Contacts of the helix formed by residues 140 - 163 (chain B) in PDB entry 4HYJ
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 THR 140 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B SER* 3.5 23.2 - - - +
133B ILE* 3.9 5.9 + - - +
136B ALA* 3.5 28.9 - - + -
138B GLY 3.5 4.4 + - - +
139B PHE* 1.3 98.6 - - - +
141B GLN* 1.3 65.9 + - - +
142B LEU* 4.1 3.6 - - - -
143B GLY* 3.1 27.0 + - - -
144B LEU 3.4 6.9 + - - -
202B LEU* 4.7 0.4 - - - +
312B LFA 6.5 0.7 - - - -
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Residues in contact with GLN 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B PHE* 3.9 11.8 - - + -
140B THR* 1.3 69.9 - - - +
142B LEU* 1.3 59.5 + - - +
144B LEU* 2.8 24.9 + - - +
145B TRP* 3.1 54.0 + - + +
312B LFA 3.3 36.3 - - + +
313B LFA 3.1 28.3 - - - +
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Residues in contact with LEU 142 (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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306A LFA 4.1 19.7 - - + -
312A LFA 6.0 5.4 - - + -
128B ILE* 3.7 31.6 - - + +
132B SER* 4.0 22.2 - - - -
140B THR* 3.3 3.0 + - - +
141B GLN* 1.3 77.6 - - - +
143B GLY* 1.3 61.8 + - - +
144B LEU 3.0 0.2 + - - -
145B TRP* 3.2 5.5 + - - -
146B SER* 2.9 39.1 + - - +
312B LFA 4.2 40.6 - - + +
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Residues in contact with GLY 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B GLY* 3.8 13.7 - - - -
132B SER* 4.3 0.8 - - - -
133B ILE* 4.4 6.5 - - - -
140B THR* 3.1 22.4 + - - -
141B GLN 3.1 0.4 - - - -
142B LEU* 1.3 77.9 - - - +
144B LEU* 1.3 55.2 + - - +
146B SER* 4.3 0.2 - - - -
147B TYR* 3.2 13.3 + - - +
198B TYR* 2.7 33.7 + - - -
202B LEU* 4.0 6.0 - - - +
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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
----------------------------------------------------------
139B PHE* 4.2 18.8 - - + -
140B THR 3.4 8.8 + - - +
141B GLN* 2.8 11.4 + - - +
143B GLY* 1.3 76.6 - - - +
145B TRP* 1.3 95.7 + - + +
147B TYR* 3.1 9.1 - - + +
148B LEU* 3.1 39.0 + - + +
202B LEU* 4.2 13.7 - - + +
305B LFA 3.9 50.0 - - + -
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Residues in contact with TRP 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B GLN* 3.1 59.8 + - + +
142B LEU* 4.3 2.5 - - + +
144B LEU* 1.3 101.3 - - + +
146B SER* 1.3 67.6 + - - +
148B LEU* 2.9 29.5 + - + +
149B ILE* 2.9 18.7 + - + +
312B LFA 3.5 34.1 - - + -
313B LFA 3.5 46.3 - - + +
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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
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125B GLY* 3.3 32.5 + - - +
128B ILE* 3.8 18.2 - - - +
129B GLY* 3.3 16.6 + - - -
142B LEU* 2.9 26.2 + - - +
145B TRP* 1.3 77.5 - - - +
147B TYR* 1.3 57.7 + - - +
149B ILE* 3.4 9.6 + - - +
150B GLY* 2.9 25.5 + - - -
312B LFA 5.8 0.9 - - - +
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Residues in contact with TYR 147 (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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125B GLY 4.4 1.3 + - - -
143B GLY 3.2 15.9 + - - +
144B LEU* 3.1 18.5 + - + +
146B SER* 1.3 81.4 + - - +
148B LEU* 1.3 75.5 + - + +
150B GLY* 3.0 3.6 + - - -
151B CYS* 2.9 46.2 + - - -
195B PRO* 2.6 48.3 + - + +
196B ILE* 4.7 0.3 - - - -
198B TYR* 3.2 38.3 + + + -
199B ALA* 3.7 16.9 - - + +
202B LEU* 4.8 3.8 - - + -
301B RET 3.6 17.2 - - + +
305B LFA 5.2 9.6 - - + -
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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
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144B LEU* 3.3 23.8 - - + +
145B TRP* 2.9 28.3 + - + +
147B TYR* 1.3 94.5 - - + +
149B ILE* 1.3 60.5 + - + +
151B CYS* 3.2 10.5 + - + +
152B PHE* 2.9 30.0 + - - +
305B LFA 5.3 5.6 - - + -
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Residues in contact with ILE 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B ILE* 4.3 20.9 - - + +
125B GLY* 5.7 3.1 - - - -
145B TRP* 2.9 21.1 + - + +
146B SER* 3.6 10.1 - - - +
148B LEU* 1.3 75.9 - - + +
150B GLY* 1.3 62.6 + - - +
152B PHE* 3.0 12.0 + - + +
153B ALA* 3.0 20.8 + - - +
312B LFA 6.4 1.8 - - + -
313B LFA 5.4 11.4 - - + -
315B LFA 5.1 7.0 - - + +
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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
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121B ILE 4.7 2.9 - - - -
122B MET* 3.5 30.1 - - - +
125B GLY* 4.9 1.1 - - - -
146B SER 2.9 14.5 + - - -
147B TYR 3.0 4.9 + - - -
149B ILE* 1.3 76.6 - - - +
151B CYS* 1.3 61.1 + - - +
153B ALA* 3.1 3.3 + - - +
154B TRP 3.0 17.8 + - - -
301B RET 3.6 18.2 - - - -
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Residues in contact with CYS 151 (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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147B TYR* 2.9 48.9 + - - -
148B LEU* 3.2 15.2 + - + +
150B GLY* 1.3 71.8 - - - +
152B PHE* 1.3 66.8 + - - +
154B TRP* 3.2 9.7 + - + +
155B ILE* 2.9 37.7 + - + +
195B PRO* 4.4 4.3 - - - -
301B RET 3.9 20.0 - - - -
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Residues in contact with PHE 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 LEU 2.9 13.6 + - - +
149B ILE* 3.2 14.8 - - + +
151B CYS* 1.3 76.8 - - - +
153B ALA* 1.3 56.5 + - - +
155B ILE* 3.0 15.7 + - + +
156B TYR* 2.9 30.3 + - + +
315B LFA 4.3 24.5 - - + -
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Residues in contact with ALA 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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118B ALA* 3.4 29.5 - - - +
121B ILE* 4.0 11.9 - - + -
122B MET* 3.8 11.0 - - + +
149B ILE 3.0 11.4 + - - +
150B GLY 3.1 8.0 + - - +
152B PHE* 1.3 76.6 - - - +
154B TRP* 1.3 61.9 + - - +
156B TYR* 3.3 9.2 + - - +
157B ILE* 3.0 28.8 + - - +
315B LFA 4.4 11.2 - - + +
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Residues in contact with TRP 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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122B MET* 3.5 28.8 - - - -
150B GLY 3.0 9.5 + - - +
151B CYS* 3.4 19.7 - - + +
153B ALA* 1.3 76.4 - - - +
155B ILE* 1.3 68.5 + - + +
157B ILE* 3.1 10.1 + - + +
158B ILE* 2.9 40.2 + - + +
187B ILE* 3.0 22.0 + - + -
188B LEU* 3.6 15.9 - - + -
191B TRP* 3.8 21.1 - + + +
192B ALA* 3.5 42.0 - - + -
195B PRO* 4.1 11.4 - - + -
301B RET 3.7 20.2 - - + -
308B LFA 6.4 0.4 - - + -
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Residues in contact with ILE 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 CYS* 2.9 27.2 + - + +
152B PHE* 3.0 15.5 + - + +
154B TRP* 1.3 89.0 - - + +
156B TYR* 1.3 58.4 + - - +
158B ILE* 3.2 10.0 + - + +
159B TYR* 2.9 28.8 + - + +
308B LFA 4.3 30.8 - - + +
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Residues in contact with TYR 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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114B LYS* 3.5 34.9 - - + +
118B ALA* 3.6 23.8 - - + -
152B PHE* 2.9 17.4 + - + +
153B ALA* 3.5 8.7 - - - +
155B ILE* 1.3 77.6 - - - +
157B ILE* 1.3 60.4 + - - +
159B TYR* 3.2 19.4 + + + +
160B LEU* 3.0 53.9 + - + +
315B LFA 3.6 43.7 - - + +
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Residues in contact with ILE 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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94B LEU* 3.7 40.2 - - + -
115B LEU* 4.0 15.3 - - + +
118B ALA* 3.6 14.6 - - + +
119B ASP* 3.6 34.3 - - - +
122B MET* 4.7 6.5 - - + -
153B ALA 3.0 19.4 + - - +
154B TRP* 3.1 15.0 + - + +
156B TYR* 1.3 77.8 - - + +
158B ILE* 1.3 63.5 + - - +
160B LEU* 3.1 10.2 + - + +
161B LEU* 2.9 23.6 + - + +
187B ILE* 4.1 13.9 - - + -
191B TRP* 5.3 1.8 - - + -
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Residues in contact with ILE 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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154B TRP* 2.9 50.5 + - + +
155B ILE* 3.5 8.3 - - - +
157B ILE* 1.3 75.9 - - - +
159B TYR* 1.3 58.8 + - - +
161B LEU* 3.1 7.6 + - - +
162B PHE* 2.9 54.8 + - + -
187B ILE* 3.9 22.0 - - + +
188B LEU* 3.8 23.3 - - + -
308B LFA 3.8 33.4 - - + -
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Residues in contact with TYR 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 ILE* 2.9 15.6 + - + +
156B TYR* 3.2 25.4 - + - +
157B ILE 3.1 0.2 - - - -
158B ILE* 1.3 76.7 - - - +
160B LEU* 1.3 71.8 + - + +
162B PHE 3.2 1.2 + - - -
163B THR* 2.6 66.6 + - + +
308B LFA 4.3 25.5 - - + +
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Residues in contact with LEU 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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111B LEU* 4.4 13.7 - - + -
114B LYS* 3.8 31.0 - - + +
115B LEU* 4.1 20.9 - - + -
156B TYR* 3.0 57.1 + - + +
157B ILE* 3.5 7.0 - - - +
159B TYR* 1.3 89.3 - - + +
161B LEU* 1.3 62.4 + - - +
163B THR* 3.7 3.6 - - - +
164B ASN* 3.0 33.5 + - + +
165B VAL* 3.1 10.2 + - - +
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Residues in contact with LEU 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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94B LEU* 4.5 0.7 - - + -
97B PHE* 3.7 41.3 - - + -
115B LEU* 4.4 15.0 - - + -
157B ILE* 2.9 21.5 + - + +
158B ILE* 3.1 8.9 + - - +
160B LEU* 1.3 76.4 - - - +
162B PHE* 1.3 61.4 + - + +
163B THR 3.3 0.2 - - - -
165B VAL* 3.3 25.1 - - + +
166B THR* 3.0 26.3 + - - -
184B ARG* 3.6 21.6 - - + +
187B ILE* 3.6 38.4 - - + -
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Residues in contact with PHE 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B ILE* 2.9 46.3 + - + +
159B TYR 3.2 0.9 + - - +
161B LEU* 1.3 81.1 - - + +
163B THR* 1.3 63.5 + - - +
166B THR* 3.3 19.6 + - - +
184B ARG* 3.6 51.4 - - + -
185B LEU* 4.5 8.3 - - + -
188B LEU* 3.8 31.4 - - + -
307B LFA 3.9 29.8 - - + +
308B LFA 3.7 34.4 - - + +
310B LFA 4.1 11.7 - - + -
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Residues in contact with THR 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B TYR* 2.6 58.5 + - + +
160B LEU* 3.6 4.3 + - - +
161B LEU 3.3 0.6 - - - -
162B PHE* 1.3 84.7 - - - +
164B ASN* 1.3 72.5 + - - +
165B VAL 3.3 0.7 - - - -
166B THR* 3.4 1.6 + - - -
167B LYS* 2.9 26.7 + - - +
308B LFA 4.0 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) + - + + + + + -
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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