Contacts of the helix formed by residues 135 - 168 (chain C) in PDB entry 3D87
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 135 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134C SER* 1.3 85.6 - - - +
136C PRO* 1.4 65.0 - - - +
137C TRP* 2.8 14.8 - - + -
138C GLN* 2.8 53.4 + - + +
139C ARG* 3.6 3.0 + - - +
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Residues in contact with PRO 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A LEU* 3.8 22.0 - - + -
93C GLU* 2.8 48.4 - - + +
134C SER 3.8 0.2 - - - -
135C GLN* 1.4 81.6 - - - +
137C TRP* 1.3 69.8 - - + +
139C ARG* 3.0 22.4 + - + +
140C LEU* 3.3 15.9 + - - +
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Residues in contact with TRP 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A GLN* 2.2 44.1 - - - +
137A TRP* 3.3 28.2 - + + +
138A GLN* 3.0 38.0 - - + +
141A LEU* 3.5 17.3 - - + +
135C GLN* 3.9 14.1 - - + -
136C PRO* 1.3 80.4 - - + +
138C GLN* 1.3 119.2 + - + +
139C ARG 3.5 0.2 + - - -
140C LEU* 3.8 7.3 + - - +
141C LEU* 4.0 18.8 + - + -
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Residues in contact with GLN 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133C PRO* 2.8 32.2 - - + +
134C SER 2.9 10.8 - - - +
135C GLN* 2.8 37.0 + - - +
137C TRP* 1.3 104.0 - - + +
139C ARG* 1.3 63.4 + - - +
141C LEU* 3.7 10.6 + - + +
142C LEU* 3.5 24.5 + - + +
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Residues in contact with ARG 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C ASP* 2.9 32.4 + - - -
89C ILE* 3.4 30.3 - - - +
92C GLY* 3.3 12.4 - - - -
93C GLU* 2.4 62.3 + - - +
133C PRO* 4.5 7.9 - - + -
134C SER* 3.7 30.1 - - - +
135C GLN 4.0 7.4 - - - +
136C PRO* 3.0 16.9 + - - +
138C GLN* 1.3 75.4 - - - +
140C LEU* 1.3 69.3 + - - +
142C LEU* 3.0 9.3 + - - +
143C ARG* 2.7 31.0 + - - +
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Residues in contact with LEU 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A LEU 3.4 26.9 - - - +
32A VAL* 3.7 15.7 - - + -
137A TRP* 3.5 19.1 - - + +
140A LEU* 4.1 15.3 - - + -
141A LEU* 3.4 46.9 - - + +
94C PRO* 3.7 20.4 - - + -
136C PRO 3.3 7.6 + - - +
137C TRP 4.1 2.0 - - - +
138C GLN 3.4 0.2 - - - -
139C ARG* 1.3 75.1 - - - +
141C LEU* 1.3 56.6 + - - +
143C ARG* 2.7 28.8 + - - +
144C PHE* 2.9 21.6 + - + -
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Residues in contact with LEU 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A TRP* 3.1 48.4 - - + +
36C ASP* 6.1 0.9 - - - +
137C TRP* 4.0 24.0 + - + +
138C GLN* 3.7 15.7 + - + +
139C ARG 3.2 0.8 - - - -
140C LEU* 1.3 79.0 - - - +
142C LEU* 1.3 63.4 + - + +
144C PHE* 3.4 3.8 + - - +
145C LYS* 3.0 43.0 + - + +
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Residues in contact with LEU 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C ILE* 3.5 34.3 - - + -
131C LEU 5.6 0.9 - - - +
132C SER 4.8 0.9 - - - +
133C PRO* 4.2 20.4 - - + -
138C GLN* 3.5 15.1 + - + +
139C ARG* 3.0 7.3 + - - +
141C LEU* 1.3 81.7 - - + +
143C ARG* 1.3 62.3 + - - +
144C PHE 3.0 2.5 - - - -
145C LYS* 4.2 15.0 - - + -
146C ILE* 2.7 56.2 + - + +
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Residues in contact with ARG 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A LEU* 2.9 58.0 + - + +
32A VAL 3.6 0.2 + - - -
89C ILE* 2.7 32.7 + - + +
90C PHE* 3.0 39.5 + - + +
92C GLY 2.9 31.1 + - - -
93C GLU 4.1 0.8 - - - -
94C PRO* 2.4 38.0 + - - +
96C LEU* 3.5 14.4 - - - +
139C ARG* 2.7 24.8 + - - +
140C LEU* 2.7 16.8 + - - +
142C LEU* 1.3 75.7 - - - +
144C PHE* 1.3 56.5 + - + +
146C ILE* 3.8 2.6 - - - +
147C LEU* 2.9 25.1 + - - +
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Residues in contact with PHE 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A HIS* 3.6 19.1 - + - -
31A LEU* 3.3 32.1 - - + -
94A PRO* 5.0 5.8 - - + -
137A TRP* 4.0 19.1 - + + -
140A LEU* 3.3 32.8 - - + -
29C HIS* 3.1 28.0 + + - +
33C GLY 5.1 1.1 - - - -
34C HIS* 4.1 24.7 - + + -
140C LEU* 2.9 29.0 + - + -
141C LEU 3.6 6.3 - - - +
143C ARG* 1.3 74.5 - - - +
145C LYS* 1.3 67.8 + - - +
146C ILE 3.1 1.1 - - - -
147C LEU* 3.8 0.2 - - - +
148C ARG* 2.8 29.1 + - - +
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Residues in contact with LYS 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C ASP* 5.7 4.5 - - - +
44C GLU* 6.1 1.4 - - - -
46C THR* 3.7 32.5 - - + +
47C ASN 5.2 2.4 - - - +
49C VAL* 6.0 3.6 - - - +
141C LEU* 3.0 35.6 + - + +
142C LEU* 3.1 18.4 + - + +
144C PHE* 1.3 74.6 - - - +
146C ILE* 1.3 62.0 + - + +
148C ARG* 3.4 3.5 + - - +
149C SER* 2.9 34.3 + - - -
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Residues in contact with ILE 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C VAL* 6.0 2.9 - - + -
81C TYR* 3.6 16.7 - - + -
84C LEU* 3.2 32.3 - - + -
85C LEU* 4.8 7.2 - - + -
89C ILE* 4.7 9.6 - - + -
90C PHE* 3.8 24.7 - - + -
142C LEU* 2.7 55.6 + - + +
143C ARG 3.8 1.6 - - - +
145C LYS* 1.3 77.7 - - + +
147C LEU* 1.3 65.9 + - + +
149C SER* 3.3 7.0 - - - -
150C LEU* 2.8 28.7 + - + +
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Residues in contact with LEU 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A LEU* 4.3 10.8 - - + -
25C ALA* 3.0 34.5 - - - +
28C ALA* 3.9 10.3 - - + +
29C HIS* 3.3 32.1 - - + -
85C LEU* 5.3 5.2 - - + -
90C PHE* 4.2 19.7 - - + -
102C VAL* 5.1 4.3 - - + -
105C LEU* 4.8 7.2 - - + -
143C ARG 2.9 21.7 + - - +
144C PHE 3.0 0.8 + - - +
146C ILE* 1.3 80.1 - - + +
148C ARG* 1.3 67.8 + - - +
150C LEU* 3.1 14.2 + - + +
151C GLN* 2.8 33.8 + - + +
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Residues in contact with ARG 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C TRP* 4.9 3.6 - - + -
29C HIS* 3.2 27.8 + - - -
30C PRO 2.6 28.7 + - - -
31C LEU* 3.2 37.2 + - - +
33C GLY* 3.1 25.3 - - - -
34C HIS 3.8 11.9 + - - +
35C MET* 5.1 2.6 - - - +
144C PHE* 2.8 17.9 + - - +
145C LYS* 4.0 3.1 - - - +
147C LEU* 1.3 75.5 - - - +
149C SER* 1.3 64.9 + - - +
151C GLN* 3.2 23.7 + - - +
152C ALA* 3.3 11.1 + - - +
208D ARG* 5.5 2.2 - - - -
209D ASP* 5.9 0.9 - - - +
293D TYR* 4.3 12.2 + - - +
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Residues in contact with SER 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C VAL* 3.7 15.6 - - - +
51C HIS* 5.1 2.2 - - - -
81C TYR* 2.3 39.3 + - - -
145C LYS* 2.9 22.5 + - - -
146C ILE* 3.3 7.2 - - - -
148C ARG* 1.3 77.5 - - - +
150C LEU* 1.3 57.0 + - - -
152C ALA* 3.0 25.7 - - - +
153C PHE 3.2 4.9 + - - -
181D GLU* 3.9 4.6 + - - +
208D ARG* 5.3 4.0 - - - +
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Residues in contact with LEU 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C LEU* 4.9 2.0 - - + -
25C ALA* 3.9 12.3 - - + -
81C TYR* 3.6 43.7 - - + -
85C LEU* 4.7 9.2 - - + -
105C LEU* 4.8 11.0 - - + -
109C LEU* 4.1 18.6 - - + -
146C ILE* 2.8 22.1 + - + +
147C LEU* 3.4 15.9 - - + +
149C SER* 1.3 69.9 + - - +
151C GLN* 1.3 61.6 + - - +
152C ALA 2.7 7.3 + - - -
153C PHE* 2.7 22.7 + - - +
154C VAL* 3.0 34.5 + - + -
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Residues in contact with GLN 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C ALA* 3.1 36.0 + - + -
26C TRP* 3.5 44.3 + - + +
29C HIS* 2.8 32.3 + - - +
147C LEU* 2.8 26.6 + - + +
148C ARG* 3.5 25.7 - - - +
150C LEU* 1.3 74.4 - - - +
152C ALA* 1.3 58.3 + - - +
154C VAL* 3.4 21.9 - - - +
155C ALA* 3.5 6.1 + - - +
292D TYR 4.6 0.3 - - - +
293D TYR* 3.4 16.0 + - + -
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Residues in contact with ALA 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148C ARG 3.3 5.7 + - - +
149C SER* 3.0 17.0 + - - +
150C LEU 2.7 0.8 + - - -
151C GLN* 1.3 79.1 - - - +
153C PHE* 1.3 64.4 + - - +
155C ALA* 3.3 14.4 + - - +
156C VAL* 3.6 11.1 + - - +
181D GLU* 4.1 13.9 - - + +
208D ARG* 3.5 41.2 - - - +
293D TYR* 3.7 10.3 - - + -
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Residues in contact with PHE 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C PRO* 4.2 8.3 - - + -
51C HIS 4.9 1.1 - - - -
52C ILE* 2.9 36.8 - - + +
73C ARG* 4.6 2.2 - - + -
74C ILE* 2.9 33.2 - - + -
77C GLY* 3.4 16.6 - - - -
78C LEU* 3.6 22.9 - - + -
81C TYR* 3.7 28.9 - + + -
149C SER 3.2 1.9 + - - +
150C LEU 2.7 13.0 + - - +
152C ALA* 1.3 78.9 - - - +
154C VAL* 1.3 76.4 + - + +
155C ALA 3.0 1.4 + - - -
156C VAL* 3.1 5.4 + - - +
157C ALA* 3.0 24.6 + - + +
181D GLU* 2.9 32.5 - - - +
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Residues in contact with VAL 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C SER* 4.7 1.7 - - - +
21C LEU* 3.3 28.5 - - + -
22C CYS* 3.4 17.2 - - - -
25C ALA* 4.2 9.0 - - + -
26C TRP* 5.8 0.4 - - - +
78C LEU* 5.2 2.0 - - + -
109C LEU* 4.7 6.5 - - + -
150C LEU* 3.1 31.2 - - + +
151C GLN* 3.4 21.3 - - - +
153C PHE* 1.3 82.6 - - + +
155C ALA* 1.3 60.0 + - - +
157C ALA* 3.2 11.5 - - + +
158C ALA* 2.7 33.8 + - - +
292D TYR 5.3 0.4 - - - +
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Residues in contact with ALA 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C CYS* 4.2 0.4 - - - -
151C GLN 3.5 12.1 - - - +
152C ALA 3.3 12.1 + - - +
153C PHE 3.0 1.0 + - - -
154C VAL* 1.3 77.0 - - - +
156C VAL* 1.3 68.8 + - + +
158C ALA* 2.7 20.4 + - - +
159C ARG* 3.1 29.2 + - - +
208D ARG* 6.1 1.6 - - - -
292D TYR* 3.9 23.4 - - + +
293D TYR* 4.1 11.2 - - + -
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Residues in contact with VAL 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C ILE* 3.0 33.0 - - + -
58C CYS* 4.2 0.2 - - + -
152C ALA 4.1 9.0 - - - +
153C PHE 3.1 7.3 + - - +
155C ALA* 1.3 77.9 - - + +
157C ALA* 1.3 55.9 + - - +
158C ALA 3.0 0.5 + - - -
159C ARG* 3.0 21.6 + - - +
160C VAL* 2.7 40.7 + - + +
179D ALA 3.1 26.0 - - - +
180D ALA 4.0 3.1 - - - +
181D GLU* 3.8 20.0 - - + +
246D TYR* 3.8 9.0 - - - +
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Residues in contact with ALA 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C SER* 4.9 2.2 - - - -
52C ILE* 4.4 2.9 - - + +
74C ILE* 4.2 26.7 - - + -
78C LEU* 5.8 1.8 - - + -
112C LEU* 6.5 0.4 - - + -
153C PHE* 3.0 13.8 + - + +
154C VAL* 3.2 24.2 - - + +
156C VAL* 1.3 78.0 - - - +
158C ALA* 1.3 61.8 + - - +
160C VAL* 3.3 3.4 + - - +
161C PHE* 2.8 37.2 + - + -
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Residues in contact with ALA 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C GLN* 5.4 0.2 - - - +
18C SER* 3.6 19.5 + - - +
22C CYS* 3.7 10.8 - - - -
154C VAL 2.7 17.1 + - - +
155C ALA 2.7 12.4 + - - +
157C ALA* 1.3 69.2 - - - +
159C ARG* 1.3 52.5 + - - +
161C PHE* 2.6 28.6 + - - +
162C ALA* 2.7 16.5 + - - +
292D TYR* 3.1 32.8 - - + -
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Residues in contact with ARG 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155C ALA* 3.3 20.7 - - - +
156C VAL* 3.6 31.7 - - - +
158C ALA* 1.3 74.3 - - - +
160C VAL* 1.3 63.6 + - - +
162C ALA* 3.4 6.8 - - - +
163C HIS 2.9 20.6 + - - -
114D TYR* 3.2 22.3 + - - -
179D ALA* 5.4 2.0 + - - +
208D ARG* 6.1 1.0 - - - +
246D TYR* 3.1 57.3 + - + +
247D PHE* 3.6 18.8 - - - +
290D ASP* 3.0 40.2 + - - -
292D TYR* 3.8 18.4 - - + +
293D TYR* 4.5 3.8 - - - +
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Residues in contact with VAL 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C TRP* 3.6 7.0 - - + -
58C CYS* 3.4 45.1 - - + +
63C LEU* 4.4 10.7 - - + +
70C CYS* 3.9 4.5 - - - -
71C LEU* 3.8 15.5 - - + -
74C ILE* 3.6 24.2 - - + -
156C VAL* 2.7 22.7 + - + +
157C ALA 3.4 10.3 - - - +
159C ARG* 1.3 76.5 - - - +
161C PHE* 1.3 66.0 + - + +
163C HIS* 3.4 3.1 + - - +
164C GLY 3.2 16.1 + - - -
246D TYR* 3.5 8.1 - - + +
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Residues in contact with PHE 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C TRP* 3.6 17.8 - + - +
14C CYS* 3.3 35.9 - - + -
15C GLN* 3.1 29.0 - - - +
18C SER* 3.7 16.6 - - - +
71C LEU* 3.8 17.3 - - + -
74C ILE* 3.9 30.5 - - + -
112C LEU* 4.6 10.5 - - + -
116C LEU* 3.7 24.2 - - + -
157C ALA* 2.8 33.2 + - + -
158C ALA 2.6 10.3 + - - +
160C VAL* 1.3 71.2 - - + +
162C ALA* 1.3 64.7 + - - +
165C ALA* 3.1 16.5 + - - +
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Residues in contact with ALA 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C GLN* 3.5 16.2 - - + +
158C ALA 2.7 15.0 + - - +
159C ARG* 3.1 12.8 + - - +
161C PHE* 1.3 71.7 - - - +
163C HIS* 1.3 64.2 + - - +
165C ALA* 3.0 7.1 + - - +
166C ALA* 2.9 20.5 + - - +
245D SER 3.6 12.8 - - - +
246D TYR 4.5 0.4 - - - +
248D SER* 4.3 2.9 - - - +
292D TYR* 3.1 29.4 - - + +
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Residues in contact with HIS 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C PRO* 3.6 37.5 + - + +
63C LEU* 4.3 11.9 - - + -
159C ARG 2.9 14.9 + - - +
160C VAL 3.6 4.7 - - - +
162C ALA* 1.3 74.9 - - - +
164C GLY* 1.3 55.0 + - - +
166C ALA* 2.7 3.2 + - - -
167C THR* 2.5 55.6 + - + +
168C LEU* 5.1 3.4 - - + -
243D PRO* 3.3 19.5 - - + +
245D SER* 2.9 51.5 + - - -
246D TYR* 3.3 10.4 + - + -
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Residues in contact with GLY 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C TRP* 3.3 34.4 - - - -
63C LEU* 5.8 0.4 - - - +
160C VAL 3.2 8.3 + - - -
163C HIS* 1.3 78.0 - - - +
165C ALA* 1.3 64.6 + - - +
168C LEU* 3.0 35.5 + - - +
169C SER 3.1 9.2 + - - -
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Residues in contact with ALA 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C TRP* 3.6 19.4 - - - +
12C THR* 4.4 8.7 - - + +
15C GLN* 3.6 28.9 - - + +
161C PHE 3.1 14.4 + - - +
162C ALA 3.0 10.8 + - - +
164C GLY* 1.3 75.7 - - - +
166C ALA* 1.3 54.0 + - - +
169C SER* 2.8 27.6 - - - +
170C PRO* 4.7 1.4 - - - +
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Residues in contact with ALA 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162C ALA 2.9 11.1 + - - +
163C HIS* 2.7 12.1 + - - +
165C ALA* 1.3 74.7 - - - +
167C THR* 1.3 61.5 + - + +
169C SER 3.9 4.4 - - - +
170C PRO* 5.5 0.9 - - - +
245D SER* 4.2 24.5 - - - +
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Residues in contact with THR 167 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163C HIS* 2.5 42.4 + - + +
166C ALA* 1.3 78.9 - - + +
168C LEU* 1.3 79.3 + - - +
169C SER 3.7 2.0 - - - +
245D SER* 4.5 20.2 - - - +
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Residues in contact with LEU 168 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C TRP* 3.4 36.8 - - + +
63C LEU* 4.0 27.4 - - + +
64C ARG* 5.3 9.9 - - - +
67C SER* 4.8 6.7 - - - -
163C HIS* 5.1 5.6 - - + -
164C GLY* 3.0 17.5 + - - +
167C THR* 1.3 100.6 - - - +
169C SER* 1.3 61.1 + - - +
170C PRO 4.0 6.2 - - - -
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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