Contacts of the helix formed by residues 122 - 149 (chain B) in PDB entry 2HKU
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 122 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B GLU* 4.7 14.0 - - - +
118B MSE 3.2 26.9 + - - +
119B THR* 3.0 13.3 + - - +
120B GLY* 3.9 17.9 + - - +
121B ARG* 1.3 74.8 - - - +
123B SER* 1.3 55.5 + - - +
124B GLU* 3.2 25.3 + - + +
125B LEU* 2.9 29.8 + - + +
126B ARG* 2.7 31.4 + - - -
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Residues in contact with SER 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B ARG 3.3 7.2 + - - -
122B ARG* 1.3 70.9 - - - +
124B GLU* 1.3 55.8 + - - +
126B ARG* 4.3 9.2 - - - +
127B ASP* 2.7 47.2 + - - -
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Residues in contact with GLU 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B SER* 5.0 5.8 + - - -
63B ARG* 4.0 30.4 + - - +
122B ARG* 3.8 25.0 + - + -
123B SER* 1.3 75.7 - - - +
125B LEU* 1.3 87.2 + - + +
127B ASP* 4.1 5.7 - - - +
128B LEU* 3.4 24.6 + - - +
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Residues in contact with LEU 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B SER* 5.4 0.4 - - - +
62B GLU* 4.2 14.6 - - + -
63B ARG* 4.1 23.8 - - + +
66B VAL* 3.8 27.3 - - + +
118B MSE 4.7 2.0 - - - +
119B THR* 4.0 18.4 - - + +
122B ARG* 2.9 43.9 + - + +
124B GLU* 1.3 103.9 - - + +
126B ARG* 1.3 66.1 + - - +
127B ASP 3.2 1.1 - - - -
128B LEU* 3.1 17.2 + - + +
129B ILE* 3.2 17.7 + - - +
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Residues in contact with ARG 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A THR 4.0 8.5 + - - -
179A ALA 3.3 15.9 + - - +
180A THR 3.9 11.3 + - - -
181A GLY* 3.5 30.5 + - - +
184A PHE* 5.0 5.8 - - + -
119B THR* 4.5 14.6 + - - -
121B ARG* 3.7 61.3 - - - +
122B ARG 2.7 19.6 + - - +
123B SER* 4.1 8.5 - - - +
125B LEU* 1.3 71.9 - - - +
127B ASP* 1.4 62.9 + - - +
129B ILE* 2.9 8.3 + - - -
130B THR* 2.8 48.8 + - + +
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Residues in contact with ASP 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A PHE* 5.6 4.9 - - - -
123B SER* 2.7 38.4 + - - +
124B GLU* 4.1 5.4 - - - +
126B ARG* 1.4 77.4 - - - +
128B LEU* 1.3 63.1 + - + +
130B THR* 3.4 8.3 + - - -
131B ASP* 3.1 35.5 + - - +
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Residues in contact with LEU 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ARG* 3.9 33.2 - - - +
66B VAL* 3.6 30.3 - - + -
67B GLU* 3.7 29.2 - - + +
70B CYS* 3.9 7.4 - - + -
124B GLU 3.4 15.4 + - - +
125B LEU* 3.1 9.4 + - + +
127B ASP* 1.3 79.2 - - + +
129B ILE* 1.3 58.6 + - - +
131B ASP* 3.7 7.8 - - - +
132B THR* 2.7 34.9 + - - -
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Residues in contact with ILE 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A ALA* 4.0 16.6 - - + +
66B VAL* 4.2 13.5 - - + -
70B CYS* 4.3 3.6 - - - -
112B PHE* 3.7 22.8 - - + -
115B ALA* 4.0 13.7 - - + +
116B MSE 3.6 42.0 - - + +
119B THR* 3.9 16.6 - - + -
125B LEU 3.5 12.8 - - - +
126B ARG* 2.9 9.7 + - - +
128B LEU* 1.3 76.0 - - - +
130B THR* 1.3 60.6 + - + +
132B THR* 3.3 3.2 + - - -
133B LEU* 2.9 35.3 + - + +
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Residues in contact with THR 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A ALA 4.5 1.3 - - - +
180A THR* 4.1 16.6 - - + -
184A PHE* 4.0 48.0 - - + +
301A EDO 5.1 1.0 + - - -
126B ARG* 2.8 37.3 + - + +
127B ASP* 3.4 14.2 + - - -
129B ILE* 1.3 77.5 - - + +
131B ASP* 1.3 66.7 + - - +
133B LEU* 3.5 7.0 + - - +
134B ARG* 3.0 32.4 + - - +
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Residues in contact with ASP 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B ASP* 3.1 30.0 + - - +
128B LEU* 3.7 9.1 - - + +
130B THR* 1.3 78.0 + - - +
132B THR* 1.3 56.8 + - - +
134B ARG* 3.3 32.1 + - - +
135B THR* 3.0 32.0 + - - -
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Residues in contact with THR 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B CYS* 3.1 25.9 - - - +
73B VAL* 3.5 31.9 - - + -
74B LEU* 3.9 18.0 - - + +
112B PHE* 3.6 13.7 - - + -
128B LEU 2.7 22.8 + - - -
129B ILE 3.5 4.5 - - - -
131B ASP* 1.3 74.2 - - - +
133B LEU* 1.3 66.0 + - - +
135B THR* 3.2 7.6 + - - -
136B LEU* 3.1 22.1 + - + +
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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
----------------------------------------------------------
176A GLN* 3.5 31.0 - - + +
179A ALA* 5.3 0.2 - - + -
180A THR* 3.6 31.0 - - + -
186A TYR* 5.1 1.1 - - + -
301A EDO 3.8 12.8 - - - +
112B PHE* 3.6 28.0 - - + -
116B MSE 3.9 17.7 - - - -
129B ILE* 2.9 27.8 + - + +
130B THR* 3.9 4.3 - - - +
132B THR* 1.3 73.9 - - - +
134B ARG* 1.3 62.8 + - - +
136B LEU* 3.4 5.5 + - + +
137B HIS* 2.8 34.3 + - + +
171B PHE* 4.0 8.7 - - + -
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Residues in contact with ARG 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A PHE* 3.6 36.8 - - + +
301A EDO 3.7 22.4 + - - +
130B THR* 3.0 20.7 + - - +
131B ASP* 3.3 35.3 + - - +
132B THR 3.2 0.2 - - - -
133B LEU* 1.3 75.0 - - - +
135B THR* 1.3 64.4 + - - +
137B HIS* 3.3 1.2 + - - +
138B SER* 2.9 38.3 + - - +
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Residues in contact with THR 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B LEU* 3.6 28.8 - - + +
131B ASP 3.0 14.6 + - - -
132B THR* 3.2 9.7 + - - -
134B ARG* 1.3 76.9 - - - +
136B LEU* 1.3 60.6 + - - +
138B SER* 4.0 4.0 - - - -
139B SER* 2.8 38.0 + - - +
214B PG4 4.3 13.9 - - - +
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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
----------------------------------------------------------
73B VAL* 4.1 37.7 - - + +
74B LEU* 3.9 19.7 - - + -
77B GLY* 4.8 0.4 - - - -
112B PHE* 4.2 7.9 - - + -
132B THR 3.1 16.7 + - - +
133B LEU* 3.7 10.5 - - + +
134B ARG 3.4 0.2 - - - -
135B THR* 1.3 77.3 - - - +
137B HIS* 1.3 61.1 + - - +
139B SER* 3.8 5.1 - - - -
140B GLY 2.9 21.5 + - - -
167B TRP* 3.1 39.3 + - + +
171B PHE* 4.1 25.6 - - + -
214B PG4 3.9 23.2 - - - +
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Residues in contact with HIS 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A GLN* 3.3 23.1 - - - -
186A TYR* 2.6 31.4 + + - -
301A EDO 3.6 24.0 - - - +
133B LEU* 2.8 35.0 + - + +
134B ARG 3.9 2.0 - - - +
136B LEU* 1.3 79.6 - - + +
138B SER* 1.3 61.5 + - - +
141B GLU* 2.9 24.4 + - - +
160B ASP 5.1 0.2 - - - -
163B SER* 2.7 28.6 + - - +
164B LYS* 3.7 32.1 - - + -
167B TRP* 3.8 17.5 - + + +
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Residues in contact with SER 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B ARG* 2.9 29.3 + - - +
135B THR* 4.0 3.4 - - - -
137B HIS* 1.3 75.0 - - - +
139B SER* 1.3 63.5 + - - +
141B GLU* 3.3 14.8 + - - +
142B VAL* 3.1 28.9 + - - +
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Residues in contact with SER 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B GLU* 4.6 6.5 - - - +
135B THR* 2.8 30.0 + - - +
136B LEU 3.9 0.4 - - - -
138B SER* 1.3 78.3 - - - +
140B GLY* 1.3 51.3 + - - +
142B VAL* 3.5 8.6 + - - +
143B ALA* 2.8 34.8 + - - +
214B PG4 3.6 37.0 - - - +
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Residues in contact with GLY 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B LEU 2.9 17.4 + - - -
138B SER 3.2 0.6 - - - -
139B SER* 1.3 73.1 - - - +
141B GLU* 1.3 64.3 + - - +
143B ALA 3.9 0.2 - - - -
144B LEU* 2.9 29.1 + - - +
163B SER* 3.7 13.9 - - - -
167B TRP* 4.4 0.4 - - - -
214B PG4 3.2 29.9 + - - -
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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
----------------------------------------------------------
301A EDO 5.4 4.3 - - - -
137B HIS* 2.9 25.3 + - - +
138B SER* 3.3 15.6 + - - +
140B GLY* 1.3 75.5 - - - +
142B VAL* 1.3 67.0 + - + +
144B LEU* 3.5 2.1 - - - +
145B ILE* 3.1 28.1 + - - +
159B ILE* 3.6 43.0 - - + +
160B ASP* 3.5 27.4 - - - +
163B SER* 3.6 6.0 + - - -
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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
----------------------------------------------------------
138B SER* 3.1 14.6 + - - +
139B SER* 3.7 10.8 - - - +
141B GLU* 1.3 82.0 - - + +
143B ALA* 1.3 58.5 + - - +
145B ILE* 4.1 3.4 - - - +
146B ARG* 3.0 69.3 + - - +
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Residues in contact with ALA 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B GLU* 4.1 10.1 - - - +
93B TYR* 3.4 23.1 - - - +
139B SER 2.8 20.9 + - - +
142B VAL* 1.3 71.5 - - - +
144B LEU* 1.3 61.4 + - - +
146B ARG* 4.0 5.1 - - - +
147B THR* 2.8 36.3 + - - -
214B PG4 3.8 24.5 - - - -
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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
----------------------------------------------------------
93B TYR* 6.0 0.9 - - - -
140B GLY 2.9 20.3 + - - +
141B GLU 3.5 0.2 - - - +
142B VAL 3.3 0.2 - - - -
143B ALA* 1.3 79.8 - - - +
145B ILE* 1.3 64.5 + - - +
147B THR* 3.4 3.9 + - - -
148B LEU* 3.2 36.3 + - + +
155B LEU* 3.9 27.4 - - + -
159B ILE* 3.3 27.4 - - + +
162B GLU* 3.9 9.9 - - + +
163B SER* 3.8 26.9 - - - +
166B PHE* 5.5 0.4 - - + -
199B LEU* 4.0 15.5 - - + -
201B ILE* 6.1 1.1 - - + -
214B PG4 3.6 19.7 - - - +
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Residues in contact with ILE 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B GLU 3.1 15.6 + - - +
142B VAL* 4.2 3.8 - - - +
144B LEU* 1.3 79.5 - - - +
146B ARG* 1.3 60.2 + - + +
148B LEU* 3.4 7.3 + - + +
149B MSE 3.1 43.6 + - + +
155B LEU* 4.3 13.0 - - + +
159B ILE* 3.7 30.7 - - + -
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Residues in contact with ARG 146 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B VAL* 3.0 46.2 + - + +
143B ALA* 4.0 4.7 - - - +
145B ILE* 1.3 76.1 - - + +
147B THR* 1.3 66.4 + - - +
149B MSE 3.6 31.2 - - + +
210B ILE* 5.4 0.3 - - - +
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Residues in contact with THR 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B VAL* 4.0 22.1 - - + +
93B TYR* 3.3 44.3 - - + -
143B ALA* 2.8 25.6 + - - -
144B LEU* 3.7 5.8 - - - -
146B ARG* 1.3 75.9 - - - +
148B LEU* 1.3 61.5 + - + +
149B MSE 3.3 1.2 + - - -
150B ARG* 4.8 2.8 + - - +
151B THR* 4.4 2.6 - - - +
210B ILE* 3.3 43.3 - - + +
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Residues in contact with LEU 148 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B VAL* 4.1 31.4 - - + -
144B LEU* 3.2 26.5 + - + +
145B ILE* 3.8 8.3 - - + +
147B THR* 1.3 75.7 - - + +
149B MSE 1.3 65.4 + - - +
150B ARG 3.4 1.6 - - - -
151B THR* 2.8 29.2 + - - +
152B GLY 3.7 2.4 + - - -
153B TRP* 4.0 35.9 - - + +
155B LEU* 3.7 37.0 - - + -
201B ILE* 5.2 4.5 - - + -
205B VAL* 4.1 8.5 - - + -
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Residues in contact with MSE 149 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B ILE* 3.1 34.4 + - + +
146B ARG* 3.6 29.8 - - + +
147B THR 3.3 2.0 - - - -
148B LEU* 1.3 77.3 - - - +
150B ARG* 1.3 67.3 + - - +
151B THR 3.2 0.3 + - - -
152B GLY* 3.6 7.3 + - - -
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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