Contacts of the helix formed by residues 146 - 172 (chain D) in PDB entry 4PP8
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 146 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71D LYS* 2.7 23.0 + - - -
75D LYS* 2.5 36.3 + - - +
142D LYS 4.1 2.2 + - - +
143D TRP 3.1 14.5 + - - +
144D LYS 3.1 3.2 - - - -
145D ASP* 1.3 75.4 - - - +
147D GLY* 1.3 62.6 + - - +
148D GLU* 3.2 16.6 + - - +
149D PHE* 3.1 24.1 + - - +
150D VAL* 3.2 15.4 + - - +
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Residues in contact with GLY 147 (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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144D LYS 5.1 1.3 - - - -
145D ASP 3.2 8.4 + - - -
146D ASP* 1.3 73.3 + - - +
148D GLU* 1.3 61.7 + - - +
150D VAL* 3.4 6.8 + - - +
151D LYS* 3.0 29.6 + - - +
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Residues in contact with GLU 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71D LYS* 4.2 14.6 - - - +
146D ASP* 3.2 11.2 + - - +
147D GLY* 1.3 76.3 + - - +
149D PHE* 1.3 61.5 + - - +
151D LYS* 3.3 7.0 + - - +
152D GLN* 2.9 38.0 + - + +
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Residues in contact with PHE 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D LEU* 4.5 4.7 - - + -
71D LYS* 4.1 25.0 - - + +
72D LEU* 3.6 23.8 - - + -
75D LYS* 3.8 8.1 - - + -
112D PHE* 3.7 27.6 - + - -
129D TRP* 4.1 19.1 - + - -
143D TRP* 3.4 46.0 - + + -
146D ASP* 3.1 26.0 + - - +
148D GLU* 1.3 79.0 - - - +
150D VAL* 1.3 67.4 + - + +
152D GLN* 3.2 16.0 + - - +
153D LEU* 3.2 33.2 + - + +
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Residues in contact with VAL 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122D PHE* 3.8 17.6 - - + -
127D MET* 3.6 29.6 - - + -
129D TRP* 4.0 13.9 - - + +
144D LYS* 3.6 31.4 - - + +
146D ASP 3.2 13.3 + - - +
147D GLY* 3.9 7.6 - - - +
149D PHE* 1.3 80.1 - - + +
151D LYS* 1.3 63.7 + - - +
153D LEU* 3.2 10.4 + - - +
154D LYS* 3.2 20.5 + - - +
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Residues in contact with LYS 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127D MET* 6.3 0.4 - - - -
147D GLY 3.0 18.1 + - - +
148D GLU* 3.5 7.6 - - - +
149D PHE 3.3 0.2 - - - -
150D VAL* 1.3 76.1 - - - +
152D GLN* 1.3 53.0 + - + +
154D LYS* 3.2 6.3 + - - +
155D PHE* 2.7 42.3 + - + +
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Residues in contact with GLN 152 (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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64D PRO 4.7 1.0 - - - +
67D ASN* 3.6 11.8 + - - +
68D LEU* 3.5 40.1 + - + +
71D LYS* 3.5 43.3 - - - +
110D TRP* 5.0 0.2 - - - -
148D GLU* 2.9 19.9 + - + +
149D PHE* 3.2 8.0 + - - +
151D LYS* 1.3 73.5 - - + +
153D LEU* 1.3 62.9 + - - +
155D PHE* 4.4 8.5 - - + -
156D LEU* 3.1 28.9 + - - +
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Residues in contact with LEU 153 (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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68D LEU* 4.0 25.4 - - + -
110D TRP* 3.1 59.9 + - + +
112D PHE* 3.8 16.6 - - + -
122D PHE* 3.7 25.6 - - + -
124D THR* 4.4 1.1 - - - -
129D TRP* 4.4 3.6 - - + -
149D PHE* 3.4 42.0 - - + +
150D VAL* 3.2 9.5 + - - +
152D GLN* 1.3 79.7 - - - +
154D LYS* 1.3 60.7 + - - +
157D ILE* 3.5 12.5 + - - +
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Residues in contact with LYS 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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122D PHE* 4.5 2.0 - - + -
124D THR* 4.2 16.5 - - - +
127D MET* 4.3 23.1 - - + -
150D VAL 3.2 10.8 + - - +
151D LYS* 3.8 7.6 - - - +
153D LEU* 1.3 77.9 - - - +
155D PHE* 1.3 64.7 + - - +
157D ILE* 3.2 15.9 + - - +
158D HIS* 3.4 30.8 + - + +
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Residues in contact with PHE 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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64D PRO* 6.1 1.8 - - + -
151D LYS* 2.7 26.8 + - + +
152D GLN* 4.2 6.7 - - + +
154D LYS* 1.3 72.0 - - - +
156D LEU* 1.3 66.9 + - - +
158D HIS* 3.2 17.1 + - + -
159D GLU* 2.8 59.7 + - + +
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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
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61D LEU* 4.1 22.7 - - + +
64D PRO* 3.6 37.5 - - + +
65D LEU* 3.8 24.9 - - + -
68D LEU* 4.8 5.2 - - + -
96D MET* 4.2 9.6 - - + -
110D TRP* 4.2 18.4 - - + -
152D GLN 3.1 19.9 + - - +
153D LEU 4.2 4.0 - - - +
154D LYS 3.4 0.2 - - - -
155D PHE* 1.3 79.0 - - - +
157D ILE* 1.3 78.2 + - + +
159D GLU* 3.5 7.4 + - - +
160D CYS* 3.2 24.1 + - - +
164D MET* 5.4 0.9 - - + -
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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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96D MET* 3.9 22.9 - - + -
98D TYR* 3.8 25.4 - - + -
106D PRO* 4.1 22.7 - - + +
107D SER* 4.3 4.3 - - - +
108D ALA* 3.3 28.3 - - + -
110D TRP* 4.4 1.1 - - - +
124D THR* 4.2 9.4 - - + +
153D LEU 3.5 17.3 - - - +
154D LYS 3.4 7.4 - - - +
155D PHE 3.1 0.8 - - - -
156D LEU* 1.3 87.2 - - + +
158D HIS* 1.3 56.9 + - + +
161D SER* 2.7 38.8 + - - -
164D MET* 4.2 9.4 - - + +
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Residues in contact with HIS 158 (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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106D PRO* 5.0 16.3 + - + -
124D THR* 6.0 2.6 - - - -
154D LYS* 3.5 32.3 + - + +
155D PHE* 3.2 18.3 + - + +
157D ILE* 1.3 83.7 - - + +
159D GLU* 1.3 63.0 + - - +
160D CYS 3.4 0.3 + - - -
161D SER* 3.8 12.4 + - - -
162D GLN 5.1 1.0 + - - -
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Residues in contact with GLU 159 (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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60D CYS* 3.4 16.8 - - - +
64D PRO* 4.2 24.5 - - - +
155D PHE* 2.8 55.3 + - + +
156D LEU* 3.8 5.5 - - - +
158D HIS* 1.3 79.3 - - - +
160D CYS* 1.3 59.9 + - - +
162D GLN* 5.4 1.3 + - - +
163D LYS* 5.5 2.4 - - - +
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Residues in contact with CYS 160 (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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60D CYS* 2.0 65.1 - - + -
61D LEU* 3.9 21.8 - - + -
64D PRO* 5.0 4.3 - - - -
156D LEU* 3.2 17.2 + - - +
157D ILE 3.6 0.4 - - - -
159D GLU* 1.3 80.7 - - - +
161D SER* 1.3 60.0 + - - +
162D GLN 3.3 2.7 - - - -
163D LYS* 3.2 5.5 + - + +
164D MET* 2.8 38.6 + - + +
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Residues in contact with SER 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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98D TYR* 3.4 9.0 + - - -
106D PRO* 3.5 36.3 - - - -
157D ILE 2.7 22.5 + - - -
158D HIS 3.8 7.8 + - - -
159D GLU 3.7 1.2 - - - -
160D CYS* 1.3 72.6 - - - +
162D GLN* 1.3 53.5 + - - +
164D MET* 3.3 6.4 + - - +
165D ASP* 2.8 42.2 + - - +
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Residues in contact with GLN 162 (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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189A SER* 6.1 2.7 - - - +
158D HIS 5.1 1.2 + - - -
159D GLU 5.4 1.1 + - - +
160D CYS 3.3 0.6 - - - -
161D SER* 1.3 78.3 - - - +
163D LYS* 1.3 63.3 + - + +
165D ASP* 3.3 8.7 + - - +
166D GLU* 2.8 30.5 + - - +
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Residues in contact with LYS 163 (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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56D GLU* 2.9 61.9 + - + +
57D VAL* 4.0 13.9 - - + +
59D LYS* 4.6 4.8 - - - +
60D CYS* 3.5 28.7 - - + +
159D GLU 5.5 1.8 - - - +
160D CYS* 3.2 8.9 + - - +
162D GLN* 1.3 78.6 - - + +
164D MET* 1.3 60.1 + - - +
166D GLU* 3.6 8.0 - - - +
167D PHE* 3.0 28.9 + - - +
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Residues in contact with MET 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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5D LEU* 4.0 30.4 - - + +
57D VAL* 3.7 22.4 - - + -
61D LEU* 4.3 15.0 - - + -
96D MET* 4.4 3.6 - - + -
98D TYR* 3.6 50.9 - - + -
156D LEU* 4.9 0.9 - - + +
157D ILE* 4.2 17.7 - - + +
160D CYS* 2.8 34.5 + - + +
161D SER* 3.6 2.9 - - - +
163D LYS* 1.3 74.5 - - - +
165D ASP* 1.3 59.0 + - - +
167D PHE* 3.3 3.3 + - - +
168D LEU* 2.9 36.8 + - - +
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Residues in contact with ASP 165 (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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98D TYR* 2.6 26.9 + - - -
100D GLN* 3.8 13.1 + - + +
101D SER* 3.1 36.9 + - - -
102D GLN 5.0 0.6 + - - -
161D SER* 2.8 24.4 + - - +
162D GLN* 3.5 8.6 - - - +
164D MET* 1.3 72.1 - - - +
166D GLU* 1.3 63.8 + - - +
168D LEU* 3.2 8.0 + - - +
169D LYS* 2.9 24.1 + - - +
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Residues in contact with GLU 166 (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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189A SER* 4.9 12.3 - - - +
190A LEU 6.1 0.7 - - - +
191A SER* 4.7 13.6 + - - +
193A ASN* 5.8 0.6 + - - -
56D GLU* 4.2 14.6 - - - +
162D GLN 2.8 20.5 + - - +
163D LYS* 3.6 10.1 - - - +
165D ASP* 1.3 71.8 - - - +
167D PHE* 1.3 60.8 + - - +
169D LYS* 3.2 21.2 - - - +
170D GLN* 3.3 7.3 + - - +
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Residues in contact with PHE 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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193A ASN* 4.5 6.5 - - - +
5D LEU* 4.8 6.5 - - + -
28D VAL* 3.8 18.6 - - + -
31D ILE* 6.0 1.8 - - + -
33D ILE* 3.5 42.8 - - + -
54D ALA* 3.8 33.7 - - + -
56D GLU* 6.1 2.0 - - + +
57D VAL* 4.3 16.8 - - + -
163D LYS 3.0 17.7 + - - +
164D MET* 3.7 4.7 - - - +
165D ASP 3.2 0.4 - - - -
166D GLU* 1.3 72.9 - - - +
168D LEU* 1.3 67.0 + - + +
170D GLN* 3.0 54.5 + - - +
171D SER* 3.3 16.9 + - - -
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Residues in contact with LEU 168 (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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3D HIS 4.2 8.5 - - - +
4D SER 4.1 3.1 - - - -
5D LEU* 4.0 21.5 - - + +
28D VAL* 3.9 32.1 - - + -
98D TYR* 4.0 24.5 - - + +
99D PRO* 4.9 0.2 - - + -
100D GLN* 3.7 46.9 - - + +
164D MET 2.9 21.6 + - - +
165D ASP 3.6 4.3 - - - +
167D PHE* 1.3 76.8 - - + +
169D LYS* 1.3 56.6 + - - +
171D SER* 3.5 7.6 + - - -
172D LYS* 3.0 24.1 + - - -
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Residues in contact with LYS 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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100D GLN* 4.2 15.2 + - - +
165D ASP 2.9 12.3 + - - +
166D GLU* 3.2 15.3 - - - +
167D PHE 3.1 0.2 - - - -
168D LEU* 1.3 74.3 - - - +
170D GLN* 1.3 67.6 + - - +
172D LYS* 3.1 19.9 + - - +
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Residues in contact with GLN 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A ASN* 2.6 43.2 + - + +
54D ALA 5.1 1.6 + - - +
166D GLU 3.3 5.5 + - - +
167D PHE* 3.0 39.8 + - - +
169D LYS* 1.3 80.5 - - - +
171D SER* 1.3 67.1 + - - +
172D LYS* 3.9 3.8 - - - +
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Residues in contact with SER 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D VAL* 3.8 25.9 - - - +
31D ILE* 5.8 6.5 - - - +
167D PHE* 3.3 21.4 + - - -
168D LEU* 3.6 10.2 + - - -
169D LYS 3.3 0.2 - - - -
170D GLN* 1.3 80.7 + - - +
172D LYS* 1.3 70.0 - - - +
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Residues in contact with LYS 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168D LEU 3.0 15.0 + - - -
169D LYS* 3.1 16.5 + - - +
170D GLN 3.9 3.6 - - - +
171D SER* 1.3 83.5 - - - +
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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