Contacts of the helix formed by residues 145 - 171 (chain D) in PDB entry 1TKP
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 ASP 145 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D MET* 3.4 30.6 - - + +
30D CYS* 3.6 22.8 - - - -
84D ARG* 2.8 24.4 + - - -
88D LEU* 4.0 5.4 - - - +
140D ALA* 2.9 19.0 + - + +
143D LEU* 3.3 4.8 - - + -
144D GLY* 1.3 73.2 - - - +
146D HIS* 1.3 60.8 + - - +
147D ALA* 3.7 2.9 + - - +
148D THR* 2.4 31.1 + - - -
149D ALA* 3.0 18.0 + - - +
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Residues in contact with HIS 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141D GLU* 2.1 49.3 + - - +
144D GLY* 3.2 34.5 + - - -
145D ASP* 1.3 69.3 - - - +
147D ALA* 1.3 56.2 + - - +
149D ALA* 3.7 0.9 - - - +
150D HIS* 2.8 36.7 + - - +
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Residues in contact with ALA 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84D ARG* 3.4 24.9 - - - +
145D ASP* 3.2 1.9 + - - +
146D HIS* 1.3 75.5 - - - +
148D THR* 1.3 60.9 - - - +
150D HIS* 3.5 8.1 + - - +
151D MET* 2.9 31.3 + - + +
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Residues in contact with THR 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D CYS* 4.5 5.2 - - + -
34D LEU* 3.9 35.7 - - + -
84D ARG* 2.7 27.3 + - + +
88D LEU* 4.1 1.2 - - - +
140D ALA* 4.0 13.2 - - + -
145D ASP* 2.4 38.3 + - - +
147D ALA* 1.3 76.7 - - - +
149D ALA* 1.3 56.7 - - - +
151D MET* 3.3 7.5 + - - +
152D LEU* 2.9 33.3 + - + +
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Residues in contact with ALA 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137D THR* 3.8 15.9 - - - +
140D ALA* 3.7 8.7 - - + +
141D GLU* 3.6 34.3 - - + +
145D ASP 3.0 14.2 + - - +
146D HIS 3.7 6.1 - - - +
148D THR* 1.3 73.7 - - - +
150D HIS* 1.3 58.5 + - - +
152D LEU* 3.2 9.0 + - - +
153D ARG* 3.0 39.0 + - - +
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Residues in contact with HIS 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146D HIS 2.8 18.4 + - - +
147D ALA* 3.6 7.2 - - - +
149D ALA* 1.3 73.5 - - - +
151D MET* 1.3 69.4 + - + +
153D ARG* 3.1 23.2 + - + +
154D GLU* 3.0 63.8 + - + +
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Residues in contact with MET 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D LEU* 5.5 2.0 - - - -
80D GLU* 3.7 54.1 - - + +
81D LEU* 4.5 12.1 - - + -
84D ARG* 3.6 40.8 - - + +
147D ALA* 2.9 19.5 + - + +
148D THR* 3.8 4.0 - - - +
150D HIS* 1.3 76.8 - - + +
152D LEU* 1.3 66.9 + - + +
154D GLU* 3.3 8.4 + - + +
155D GLY* 2.9 21.1 + - - -
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Residues in contact with LEU 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D LEU* 3.8 17.5 - - + -
37D ASP* 4.1 10.1 - - - +
81D LEU* 3.7 30.5 - - + -
133D THR* 3.6 14.9 - - + +
136D HIS* 3.7 17.7 - - + +
137D THR* 3.5 37.9 - - + +
140D ALA* 4.7 0.2 - - + -
148D THR* 2.9 29.5 + - + +
149D ALA* 3.4 7.6 - - - +
150D HIS 3.2 0.2 - - - -
151D MET* 1.3 75.3 - - + +
153D ARG* 1.4 52.4 + - - +
155D GLY* 3.3 2.2 + - - +
156D LEU* 2.6 37.4 + - - +
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Residues in contact with ARG 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137D THR* 4.5 18.6 + - + +
141D GLU* 3.1 45.9 + - - +
149D ALA* 3.0 18.6 + - - +
150D HIS* 3.1 32.6 + - - +
152D LEU* 1.4 70.6 - - - +
154D GLU* 1.3 65.9 + - + +
156D LEU* 3.7 10.9 - - + +
157D ILE* 3.1 26.3 + - - +
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Residues in contact with GLU 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150D HIS* 3.0 53.9 + - + +
151D MET* 3.7 7.2 - - + +
153D ARG* 1.3 76.5 - - + +
155D GLY* 1.3 60.8 + - - +
157D ILE* 3.7 11.6 - - - +
158D GLU* 3.7 16.8 - - - +
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Residues in contact with GLY 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77D VAL* 4.2 22.9 - - - +
151D MET 2.9 14.6 + - - -
152D LEU* 3.6 2.2 - - - -
154D GLU* 1.3 75.7 - - - +
156D LEU* 1.3 67.9 + - - +
158D GLU* 2.9 15.2 + - - +
159D LEU* 3.0 21.5 + - - +
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Residues in contact with LEU 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130D ILE* 4.0 19.7 - - + +
133D THR* 3.6 30.0 - - + +
134D ARG* 4.1 19.3 - - + +
137D THR* 5.0 4.9 - - + -
152D LEU 2.6 21.2 + - - +
153D ARG* 3.2 13.8 + - + +
155D GLY* 1.3 73.2 - - - +
157D ILE* 1.3 59.0 + - - +
159D LEU* 3.0 7.6 + - + +
160D GLU* 2.7 67.1 + - + +
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Residues in contact with ILE 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153D ARG 3.1 12.7 + - - +
154D GLU* 3.7 12.8 - - - +
156D LEU* 1.3 79.1 - - - +
158D GLU* 1.3 81.9 + - - +
160D GLU* 4.0 9.8 - - + +
161D ASP* 3.2 25.4 + - + +
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Residues in contact with GLU 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73D THR* 3.7 27.9 + - + +
77D VAL* 5.0 2.0 - - + -
154D GLU 3.7 13.4 - - - +
155D GLY* 2.9 10.3 + - - +
157D ILE* 1.3 98.0 - - - +
159D LEU* 1.3 66.8 + - - +
161D ASP* 3.3 8.5 + - - +
162D ASP* 3.0 27.3 + - - -
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Residues in contact with LEU 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D VAL* 4.9 3.1 - - + -
44D LEU* 4.7 10.5 - - + -
73D THR* 4.5 9.9 - - + -
74D ALA* 4.8 5.8 - - + -
77D VAL* 4.0 35.2 - - + -
126D TYR* 3.7 26.9 - - + -
129D ILE* 3.8 28.3 - - + -
130D ILE* 4.3 13.2 - - + -
133D THR* 4.7 6.5 - - + +
155D GLY 3.0 16.6 + - - +
156D LEU* 3.0 12.0 + - + +
158D GLU* 1.3 78.2 - - - +
160D GLU* 1.3 59.0 + - - +
162D ASP 3.2 1.6 + - - -
163D ALA* 2.9 29.8 + - - +
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Residues in contact with GLU 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130D ILE* 3.7 23.3 - - + -
134D ARG* 3.1 30.6 + - - -
156D LEU* 2.7 49.7 + - + +
157D ILE* 4.1 10.4 - - + +
159D LEU* 1.3 80.3 - - - +
161D ASP* 1.3 56.5 + - - +
163D ALA* 3.6 1.2 - - - +
164D HIS* 2.7 32.4 + - - +
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Residues in contact with ASP 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157D ILE* 3.2 23.3 + - + +
158D GLU* 3.9 9.7 - - - +
159D LEU 3.3 0.2 - - - -
160D GLU* 1.3 75.5 - - - +
162D ASP* 1.4 69.5 + - - +
164D HIS* 3.2 8.8 + - - +
165D HIS* 3.0 64.6 + - - -
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Residues in contact with ASP 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66D PHE* 3.7 14.2 - - + -
69D GLU 5.0 0.2 - - - -
70D ALA* 3.5 31.5 - - + +
73D THR* 3.6 23.9 + - - +
126D TYR* 3.4 27.6 + - + +
158D GLU 3.0 11.8 + - - +
159D LEU* 5.5 0.3 - - - +
161D ASP* 1.4 81.4 - - - +
163D ALA* 1.3 63.0 + - - +
165D HIS* 3.2 10.5 + - - +
166D ILE* 3.1 26.3 + - - +
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Residues in contact with ALA 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123D MET* 4.7 9.2 - - + +
126D TYR* 3.6 34.1 - - + -
127D GLY* 6.1 0.2 - - - -
130D ILE* 3.8 13.5 - - + -
159D LEU 2.9 16.8 + - - +
160D GLU 3.6 4.0 - - - +
162D ASP* 1.3 77.7 - - - +
164D HIS* 1.3 64.2 + - - +
166D ILE* 3.4 6.0 + - - +
167D GLU* 3.0 22.2 + - - +
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Residues in contact with HIS 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160D GLU 2.7 18.0 + - - +
161D ASP* 3.7 9.3 + - - +
162D ASP 3.1 0.4 - - - -
163D ALA* 1.3 80.0 - - - +
165D HIS* 1.3 74.1 + + - +
167D GLU* 3.1 21.4 + - - +
168D HIS* 2.9 64.2 + + - +
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Residues in contact with HIS 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66D PHE* 3.5 31.9 - + + -
161D ASP* 3.0 47.0 + - - -
162D ASP* 3.4 11.2 - - - +
164D HIS* 1.3 85.7 + + - +
166D ILE* 1.3 60.3 + - - +
168D HIS* 2.9 10.7 + - - +
169D TYR* 2.8 36.4 + - + -
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Residues in contact with ILE 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D LEU* 4.9 3.1 - - + -
66D PHE* 3.7 21.8 - - + -
67D LEU* 5.3 0.2 - - + -
119D LEU* 3.5 34.8 - - + +
122D ASP* 3.9 17.5 - - + +
123D MET* 3.9 15.0 - - + +
126D TYR* 3.3 39.5 - - + +
162D ASP 3.1 8.6 + - - +
163D ALA* 3.6 7.2 - - - +
165D HIS* 1.3 76.3 - - - +
167D GLU* 1.3 63.8 + - - +
169D TYR* 3.1 20.1 + - - +
170D LEU* 3.2 22.6 + - + +
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Residues in contact with GLU 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D MET* 4.0 25.4 - - + +
163D ALA 3.0 15.1 + - - +
164D HIS* 3.4 25.1 - - - +
165D HIS 3.1 0.6 - - - -
166D ILE* 1.3 77.1 - - - +
168D HIS* 1.3 67.5 + - + +
170D LEU* 3.3 13.1 + - - +
171D GLU* 3.4 21.3 + - + +
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Residues in contact with HIS 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164D HIS* 2.9 45.9 + + - +
165D HIS* 2.9 12.8 + - - +
167D GLU* 1.3 80.5 - - + +
169D TYR* 1.3 64.5 + - - +
170D LEU 3.1 0.9 + - - -
171D GLU* 3.3 29.5 + - + +
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Residues in contact with TYR 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A LEU* 3.5 40.0 - - + +
59D GLU* 5.9 1.3 - - + -
62D ASP* 2.5 34.1 + - - -
63D LEU* 3.7 20.4 - - + -
66D PHE* 3.5 45.4 - + - +
116D ARG* 4.3 1.0 + - - -
119D LEU* 3.9 16.2 - - + -
165D HIS* 2.8 24.9 + - + -
166D ILE* 3.1 13.6 + - - +
168D HIS* 1.3 76.8 - - - +
170D LEU* 1.4 60.5 + - - +
171D GLU 3.6 4.5 + - - +
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Residues in contact with LEU 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A LEU* 4.3 1.8 - - + -
116D ARG* 2.9 75.3 + - + +
119D LEU* 3.9 14.8 - - + -
120D ALA* 4.0 25.6 - - + +
123D MET* 4.1 16.8 - - + -
166D ILE* 3.2 30.8 + - + +
167D GLU* 3.3 6.0 + - - +
168D HIS 3.1 0.8 - - - -
169D TYR* 1.4 74.0 - - - +
171D GLU* 1.3 67.1 + - - +
172D ASP* 3.9 0.5 + - - +
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Residues in contact with GLU 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A ALA* 4.8 1.0 - - - +
116D ARG* 4.7 3.5 + - - -
167D GLU* 3.4 21.9 + - + +
168D HIS* 3.3 28.9 + - + +
169D TYR 4.1 5.4 - - - +
170D LEU* 1.3 83.7 - - - +
172D ASP* 1.3 76.6 + - - +
173D ASP* 3.1 19.9 + - + +
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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
------------------------------------------------------------
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