Contacts of the helix formed by residues 153 - 176 (chain B) in PDB entry 3RKR
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 GLY 153 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B TRP* 4.0 8.5 - - - -
96B PHE* 3.9 21.5 - - - -
150B VAL* 2.9 15.8 + - - +
151B ALA 3.1 0.6 - - - -
152B ASP* 1.3 78.4 - - - +
154B ALA* 1.3 52.6 + - - +
155B ALA 3.4 2.0 - - - -
156B TYR* 3.3 5.3 + - - +
157B THR* 2.8 40.0 + - - -
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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
----------------------------------------------------------
95B TRP* 6.0 2.0 - - - -
100B LEU* 3.9 26.2 - - + -
152B ASP 3.8 1.2 - - - -
153B GLY* 1.3 76.6 - - - +
155B ALA* 1.3 58.9 + - - +
157B THR* 3.2 3.3 + - - -
158B ALA* 2.9 28.9 + - - +
166C LEU* 3.7 19.1 - - + +
169C SER* 3.5 26.7 - - - -
170C ALA 4.3 1.3 - - - +
173C GLU* 3.8 13.2 + - - +
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Residues in contact with ALA 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B TRP* 5.9 1.7 - - + -
100B LEU* 4.4 2.3 - - + +
103B MET* 3.5 39.0 - - + -
108B TRP* 3.7 21.8 - - + -
111B LEU* 3.6 14.8 - - + +
112B ILE* 4.5 2.6 - - + +
154B ALA* 1.3 78.3 - - - +
156B TYR* 1.3 57.4 + - - +
158B ALA* 3.2 3.0 + - - +
159B SER* 2.9 24.9 + - - -
166C LEU* 4.0 10.0 - - - +
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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
----------------------------------------------------------
92B GLY 6.1 0.2 - - - -
93B VAL 3.4 27.4 - - - -
94B GLY* 3.9 10.5 - - - -
95B TRP 4.3 5.1 + - - +
96B PHE* 3.8 32.1 - + + -
111B LEU* 3.9 13.0 - - + +
115B ASN* 3.8 5.2 - - - -
143B SER* 2.3 37.8 + - - -
144B LEU* 3.8 20.9 - - + -
150B VAL* 5.2 3.8 - - + -
153B GLY 3.5 12.1 - - - +
155B ALA* 1.3 79.3 - - - +
157B THR* 1.3 63.8 + - - +
159B SER* 2.7 22.1 + - - -
160B LYS* 3.0 31.5 + - + +
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Residues in contact with THR 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B LEU* 3.9 11.4 - - + -
149B PRO* 4.0 10.1 - - + -
150B VAL* 3.3 27.9 + - - +
153B GLY 2.8 26.3 + - - -
154B ALA 3.6 2.0 - - - -
156B TYR* 1.3 71.3 - - - +
158B ALA* 1.3 64.6 + - - +
160B LYS* 3.1 2.4 + - - -
161B TRP* 2.9 61.5 + - + +
165C GLY* 3.7 15.9 - - - +
169C SER* 3.4 11.6 + - - +
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Residues in contact with ALA 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B TRP* 5.0 2.9 - - + -
112B ILE* 5.3 1.3 - - + -
116B LEU* 5.1 1.7 - - - +
154B ALA 2.9 13.7 + - - +
155B ALA* 3.2 8.9 + - - +
157B THR* 1.3 76.2 - - - +
159B SER* 1.3 56.9 + - - +
162B GLY* 2.8 29.6 + - - -
116C LEU* 4.3 12.7 - - + +
162C GLY* 3.3 34.2 - - - +
165C GLY* 4.5 1.3 - - - -
166C LEU* 3.8 20.1 - - + +
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Residues in contact with SER 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B LEU* 3.6 9.3 - - - +
112B ILE* 4.1 13.2 - - - +
115B ASN* 3.1 43.8 + - - +
116B LEU* 3.9 13.8 - - - +
155B ALA 2.9 13.9 + - - -
156B TYR 2.7 17.7 + - - -
158B ALA* 1.3 77.1 - - - +
160B LYS* 1.3 60.8 + - - +
162B GLY 3.8 0.2 - - - -
163B LEU* 2.9 27.0 + - - +
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Residues in contact with LYS 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B ASN 5.9 0.2 + - - -
91B ALA 5.2 1.8 + - - -
92B GLY* 4.6 10.5 - - - -
115B ASN* 3.8 30.6 + - - +
141B ILE 4.6 10.5 + - - -
142B SER* 4.0 8.9 + - - +
143B SER* 3.8 25.2 - - - +
144B LEU* 3.9 21.8 - - + -
156B TYR* 3.0 49.8 + - + +
157B THR 3.8 2.9 - - - +
159B SER* 1.3 77.6 + - - +
161B TRP* 1.3 67.3 + - - +
162B GLY 3.2 0.9 - - - -
163B LEU* 3.3 11.6 + - + +
164B ASN* 3.0 29.5 + - - +
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Residues in contact with TRP 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B LEU* 4.3 14.1 - - + +
146B GLY* 3.3 47.5 - - - +
147B LYS 3.6 25.1 - - - +
148B ASN 3.7 3.7 + - - -
149B PRO* 3.8 20.0 - - + -
157B THR* 2.9 39.7 + - + +
158B ALA 4.2 1.1 - - - +
160B LYS* 1.3 73.7 - - - +
162B GLY* 1.3 62.8 + - - +
164B ASN* 3.3 10.6 + - - +
165B GLY 3.1 17.7 + - - -
242B SO4 4.5 1.8 + - - -
146C GLY* 6.5 1.1 - - - -
161C TRP* 3.5 33.8 - - + +
162C GLY* 4.5 0.4 - - - -
164C ASN* 3.9 15.0 - - + -
165C GLY* 3.3 31.4 - - - -
168C THR* 4.3 8.3 - - + -
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Residues in contact with GLY 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B LEU* 3.6 13.2 - - - -
158B ALA 2.8 18.8 + - - -
159B SER 3.9 1.1 - - - -
161B TRP* 1.3 78.6 - - - +
163B LEU* 1.3 50.7 + - - +
165B GLY* 3.0 2.1 + - - -
166B LEU* 2.8 35.7 + - - +
158C ALA* 3.4 28.4 - - - +
162C GLY* 4.0 1.4 - - - +
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Residues in contact with LEU 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B ASN* 5.6 2.9 - - + +
115B ASN 4.3 9.2 - - - +
116B LEU* 3.5 6.9 - - + +
119B PRO* 3.8 35.4 - - + -
140B ASN* 4.3 11.9 - - + +
141B ILE 3.9 23.1 - - - +
142B SER* 4.3 16.8 - - - +
159B SER 2.9 20.9 + - - +
160B LYS* 3.3 16.5 + - + +
162B GLY* 1.3 72.8 - - - +
164B ASN* 1.4 64.8 + - - +
166B LEU* 3.2 6.5 + - + +
167B MET* 3.0 41.8 + - + +
183B LEU* 4.8 2.9 - - + -
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Residues in contact with ASN 164 (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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142B SER* 2.9 23.4 + - - -
144B LEU 2.9 22.2 + - - -
145B ALA* 3.6 19.6 + - - +
146B GLY* 3.7 7.1 - - - +
160B LYS 3.0 10.8 + - - +
161B TRP* 3.5 8.7 - - - +
163B LEU* 1.4 76.1 - - - +
165B GLY* 1.3 61.1 + - - +
168B THR* 2.8 34.2 + - + +
183B LEU* 3.4 31.4 - - + +
230B GLU* 5.7 0.6 + - - -
161C TRP* 3.9 13.9 - - + -
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Residues in contact with GLY 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B TRP 3.1 7.7 + - - -
162B GLY 3.0 5.6 + - - -
164B ASN* 1.3 74.0 - - - +
166B LEU* 1.3 64.9 + - - +
168B THR* 3.8 1.8 + - - -
169B SER* 2.8 32.1 + - - -
157C THR* 3.7 13.5 - - - +
158C ALA* 4.4 2.2 - - - -
161C TRP* 3.3 27.9 - - - -
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Residues in contact with LEU 166 (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 27.6 - - + +
120B TYR* 3.9 14.6 - - + +
162B GLY 2.8 20.0 + - - +
163B LEU* 3.5 9.9 - - + +
165B GLY* 1.3 73.2 - - - +
167B MET* 1.3 77.0 + - + +
170B ALA* 2.9 28.1 + - - +
100C LEU* 3.6 27.8 - - + -
108C TRP* 3.7 24.2 - - + -
154C ALA* 3.7 27.6 - - - +
155C ALA* 4.0 0.7 - - - +
158C ALA* 3.8 7.2 - - + +
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Residues in contact with MET 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B ASN* 4.0 3.6 - - - +
119B PRO* 3.5 39.7 - - + +
120B TYR* 4.6 0.9 - - - -
123B LEU* 3.9 28.9 - - + -
138B ILE* 4.7 1.1 - - + -
140B ASN* 3.4 45.3 - - + +
163B LEU* 3.0 25.2 + - + +
166B LEU* 1.3 86.5 - - + +
168B THR* 1.3 61.8 + - - +
170B ALA* 4.2 2.7 - - - -
171B ALA* 2.7 30.0 + - - +
181B VAL* 3.4 12.7 - - + +
182B SER 5.3 0.7 - - - +
183B LEU* 4.4 11.2 - - + -
100C LEU* 5.0 0.7 - - + -
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Residues in contact with THR 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B ASN* 2.8 23.7 + - + +
165B GLY 3.8 1.0 + - - -
167B MET* 1.3 73.2 - - - +
169B SER* 1.3 65.9 + - - +
171B ALA* 3.6 16.9 - - - +
172B GLU* 3.7 6.8 + - - +
183B LEU* 4.1 25.8 - - + -
229B SER* 4.9 12.1 - - - +
230B GLU* 4.8 9.2 - - + +
149C PRO* 3.5 29.0 - - - +
161C TRP* 3.9 10.8 - - + -
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Residues in contact with SER 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B GLY 2.8 24.3 + - - -
168B THR* 1.3 73.9 - - - +
170B ALA* 1.3 65.0 + - - +
172B GLU* 3.0 17.2 + - - +
173B GLU* 3.4 14.3 + - - +
149C PRO* 3.4 8.9 - - - +
150C VAL 3.2 28.3 + - - -
151C ALA* 4.3 1.8 - - - +
154C ALA* 3.5 16.6 - - - -
157C THR* 3.3 22.2 + - - -
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Residues in contact with ALA 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B LEU* 3.8 28.7 - - + -
166B LEU 2.9 17.8 + - - +
167B MET* 3.7 7.6 - - - +
169B SER* 1.3 75.5 - - - +
171B ALA* 1.3 62.8 + - - +
173B GLU* 3.1 20.1 + - - +
174B LEU* 3.0 26.3 + - + +
181B VAL* 4.3 2.9 - - + -
100C LEU* 4.0 14.4 - - + -
154C ALA* 4.2 0.8 - - - +
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Residues in contact with ALA 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B MET 2.7 21.1 + - - +
168B THR* 3.6 12.3 - - - +
169B SER 3.1 0.2 - - - -
170B ALA* 1.3 73.2 - - - +
172B GLU* 1.3 60.8 + - - +
174B LEU* 4.1 0.3 - - - +
175B ARG* 3.2 26.7 + - - +
179B VAL 4.8 0.5 - - - +
181B VAL* 3.6 34.1 - - + +
227B PHE* 4.2 16.1 - - + -
229B SER* 5.1 7.2 - - - +
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Residues in contact with GLU 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B THR 3.7 6.0 + - - +
169B SER* 3.0 11.2 + - - +
171B ALA* 1.3 78.9 - - - +
173B GLU* 1.3 64.1 + - - +
174B LEU 3.5 0.2 + - - -
175B ARG* 2.9 50.7 + - - +
176B GLN* 4.5 3.8 + - - +
149C PRO* 6.2 1.8 - - + -
151C ALA* 3.7 23.3 - - + +
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Residues in contact with GLU 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B SER 3.7 5.5 - - - +
170B ALA* 3.1 24.6 + - - +
172B GLU* 1.3 77.9 - - - +
174B LEU* 1.3 61.9 + - + +
176B GLN* 3.4 32.1 + - - +
177B HIS* 4.1 3.8 - - - -
99C PRO* 3.3 19.5 - - + +
100C LEU* 2.7 34.2 + - - +
101C HIS* 5.3 0.5 + - - -
151C ALA* 4.0 5.2 - - + -
152C ASP* 3.0 43.2 + - - +
154C ALA* 3.6 16.3 + - - +
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Residues in contact with LEU 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B LEU* 3.9 25.4 - - + -
127B ALA* 4.4 6.1 - - + -
131B ILE* 3.8 35.2 - - + -
138B ILE* 4.3 5.6 - - + -
170B ALA* 3.0 14.7 + - + +
171B ALA 4.4 0.2 - - - +
173B GLU* 1.3 79.7 - - + +
175B ARG* 1.3 57.8 + - - +
176B GLN 3.2 2.5 - - - -
177B HIS* 2.8 27.6 + - + +
179B VAL* 3.2 41.2 + - + +
181B VAL* 3.5 26.7 - - + -
101C HIS* 3.8 17.5 - - + +
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Residues in contact with ARG 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B ALA 3.2 16.2 + - - +
172B GLU* 2.9 44.1 + - - +
174B LEU* 1.3 75.7 - - - +
176B GLN* 1.3 57.3 + - - +
178B GLN* 3.0 24.2 + - - +
179B VAL 3.5 9.3 + - - -
180B ARG* 6.2 0.4 - - - -
227B PHE* 3.6 33.2 - - + -
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Residues in contact with GLN 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B GLU 4.5 2.6 + - - +
173B GLU* 3.4 24.6 + - - +
175B ARG* 1.3 79.1 - - - +
177B HIS* 1.3 86.4 + - + +
178B GLN* 3.4 11.0 + - - +
99C PRO* 5.5 8.1 - - - +
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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