Contacts of the helix formed by residues 138 - 167 (chain A) in PDB entry 4NY4
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 138 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A SER 4.1 3.8 - - - +
135A PRO* 2.7 38.8 + - + +
136A THR 3.4 1.4 + - - +
137A PHE* 1.3 80.1 - - - +
139A SER* 1.3 64.0 + - - +
140A GLY* 4.3 4.0 - - - -
141A LYS* 3.4 20.8 + - - +
142A LEU* 3.2 24.0 + - - +
446A ARG* 3.9 4.5 - - - +
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Residues in contact with SER 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A THR* 1.3 72.0 - - - +
140A GLY* 1.3 63.2 + - - +
142A LEU* 3.5 13.0 + - - +
143A LYS* 3.5 20.1 + - - +
347A TYR* 3.6 18.4 + - - -
446A ARG* 3.2 35.2 + - - +
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Residues in contact with GLY 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A THR* 3.3 3.9 - - - -
139A SER* 1.3 81.6 + - - +
141A LYS* 1.4 59.6 + - - +
143A LYS* 3.4 19.6 + - - +
144A GLU* 3.0 21.1 - - - +
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Residues in contact with LYS 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A PRO* 3.3 30.7 - - - +
136A THR* 4.2 13.0 - - - +
138A THR* 3.4 15.8 + - - +
139A SER 3.5 0.4 - - - -
140A GLY* 1.4 72.2 - - - +
142A LEU* 1.4 61.3 + - - +
144A GLU* 3.5 12.5 + - - +
145A MET* 3.4 27.0 + - + +
274A LEU* 3.8 37.2 - - + +
277A ASP* 5.6 1.6 + - - -
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Residues in contact with LEU 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A PHE* 5.6 6.1 - - - +
138A THR 3.2 18.5 + - - +
139A SER* 3.6 9.0 - - - +
140A GLY 3.3 0.4 - - - -
141A LYS* 1.4 74.3 - - - +
143A LYS* 1.4 63.0 + - - +
145A MET* 3.2 25.8 + - + +
146A VAL* 3.2 26.1 + - - +
347A TYR* 3.7 22.7 - - + +
446A ARG* 3.8 30.5 - - + +
447A PHE* 3.9 32.8 - - + +
450A MET* 4.1 19.7 - - + -
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Residues in contact with LYS 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A SER 3.5 15.7 - - - +
140A GLY* 3.4 13.7 - - - +
141A LYS 3.3 0.4 - - - -
142A LEU* 1.4 76.7 - - - +
144A GLU* 1.4 65.4 + - - +
146A VAL* 3.3 18.6 + - - +
147A PRO* 3.5 7.1 - - - +
347A TYR* 3.6 44.3 - - + +
348A ASP* 4.0 21.3 + - - -
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Residues in contact with GLU 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A GLY 3.0 23.3 - - - +
141A LYS* 3.5 12.3 + - - +
142A LEU 3.3 0.4 - - - -
143A LYS* 1.4 80.9 - - - +
145A MET* 1.3 59.8 + - + +
147A PRO* 3.4 12.2 - - - +
148A ILE* 3.5 15.2 - - - +
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Residues in contact with MET 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A THR* 3.8 22.2 - - + +
137A PHE* 5.4 2.0 - - + -
141A LYS* 3.4 18.8 + - + +
142A LEU* 3.2 36.2 + - + +
144A GLU* 1.3 75.8 - - + +
146A VAL* 1.4 64.1 + - - +
147A PRO 3.6 0.2 - - - -
148A ILE* 3.3 24.0 + - + +
149A ILE* 3.4 19.7 + - + +
187A THR* 4.2 22.0 - - + +
271A PHE* 4.3 18.4 - - + -
274A LEU* 5.8 8.5 - - + -
447A PHE* 3.9 26.7 - - + -
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Residues in contact with VAL 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A LEU 3.2 15.3 + - - +
143A LYS 3.3 10.7 + - - +
145A MET* 1.4 75.2 - - - +
147A PRO* 1.4 67.4 - - + +
148A ILE 3.2 0.9 + - - -
149A ILE* 3.4 11.3 - - + +
150A ALA* 3.3 19.7 + - + +
345A PRO 4.6 4.7 - - - +
346A THR* 4.1 12.8 - - + -
347A TYR* 3.8 48.5 - - + +
450A MET* 4.2 20.4 - - + -
454A LEU* 4.5 10.3 - - + +
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Residues in contact with PRO 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A LYS 3.5 10.5 - - - +
144A GLU* 3.4 18.2 - - - +
146A VAL* 1.4 93.9 - - + +
148A ILE* 1.4 60.5 + - + +
150A ALA* 3.5 18.3 + - + +
151A GLN* 3.7 8.8 + - - +
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Residues in contact with ILE 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A GLU 3.5 22.7 - - - +
145A MET* 3.5 20.2 - - + +
146A VAL 3.2 1.0 - - - -
147A PRO* 1.4 79.4 - - + +
149A ILE* 1.4 61.0 + - - +
150A ALA 3.2 0.9 + - - -
151A GLN* 3.5 8.8 - - - +
152A TYR* 3.3 20.3 - - + -
186A SER* 3.9 38.6 - - - +
187A THR* 4.3 13.0 - - + +
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Residues in contact with ILE 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A MET* 3.4 24.2 + - + +
146A VAL* 3.4 22.7 - - + +
148A ILE* 1.4 72.8 - - - +
150A ALA* 1.3 62.6 + - - +
151A GLN 3.4 0.4 - - - -
152A TYR* 3.5 18.3 + - - +
153A GLY* 3.5 8.5 + - - -
179A TYR* 4.4 11.3 + - - +
183A VAL* 3.7 38.1 - - + +
186A SER* 4.6 1.1 - - - +
187A THR* 3.8 25.8 - - + -
447A PHE* 5.1 5.6 - - + -
450A MET* 5.1 4.0 - - + -
451A ASN* 4.2 19.5 - - + -
454A LEU* 3.8 24.9 - - + +
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Residues in contact with ALA 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A VAL* 3.3 19.0 + - + +
147A PRO* 3.5 13.0 - - + +
148A ILE 3.2 0.6 - - - -
149A ILE* 1.3 75.2 - - - +
151A GLN* 1.4 58.8 + - - +
152A TYR 3.2 0.2 - - - -
153A GLY* 3.1 17.5 + - - -
154A ASP* 3.3 13.1 - - - +
344A PRO* 6.4 0.7 - - + -
345A PRO* 5.2 7.6 - - + +
454A LEU* 4.3 18.8 - - + -
458A ARG* 3.6 16.9 + - - +
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Residues in contact with GLN 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A PRO 3.7 6.5 + - - +
148A ILE* 3.5 16.7 + - - +
150A ALA* 1.4 77.6 - - - +
152A TYR* 1.3 71.7 + - + +
153A GLY 3.3 0.2 - - - -
154A ASP* 3.7 13.6 + - - +
155A VAL* 3.3 32.3 + - - +
158A ARG* 5.7 0.2 + - - -
192A ASN* 3.2 35.3 + - - +
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Residues in contact with TYR 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A ILE* 3.3 22.2 - - + -
149A ILE* 3.5 11.8 + - - +
150A ALA 3.2 1.0 - - - -
151A GLN* 1.3 85.3 - - + +
153A GLY* 1.3 54.8 + - - +
154A ASP 3.3 0.9 - - - -
155A VAL* 3.6 17.3 - - + +
156A LEU* 2.8 34.1 + - - +
179A TYR* 3.8 7.5 - - + -
182A ASP* 3.3 45.8 - - + +
183A VAL* 4.2 11.7 - - + -
186A SER* 3.4 32.7 - - - -
190A GLY 4.8 0.2 + - - -
191A VAL 3.7 0.5 + - - -
192A ASN* 2.8 55.4 + - - -
193A ILE 4.6 0.2 - - - -
194A ASP* 5.8 1.3 - - - -
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Residues in contact with GLY 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A ILE 3.5 7.2 + - - -
150A ALA* 3.1 11.3 + - - -
152A TYR* 1.3 77.6 - - - +
154A ASP* 1.4 55.4 + - - +
156A LEU* 3.5 8.5 + - - +
157A VAL* 3.2 32.2 + - - +
179A TYR* 4.3 6.9 - - - -
454A LEU* 5.4 4.7 - - - -
455A ALA* 5.7 1.3 - - - -
458A ARG* 3.7 22.0 - - - +
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Residues in contact with ASP 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A ALA 3.3 9.7 + - - +
151A GLN* 3.8 13.0 - - - +
152A TYR 3.3 0.4 - - - -
153A GLY* 1.4 74.3 - - - +
155A VAL* 1.4 53.2 + - - +
157A VAL* 3.3 8.7 + - - +
158A ARG* 2.8 54.7 + - - +
161A ARG* 5.7 0.2 + - - -
458A ARG* 3.0 39.9 + - - +
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Residues in contact with VAL 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A GLN* 3.3 25.3 + - - +
152A TYR* 3.4 24.6 + - + +
153A GLY 3.4 0.6 - - - -
154A ASP* 1.4 72.6 - - - +
156A LEU* 1.4 54.5 + - - +
158A ARG* 3.3 19.8 + - - +
159A ASN* 2.8 49.6 + - - +
182A ASP* 5.1 5.8 - - - +
194A ASP* 3.4 32.5 - - - +
----------------------------------------------------------
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Residues in contact with LEU 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A TYR 2.8 17.5 + - - +
153A GLY* 3.6 7.6 - - - +
154A ASP 3.3 0.2 - - - -
155A VAL* 1.4 75.5 - - - +
157A VAL* 1.4 56.7 + - - +
159A ASN* 3.5 5.1 + - + +
160A LEU* 2.9 32.6 + - + +
175A VAL* 3.6 44.1 - - + +
176A PHE* 4.3 9.9 - - + -
179A TYR* 3.7 32.8 - - + -
455A ALA* 4.2 18.4 - - + +
458A ARG* 6.1 0.2 - - + -
459A VAL* 3.7 28.9 - - + -
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Residues in contact with VAL 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A GLY 3.2 15.2 + - - +
154A ASP* 3.3 9.8 + - - +
156A LEU* 1.4 70.7 - - - +
158A ARG* 1.4 59.6 + - - +
160A LEU* 3.4 0.8 + - - -
161A ARG* 2.9 61.4 + - - +
458A ARG* 3.5 38.1 - - + +
459A VAL* 4.2 5.8 - - + +
462A ASN* 3.8 13.0 - - - +
463A PHE* 3.4 23.0 - - + -
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Residues in contact with ARG 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A GLN 5.7 0.2 + - - -
154A ASP* 2.8 33.5 + - - +
155A VAL* 3.4 20.7 - - - +
157A VAL* 1.4 77.8 - - - +
159A ASN* 1.3 62.6 + - - +
161A ARG* 3.5 31.8 - - - +
162A ARG* 3.9 26.5 + - - +
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Residues in contact with ASN 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A VAL* 2.8 44.2 + - - +
156A LEU* 3.9 5.6 - - + +
158A ARG* 1.3 77.4 - - - +
160A LEU* 1.3 62.8 + - - +
161A ARG 3.2 0.7 + - - -
162A ARG* 3.3 29.2 + - - +
163A GLU* 3.6 13.7 + - - +
175A VAL* 5.8 3.4 - - + -
194A ASP* 3.9 4.1 + - - -
196A LEU* 3.4 35.5 - - + +
197A ASN* 3.2 30.8 + - - +
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Residues in contact with LEU 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A LEU* 2.9 18.0 + - + +
157A VAL 3.4 3.6 + - - +
159A ASN* 1.3 73.0 - - - +
161A ARG* 1.4 57.6 + - - +
163A GLU* 3.5 5.4 + - + +
164A ALA* 3.1 28.1 + - - +
170A VAL* 3.9 24.9 - - + -
172A LEU* 6.0 1.8 - - + -
175A VAL* 3.8 29.3 - - + +
176A PHE* 6.3 0.9 - - + -
459A VAL* 4.3 16.4 - - + -
463A PHE* 3.8 27.4 - - + -
465A PHE* 3.7 27.8 - - + -
493A VAL* 4.4 15.3 - - + -
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Residues in contact with ARG 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A ASP 5.7 0.4 + - - -
157A VAL* 2.9 33.8 + - - +
158A ARG* 3.5 25.0 - - - +
159A ASN 3.2 0.4 - - - -
160A LEU* 1.4 75.7 - - - +
162A ARG* 1.4 52.3 + - + +
164A ALA* 3.2 3.3 + - - +
165A GLU* 2.8 54.9 + - + +
342A LYS* 5.1 2.8 - - - +
462A ASN* 3.5 26.7 + - - +
463A PHE* 3.6 20.6 - - + -
495A SER* 4.9 10.3 - - - +
----------------------------------------------------------
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Residues in contact with ARG 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A ARG* 3.9 25.0 + - - +
159A ASN* 3.3 37.2 + - - +
160A LEU 3.5 0.4 - - - -
161A ARG* 1.4 74.6 - - + +
163A GLU* 1.3 55.4 + - - +
165A GLU* 3.5 19.1 + - - +
166A THR* 2.9 32.7 + - - -
197A ASN* 3.5 22.4 + - - +
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Residues in contact with GLU 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A ASN 3.6 10.9 + - - +
160A LEU* 3.5 12.3 + - + +
161A ARG 3.4 0.6 - - - -
162A ARG* 1.3 77.4 - - - +
164A ALA* 1.4 58.4 + - - +
166A THR* 4.0 5.6 + - - -
167A GLY 3.9 7.4 + - - -
168A LYS* 3.6 39.4 + - + +
169A PRO 4.9 2.0 - - - +
170A VAL* 3.7 37.8 - - + +
171A THR 6.1 0.2 - - - -
175A VAL* 4.9 10.0 - - + +
196A LEU* 5.4 6.6 - - - +
----------------------------------------------------------
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Residues in contact with ALA 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A LEU 3.1 18.3 + - - +
161A ARG 3.6 4.7 - - - +
163A GLU* 1.4 74.6 - - - +
165A GLU* 1.4 61.4 + - - +
166A THR 3.3 2.2 - - - -
167A GLY* 3.3 14.4 + - - +
168A LYS 5.6 0.2 - - - -
170A VAL* 5.2 0.4 - - - -
463A PHE* 4.3 10.5 - - + -
493A VAL* 3.4 42.1 - - + +
494A GLU* 5.8 0.2 - - - -
495A SER* 4.8 11.0 + - - +
----------------------------------------------------------
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Residues in contact with GLU 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A ARG* 2.8 29.9 + - + +
162A ARG* 3.5 28.4 + - - +
164A ALA* 1.4 76.8 - - - +
166A THR* 1.3 60.4 + - - +
167A GLY* 4.7 0.2 - - - -
495A SER* 6.4 2.5 - - - -
----------------------------------------------------------
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Residues in contact with THR 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A ARG 2.9 17.0 + - - -
163A GLU* 4.1 8.2 - - - -
164A ALA 3.3 0.6 - - - -
165A GLU* 1.3 76.8 - - - +
167A GLY* 1.3 59.1 + - - +
168A LYS* 3.2 24.1 + - + -
----------------------------------------------------------
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Residues in contact with GLY 167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A GLU 3.9 0.6 + - - -
164A ALA* 3.3 18.5 + - - -
165A GLU 4.7 0.2 - - - -
166A THR* 1.3 77.3 - - - +
168A LYS* 1.3 63.1 + - - +
169A PRO* 4.0 1.7 - - - +
492A LYS* 4.3 24.2 - - - +
493A VAL 5.7 2.2 - - - -
----------------------------------------------------------
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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