -
196B ASP* 6.0 0.2 - - + -
197B ARG* 4.1 13.2 - - + -
200B SER* 4.7 1.8 - - - +
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Residues in contact with LEU 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B LEU* 3.0 19.7 + - + +
145B HIS* 4.3 1.3 - - - +
147B VAL* 1.3 78.9 - - - +
149B LEU* 1.3 65.6 + - + +
151B ASP* 3.7 1.2 - - - +
152B ALA* 2.8 31.8 + - + +
167B PHE* 4.4 6.5 - - + -
171B PHE* 3.5 47.7 - - + -
454B PHE* 3.6 26.0 - - + -
457B LEU* 5.6 9.0 - - + -
458B VAL* 4.5 4.7 - - + -
462B LEU* 3.7 30.1 - - + -
496B TYR* 4.3 11.4 - - + -
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Residues in contact with LEU 149 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B HIS* 2.9 55.4 + - + +
146B ALA* 5.2 0.2 - - - -
148B LEU* 1.3 82.4 - - + +
150B GLY* 1.3 53.9 + - - +
152B ALA* 4.4 3.4 - - - -
153B THR* 2.8 44.4 + - - +
457B LEU* 5.0 4.5 - - + -
461B HIS* 4.5 19.1 - - + -
462B LEU* 4.4 21.8 - - + -
498B ILE* 4.8 19.5 - - + -
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Residues in contact with GLY 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B ALA 2.9 21.6 + - - -
149B LEU* 1.3 75.5 - - - +
151B ASP* 1.3 63.7 + - - +
153B THR* 3.9 3.2 - - - -
154B GLU* 3.0 25.6 + - - +
197B ARG* 3.3 19.2 + - - -
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Residues in contact with ASP 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B VAL 2.9 21.4 + - - +
148B LEU 3.7 3.1 - - - +
150B GLY* 1.3 72.2 - - - +
152B ALA* 1.3 57.4 + - - +
154B GLU* 3.5 3.1 + - - +
155B ALA* 3.0 29.5 + - - +
171B PHE* 3.8 15.5 - - + -
174B ARG* 2.8 37.7 + - - -
197B ARG* 2.9 31.4 + - - +
496B TYR* 5.0 4.3 - - - +
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Residues in contact with ALA 152 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B LEU* 2.8 24.7 + - + +
149B LEU* 4.0 2.9 - - - +
151B ASP* 1.3 70.3 - - - +
153B THR* 1.3 65.9 + - - +
155B ALA* 3.0 12.9 + - - +
156B GLY 3.0 22.7 + - - +
160B HIS* 3.8 3.8 - - + -
462B LEU* 5.3 1.8 - - + -
496B TYR* 4.2 25.4 - - + -
498B ILE* 3.6 27.1 - - + -
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Residues in contact with THR 153 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B LEU* 2.8 30.2 + - - +
150B GLY* 3.9 4.5 - - - -
152B ALA* 1.3 75.1 - - - +
154B GLU* 1.3 63.4 + - - +
156B GLY* 3.2 14.5 + - - +
498B ILE* 3.7 16.1 - - - +
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Residues in contact with GLU 154 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B GLY 3.0 18.1 + - - +
151B ASP 3.8 3.4 - - - +
153B THR* 1.3 77.1 - - - +
155B ALA* 1.3 60.1 + - - +
156B GLY 3.5 0.3 + - - -
197B ARG* 2.5 33.1 + - - +
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Residues in contact with ALA 155 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B ASP 3.0 17.2 + - - +
152B ALA* 3.0 3.4 + - - +
154B GLU* 1.3 77.2 - - - +
156B GLY* 1.3 56.3 + - - +
160B HIS* 2.9 43.8 + - + +
496B TYR* 5.3 2.5 - - - +
----------------------------------------------------------
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Residues in contact with GLY 156 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B ALA 3.0 16.6 + - - +
153B THR* 3.2 12.2 + - - -
154B GLU 3.3 1.8 + - - -
155B ALA* 1.3 78.3 - - - +
157B SER* 1.3 58.4 + - - -
158B GLY 3.3 6.2 - - - +
160B HIS* 3.0 16.2 - - - -
498B ILE* 4.6 2.4 - - - +
----------------------------------------------------------
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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