Contacts of the helix formed by residues 145 - 170 (chain A) in PDB entry 1V3W
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 145 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A ARG* 4.2 11.4 - - - +
143A GLN 4.9 0.7 - - - +
144A LEU* 1.3 73.6 - - - +
146A GLU* 1.3 65.1 + - - +
147A GLU* 3.5 20.1 + - - +
148A GLU* 2.8 43.6 + - - +
149A ILE* 2.9 26.2 + - - +
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Residues in contact with GLU 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A THR* 1.3 73.8 - - - +
147A GLU* 1.3 70.6 + - + +
149A ILE* 3.3 13.2 + - + +
150A GLU* 3.0 32.5 + - + +
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Residues in contact with GLU 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A THR* 3.2 15.4 + - - +
146A GLU* 1.3 92.2 + - + +
148A GLU* 1.3 57.9 + - + +
150A GLU* 3.4 8.1 + - - +
151A TRP* 3.0 26.5 + - - +
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Residues in contact with GLU 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A ILE* 3.8 19.7 - - + +
132A LEU* 4.9 3.1 - - - +
142A ARG* 2.9 37.4 + - - -
144A LEU* 3.3 14.6 - - + +
145A THR* 2.8 40.6 + - - +
147A GLU* 1.3 75.4 - - + +
149A ILE* 1.3 60.4 + - - +
151A TRP* 3.1 10.2 + - - +
152A THR* 3.0 32.9 + - - +
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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
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112A HIS* 3.9 23.8 + - + +
130A TYR* 3.6 32.1 - - + -
144A LEU* 3.8 23.1 - - + +
145A THR 2.9 24.1 + - - +
146A GLU* 3.5 15.0 - - + +
147A GLU 3.2 0.2 - - - -
148A GLU* 1.3 77.2 - - - +
150A GLU* 1.3 64.6 + - + +
152A THR* 2.5 29.0 + - - -
153A LYS* 3.9 2.9 + - - +
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Residues in contact with GLU 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A GLU* 3.0 21.8 + - + +
147A GLU* 3.8 7.0 - - - +
148A GLU 3.3 0.2 - - - -
149A ILE* 1.3 81.4 - - + +
151A TRP* 1.3 57.8 + - - +
153A LYS* 3.3 7.2 + - - +
154A LYS* 3.1 30.7 + - + +
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Residues in contact with TRP 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A ILE* 3.3 29.9 - - + +
114A ILE* 4.8 6.7 - - + -
147A GLU 3.0 14.6 + - - +
148A GLU* 3.3 13.2 - - - +
149A ILE 3.1 0.2 - - - -
150A GLU* 1.3 75.0 - - - +
152A THR* 1.3 63.5 + - - +
153A LYS 3.0 2.0 - - - -
154A LYS* 3.5 48.2 - - + +
155A ASN* 3.0 53.5 + - - +
158A ILE* 3.7 23.8 - - + -
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Residues in contact with THR 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A TYR 3.5 20.3 - - - +
79A THR* 5.3 0.7 + - - -
94A TYR* 3.3 29.7 - - - +
96A ILE* 3.9 14.4 - - + +
112A HIS* 3.0 20.0 + - - -
113A VAL 4.3 2.9 - - - +
114A ILE* 3.9 16.6 - - + -
144A LEU* 3.9 22.7 - - + -
148A GLU 3.0 19.0 + - - +
149A ILE* 2.5 19.9 + - - +
151A TRP* 1.3 76.8 - - - +
153A LYS* 1.3 57.2 + - - +
155A ASN* 4.7 0.7 - - - +
156A ALA* 4.6 3.8 + - - +
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Residues in contact with LYS 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A TYR* 4.0 29.5 + - + -
94A TYR* 3.8 32.4 + - + +
112A HIS* 5.8 1.1 - - + -
149A ILE 4.9 1.6 - - - +
150A GLU* 3.3 9.0 + - - +
151A TRP 3.0 0.4 - - - -
152A THR* 1.3 81.4 + - - +
154A LYS* 1.3 64.9 + - - +
155A ASN 3.3 1.8 - - - -
156A ALA* 3.0 7.6 + - - +
157A GLU* 3.0 49.4 + - - +
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Residues in contact with LYS 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A GLU* 3.1 20.6 + - + +
151A TRP* 3.5 37.2 - - + +
153A LYS* 1.3 76.8 - - - +
155A ASN* 1.3 63.0 + - - +
157A GLU* 3.1 16.3 + - - +
158A ILE* 2.9 35.9 + - + +
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Residues in contact with ASN 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A GLN* 4.6 0.5 + - - -
79A THR* 3.5 32.8 + - - +
96A ILE* 3.7 19.1 - - + +
151A TRP* 3.0 57.6 + - + +
152A THR 4.9 1.3 - - - +
154A LYS* 1.3 77.5 - - - +
156A ALA* 1.3 61.6 + - - +
158A ILE* 3.4 7.1 + - - +
159A TYR* 3.3 30.5 + - - -
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Residues in contact with ALA 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A TYR 3.6 20.1 - - - +
57A ASN* 4.0 7.4 - - - +
77A TYR* 3.6 35.7 - - + +
79A THR* 3.7 10.0 + - - +
152A THR 4.6 1.0 + - - +
153A LYS 3.0 9.6 + - - +
155A ASN* 1.3 79.0 - - - +
157A GLU* 1.3 64.4 + - - +
159A TYR* 3.1 5.2 + - - +
160A VAL* 3.0 25.5 + - - +
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Residues in contact with GLU 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A TYR* 4.1 17.0 + - + -
153A LYS* 3.0 45.7 + - - +
154A LYS* 3.1 18.1 + - - +
156A ALA* 1.3 72.7 - - - +
158A ILE* 1.3 67.2 + - + +
160A VAL* 3.2 18.4 + - + +
161A GLU* 3.2 19.8 + - + +
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Residues in contact with ILE 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A TRP* 3.7 35.0 - - + -
154A LYS* 2.9 22.0 + - + +
155A ASN* 3.5 9.2 - - - +
156A ALA 3.2 0.2 - - - -
157A GLU* 1.3 76.7 - - - +
159A TYR* 1.3 67.0 + - + +
161A GLU* 3.3 7.5 + - - +
162A LEU* 3.0 34.4 + - + +
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Residues in contact with TYR 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A SER* 4.3 1.9 + - - +
38A TRP* 3.4 46.7 - + - -
55A TYR 5.9 0.2 - - - +
57A ASN* 3.6 25.6 - - + +
59A GLN* 3.2 39.4 - - + +
60A ASP* 5.0 0.5 + - - -
82A HIS* 3.8 15.9 + - - -
155A ASN* 3.3 23.6 + - - -
156A ALA 3.1 9.7 + - - +
158A ILE* 1.3 84.4 - - + +
160A VAL* 1.3 59.9 + - - +
162A LEU* 3.6 23.0 - - + +
163A ALA* 2.8 31.7 + - - +
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Residues in contact with VAL 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A LYS* 3.8 50.3 - - + +
36A SER* 5.7 0.2 - - - -
55A TYR* 4.1 27.1 - - + +
77A TYR* 5.8 0.7 - - + -
156A ALA 3.0 20.5 + - - +
157A GLU* 3.2 12.0 + - + +
159A TYR* 1.3 75.7 - - - +
161A GLU* 1.3 74.6 + - - +
163A ALA* 3.5 6.6 + - - +
164A GLU* 3.3 20.1 + - - +
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Residues in contact with GLU 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A GLU* 3.2 14.5 + - + +
158A ILE* 3.6 9.0 - - - +
159A TYR 3.2 0.4 - - - -
160A VAL* 1.3 87.8 - - - +
162A LEU* 1.3 64.1 + - - +
164A GLU* 3.2 13.7 + - - +
165A LYS* 3.0 27.1 + - + +
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Residues in contact with LEU 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A TRP* 4.0 13.9 - - + -
158A ILE* 3.0 24.6 + - + +
159A TYR* 3.2 37.6 + - + +
161A GLU* 1.3 75.1 - - - +
163A ALA* 1.3 63.6 + - - +
165A LYS* 3.0 25.6 + - + +
166A HIS* 3.0 38.1 + - + +
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Residues in contact with ALA 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A SER 5.8 1.1 - - - +
18A PHE* 3.9 11.8 - - + +
34A LYS 5.5 1.8 - - - +
35A THR 4.7 3.8 - - - +
36A SER* 3.7 26.2 - - - -
38A TRP* 3.9 11.6 - - - -
159A TYR 2.8 17.5 + - - +
160A VAL* 3.6 7.9 - - - +
162A LEU* 1.3 77.7 - - - +
164A GLU* 1.3 56.8 + - - +
166A HIS* 3.2 4.2 + - - +
167A ILE* 2.9 36.0 + - + +
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Residues in contact with GLU 164 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160A VAL* 3.3 9.3 + - - +
161A GLU* 3.2 17.5 + - - +
163A ALA* 1.3 78.4 - - - +
165A LYS* 1.3 63.9 + - - +
167A ILE* 3.3 13.0 + - + +
168A LYS* 3.0 57.5 + - + +
3004A CA 2.5 30.8 - - - -
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Residues in contact with LYS 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A GLU* 3.0 19.7 + - + +
162A LEU* 3.0 27.1 + - + +
164A GLU* 1.3 77.7 - - + +
166A HIS* 1.3 56.6 + - + +
168A LYS* 4.2 3.3 - - - +
169A GLY* 2.7 33.4 + - - -
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Residues in contact with HIS 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A PHE* 3.8 18.8 - - + -
38A TRP* 3.4 29.4 - + - -
39A PRO* 6.3 0.4 - - + -
162A LEU* 3.0 40.1 + - + +
163A ALA 3.2 7.4 + - - +
165A LYS* 1.3 79.7 - - + +
167A ILE* 1.3 65.6 + - - +
170A ARG* 2.9 72.4 + - + +
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Residues in contact with ILE 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A PRO 5.6 1.1 - - - +
16A SER* 3.7 24.5 - - - +
17A ALA 4.2 5.6 - - - +
18A PHE* 3.7 30.1 - - + -
163A ALA* 2.9 24.6 + - + +
164A GLU* 3.6 13.2 - - + +
166A HIS* 1.3 78.5 - - - +
168A LYS* 1.3 66.6 + - + +
170A ARG 5.0 0.5 + - - +
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Residues in contact with LYS 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A GLU* 3.0 52.6 + - + +
165A LYS* 4.2 2.5 - - - +
167A ILE* 1.3 87.9 - - + +
169A GLY* 1.3 58.0 + - - +
170A ARG 3.8 1.9 - - - +
3004A CA 4.1 4.6 - - - -
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Residues in contact with GLY 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A LYS 2.7 21.0 + - - -
168A LYS* 1.3 75.2 - - - +
170A ARG* 1.3 63.6 + - - +
171A LYS* 3.6 5.4 + - - +
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Residues in contact with ARG 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A PHE* 3.8 10.2 - - + -
20A ASP* 2.8 34.5 + - - -
21A GLU* 5.1 6.9 + - - +
22A ASN* 4.2 9.7 - - - +
38A TRP* 5.2 0.2 - - - -
39A PRO* 4.9 6.2 - - - +
166A HIS* 2.9 67.6 + - + +
167A ILE 5.0 0.8 + - - +
168A LYS 3.8 1.8 - - - +
169A GLY* 1.3 78.3 - - - +
171A LYS* 1.3 63.9 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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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