Contacts of the helix formed by residues 140 - 161 (chain B) in PDB entry 1YXU
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 GLN 140 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B ALA 3.7 3.2 + - - +
139B LEU* 1.3 73.4 - - - +
141B GLU* 1.3 66.1 + - - +
142B GLU* 3.2 7.3 - - + +
143B LEU* 3.0 9.7 + - + +
144B ALA* 3.0 16.1 + - - +
303B HIS* 3.5 32.3 + - + +
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Residues in contact with GLU 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B LEU 3.4 2.2 + - - +
140B GLN* 1.3 71.9 - - - +
142B GLU* 1.3 57.1 + - - +
144B ALA* 4.3 3.8 - - - -
145B ARG* 2.8 37.4 + - - +
236B VAL* 4.9 7.6 - - + -
258B ARG* 4.5 5.6 + - - +
259B VAL* 3.4 13.1 - - - +
260B SER* 2.8 44.8 + - - -
263B CYS* 3.8 7.5 - - - +
289B TRP* 2.7 41.1 + - + +
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Residues in contact with GLU 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B GLN* 3.1 5.1 + - + +
141B GLU* 1.3 78.8 - - - +
143B LEU* 1.3 61.6 + - - +
145B ARG* 3.5 22.5 + - - +
146B SER* 3.2 21.1 + - - -
294B LEU* 3.4 39.5 + - + +
302B ILE* 4.1 10.0 - - - +
303B HIS* 2.6 32.7 + - + +
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Residues in contact with LEU 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B PHE* 4.0 26.9 - - + -
136B ARG* 4.9 3.8 - - - +
139B LEU* 4.2 20.6 - - + -
140B GLN* 3.0 12.2 + - + +
142B GLU* 1.3 77.6 - - - +
144B ALA* 1.3 60.5 + - - +
146B SER* 3.2 5.4 + - - -
147B PHE* 2.9 47.6 + - + +
299B THR* 3.4 28.3 - - + -
303B HIS* 3.6 43.4 + - + +
304B LEU* 4.7 2.2 - - + -
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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
----------------------------------------------------------
139B LEU* 4.2 9.8 - - + +
140B GLN 3.0 14.6 + - - +
141B GLU 3.9 3.1 - - - +
143B LEU* 1.3 77.0 - - - +
145B ARG* 1.3 56.6 + - - +
147B PHE* 4.4 1.3 - - - -
148B PHE* 2.9 31.9 + - - +
232B LEU* 4.6 0.7 - - + -
235B MET* 3.7 26.0 - - + +
236B VAL* 3.8 27.8 - - + -
289B TRP* 3.8 6.5 - - + -
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Residues in contact with ARG 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B GLU* 2.8 21.5 + - - +
142B GLU* 3.7 31.7 - - - +
143B LEU 3.2 0.2 - - - -
144B ALA* 1.3 75.5 - - - +
146B SER* 1.3 66.5 + - - +
149B TRP* 3.0 26.2 + - - +
289B TRP* 2.7 68.1 + - + +
290B MET* 3.5 16.2 - - + +
291B GLN 3.4 22.6 + - - -
292B ASP* 4.3 5.2 + - - +
293B VAL* 4.0 22.4 - - + +
294B LEU* 5.3 0.4 - - - +
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Residues in contact with SER 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B GLU 3.2 12.7 + - - -
143B LEU 3.2 6.7 + - - -
145B ARG* 1.3 78.9 - - - +
147B PHE* 1.3 64.1 + - - +
149B TRP* 3.3 3.3 + - - +
150B GLN* 3.1 35.3 + - - +
293B VAL* 3.7 13.8 - - - +
294B LEU* 3.8 13.6 + - - +
299B THR* 2.7 40.5 + - - +
254C PHE* 5.6 0.5 - - - -
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Residues in contact with PHE 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B LEU* 3.9 15.5 - - + -
132B PHE* 4.2 4.9 - + - -
139B LEU* 3.8 23.6 - - + -
143B LEU* 2.9 41.2 + - + +
146B SER* 1.3 81.2 - - - +
148B PHE* 1.3 63.3 + - - +
150B GLN* 3.0 17.6 + - - +
151B VAL* 3.0 15.6 + - - +
175B ILE* 3.7 38.1 - - + -
180B GLY 4.8 2.9 - - - -
182B LEU* 3.5 32.0 - - + +
235B MET* 3.6 18.6 - - + -
299B THR* 4.2 8.5 - - + -
304B LEU* 4.4 13.9 - - + -
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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
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144B ALA 2.9 24.8 + - - +
145B ARG* 4.1 3.6 - - - +
147B PHE* 1.3 72.3 - - - +
149B TRP* 1.3 62.3 + - - +
151B VAL* 3.2 5.1 + - + +
152B LEU* 3.1 51.9 + - + +
228B LEU* 3.4 45.1 - - + -
231B LEU* 4.8 7.0 - - + -
232B LEU* 3.6 46.0 - - + -
235B MET* 4.0 10.0 - - - +
266B LEU* 4.3 2.9 - - + -
270B CYS* 4.9 6.7 - - - -
284B ILE* 3.9 18.6 - - + -
289B TRP* 4.3 1.6 - + + -
290B MET* 3.5 22.9 - - + -
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Residues in contact with TRP 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B ARG 3.0 20.1 + - - +
146B SER 3.5 3.6 - - - +
148B PHE* 1.3 75.9 - - - +
150B GLN* 1.3 62.3 + - - +
152B LEU* 3.2 8.2 + - - +
153B GLU* 3.1 31.0 + - + +
285B GLN* 3.4 56.5 + - + -
290B MET* 3.9 38.7 - - + +
291B GLN* 5.2 2.9 - - - -
293B VAL* 3.8 12.3 - - + +
254C PHE* 3.6 27.1 - + - -
255C PHE 2.8 19.3 + - - -
256C ARG 3.6 13.2 - - - -
257C GLN* 3.4 24.2 - - - -
258C ARG* 3.5 19.5 - - - -
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Residues in contact with GLN 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B PHE* 5.1 1.4 - - - -
102B GLY* 5.6 0.3 - - - -
146B SER* 3.1 33.1 + - - +
147B PHE* 3.0 10.3 + - - +
149B TRP* 1.3 73.9 - - - +
151B VAL* 1.3 65.8 + - - +
153B GLU* 3.4 9.0 + - - +
154B ALA* 3.1 23.0 + - - +
180B GLY 2.7 24.8 + - - -
181B GLU* 3.3 7.1 - - - +
182B LEU* 2.8 47.8 + - + +
296B PRO* 3.7 19.8 - - - +
254C PHE* 3.9 18.0 - - + -
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Residues in contact with VAL 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B PHE 3.0 15.0 + - - +
148B PHE* 3.2 8.9 + - + +
150B GLN* 1.3 76.8 - - - +
152B LEU* 1.3 56.6 + - - +
154B ALA* 3.3 6.6 + - + +
155B VAL* 2.9 36.6 + - + +
168B ILE* 4.4 5.8 - - + -
173B ILE* 3.9 26.9 - - + -
182B LEU* 4.2 16.8 - - + -
184B LEU* 5.5 3.8 - - + -
228B LEU* 3.8 25.4 - - + -
231B LEU* 3.8 17.7 - - + -
235B MET* 4.7 2.5 - - + -
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Residues in contact with LEU 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B PHE* 3.1 57.4 + - + +
149B TRP* 3.2 10.7 + - - +
151B VAL* 1.3 77.4 - - - +
153B GLU* 1.3 56.0 + - - +
155B VAL* 3.3 3.9 + - + +
156B ARG* 2.9 36.4 + - - +
228B LEU* 4.1 17.9 - - + -
281B PHE* 3.5 38.4 - - + -
284B ILE* 4.1 22.4 - - + -
285B GLN* 3.8 21.1 - - + +
290B MET* 5.5 0.7 - - - -
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Residues in contact with GLU 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B PHE* 4.0 18.5 - - + -
149B TRP* 3.1 38.6 + - + +
150B GLN* 3.6 10.3 - - - +
152B LEU* 1.3 76.1 - - - +
154B ALA* 1.3 56.6 + - - +
156B ARG* 3.5 19.6 + - - +
157B HIS* 2.9 27.9 + - - +
285B GLN* 3.0 22.1 + - - -
254C PHE* 5.3 4.7 - - + -
255C PHE* 4.5 13.5 - - + +
257C GLN 4.9 1.0 - - - +
259C VAL 5.5 0.2 + - - -
264C GLN* 3.0 34.7 + - - +
268C ARG* 4.9 0.9 + - - -
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Residues in contact with ALA 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B PHE* 3.6 12.7 - - + -
102B GLY* 3.3 32.3 - - - +
103B VAL* 3.8 4.2 - - + +
150B GLN 3.1 13.8 + - - +
151B VAL* 3.7 7.0 - - - +
153B GLU* 1.3 78.2 - - - +
155B VAL* 1.3 59.7 + - - +
157B HIS* 3.4 2.6 + - - +
158B CYS* 3.1 31.8 + - - -
182B LEU 5.5 0.7 - - - +
184B LEU* 4.5 10.5 - - + +
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Residues in contact with VAL 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B VAL* 2.9 32.7 + - + +
152B LEU* 3.8 5.6 - - - +
154B ALA* 1.3 73.7 - - - +
156B ARG* 1.3 61.1 + - - +
158B CYS* 3.2 9.0 + - + +
159B HIS* 3.0 39.9 + - + +
165B HIS* 5.9 1.1 - - + -
168B ILE* 3.7 34.8 - - + -
184B LEU* 4.3 10.5 - - + -
224B ALA* 5.0 0.4 - - + -
228B LEU* 4.7 6.5 - - + -
281B PHE* 3.8 30.3 - - + -
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Residues in contact with ARG 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B LEU* 2.9 19.6 + - + +
153B GLU* 3.5 14.6 + - - +
155B VAL* 1.3 75.9 - - - +
157B HIS* 1.3 59.7 + - - +
159B HIS* 3.8 5.6 - - - +
160B ASN* 2.9 32.7 + - - +
281B PHE* 4.0 35.6 - - + +
285B GLN* 3.0 31.0 + - - -
258C ARG* 3.8 19.4 - - - +
259C VAL 2.8 32.5 + - - +
260C SER* 3.5 2.6 - - - +
261C SER* 3.0 38.4 + - - +
264C GLN* 3.2 16.9 - - - +
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Residues in contact with HIS 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B VAL* 3.1 36.0 - - + +
98B SER* 3.6 21.1 + - - -
100B PHE* 3.6 35.4 - + + -
103B VAL* 3.9 13.7 - - + +
153B GLU 2.9 18.4 + - - +
154B ALA 3.5 5.2 - - - +
155B VAL 3.2 0.2 - - - -
156B ARG* 1.3 77.1 - - - +
158B CYS* 1.3 64.0 + - - +
160B ASN* 3.3 20.8 + - - +
161B CYS* 3.1 36.9 + - - -
268C ARG* 6.2 1.3 - - - -
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Residues in contact with CYS 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B VAL* 4.0 15.0 - - + -
103B VAL* 3.9 12.6 - - - -
154B ALA 3.1 18.4 + - - -
155B VAL* 3.2 10.1 + - - +
157B HIS* 1.3 75.3 - - - +
159B HIS* 1.3 58.4 + - + +
161B CYS* 2.9 19.1 + - - +
162B GLY 3.1 0.3 + - - -
163B VAL* 3.1 31.2 + - + +
165B HIS* 5.3 5.2 - - + +
184B LEU* 4.2 8.1 - - - -
187B PHE* 3.5 38.1 - - - -
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Residues in contact with HIS 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B VAL* 3.0 26.9 + - + +
156B ARG* 4.1 3.8 - - - +
158B CYS* 1.3 75.6 - - + +
160B ASN* 1.3 62.1 + - - +
162B GLY* 3.0 10.7 + - - -
163B VAL 3.1 21.5 - - - -
164B LEU* 3.3 31.9 - - + +
165B HIS 4.9 2.0 + - - -
168B ILE* 6.0 0.6 - - - +
193B LEU* 3.4 29.4 - - + +
221B ARG* 4.2 16.0 - - + +
224B ALA* 4.0 10.4 - - + +
281B PHE* 3.1 42.9 - + + -
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Residues in contact with ASN 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B ARG 2.9 18.3 + - - +
157B HIS* 3.5 30.3 + - - +
159B HIS* 1.3 75.6 - - - +
161B CYS* 1.3 61.2 + - - +
261C SER* 4.1 26.5 - - - +
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Residues in contact with CYS 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B LYS* 3.1 58.6 + - - +
96B VAL* 4.1 8.1 - - + -
98B SER* 6.2 0.9 - - - -
157B HIS* 3.1 43.0 + - - +
158B CYS 2.9 10.7 + - - +
160B ASN* 1.3 81.5 - - - +
162B GLY* 1.3 55.3 + - - +
163B VAL* 4.6 0.7 - - + -
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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
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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) + - + + + + + -
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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