Contacts of the helix formed by residues 155 - 182 (chain D) in PDB entry 3P8C
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 SER 155 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149D LYS* 4.6 8.6 + - - +
153D ASN* 2.8 23.5 + - - -
154D PRO* 1.3 75.3 - - - +
156D TYR* 1.3 62.2 + - - +
157D PHE 3.3 1.1 + - - -
158D PHE* 3.5 8.9 + - - +
159D ASP* 3.0 37.7 + - - +
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Residues in contact with TYR 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634A ARG 5.3 1.3 + - - -
635A ARG* 2.8 37.3 + - - +
636A ILE* 3.5 27.4 - - + -
637A GLN* 3.2 39.3 - - + -
639A PRO 4.2 7.2 - - - -
153D ASN* 3.0 32.0 + - + +
154D PRO 3.1 0.2 - - - -
155D SER* 1.3 76.0 + - - +
157D PHE* 1.3 75.5 + + + +
159D ASP* 3.8 4.8 - - - +
160D LEU* 3.0 60.3 + - + +
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Residues in contact with PHE 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622A TRP* 4.5 1.1 - + - -
624A ARG* 3.5 11.2 - - - -
637A GLN* 3.7 33.9 - - + -
638A PHE 3.3 27.8 - - - -
639A PRO* 4.6 5.1 - - + +
640A ILE* 4.3 16.2 + - + +
690A GLU* 3.2 40.6 - - + -
693A ALA* 4.1 3.4 - - + +
694A GLU* 3.6 29.4 - - + -
697A LEU* 3.4 16.3 - - + +
153D ASN 5.2 1.3 - - - -
154D PRO* 3.4 22.2 - - + +
155D SER 3.3 1.0 - - - -
156D TYR* 1.3 81.0 - + + +
158D PHE* 1.3 60.6 + - - +
160D LEU* 4.0 2.8 - - - +
161D TRP* 3.1 24.9 + - - +
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Residues in contact with PHE 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697A LEU* 3.7 28.3 - - + +
110D GLN* 6.0 4.3 - - - -
154D PRO 4.9 0.4 + - - -
155D SER* 3.5 10.8 + - - +
156D TYR 3.4 0.2 - - - -
157D PHE* 1.3 77.2 - - - +
159D ASP* 1.3 69.5 + - - +
161D TRP* 3.1 5.5 + + - -
162D LYS* 2.8 45.4 + - + +
249D ASN* 3.3 56.1 - - + -
251D VAL* 4.1 16.4 - - + -
254D ILE* 3.9 21.1 - - + -
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Residues in contact with ASP 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153D ASN* 4.8 5.2 + - - -
155D SER* 3.0 36.6 + - - +
156D TYR* 3.3 6.0 + - + +
158D PHE* 1.3 88.0 - - - +
160D LEU* 1.3 63.0 - - + +
162D LYS* 3.8 6.8 + - - +
163D GLU* 3.1 28.3 + - - +
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Residues in contact with LEU 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635A ARG* 3.3 31.0 - - - +
639A PRO* 4.0 22.0 - - + -
156D TYR* 3.0 54.1 + - + +
157D PHE* 4.2 2.7 - - - +
159D ASP* 1.3 79.7 - - + +
161D TRP* 1.3 61.8 + - - +
163D GLU* 3.5 20.9 + - - +
164D LYS* 2.8 30.1 + - - +
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Residues in contact with TRP 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639A PRO* 5.9 0.8 - - - +
640A ILE* 3.9 17.9 - - + -
641A GLU* 5.6 4.0 - - - +
697A LEU* 3.8 19.5 - - + -
701A GLN* 3.1 40.2 + - - +
157D PHE 3.1 19.5 + - - +
158D PHE* 3.1 9.4 + + - +
160D LEU* 1.3 74.7 - - - +
162D LYS* 1.3 71.8 + - - +
164D LYS* 3.2 10.2 + - + +
165D MET* 2.8 64.3 + - + +
251D VAL* 3.7 43.5 - - + -
254D ILE* 3.8 32.5 - - + -
255D LEU* 3.8 15.3 - - + -
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Residues in contact with LYS 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158D PHE* 2.8 36.1 + - + +
159D ASP* 3.9 6.3 - - - +
161D TRP* 1.3 80.4 - - - +
163D GLU* 1.3 57.6 + - - +
165D MET* 3.3 4.8 + - - +
166D LEU* 3.0 57.5 + - + +
248D GLU 3.5 15.6 + - - +
249D ASN* 3.1 44.5 + - - +
254D ILE* 3.9 15.3 - - + +
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Residues in contact with GLU 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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159D ASP 3.1 18.3 + - - +
160D LEU* 3.6 20.5 - - - +
162D LYS* 1.3 79.3 - - - +
164D LYS* 1.3 63.0 + - - +
166D LEU* 3.4 9.2 + - - +
167D GLN* 3.0 24.5 + - + +
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Residues in contact with LYS 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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440A ARG* 4.5 22.2 - - - +
641A GLU* 4.0 33.1 + - - +
160D LEU 2.8 21.4 + - - +
161D TRP* 3.6 9.2 - - + +
163D GLU* 1.3 74.4 - - - +
165D MET* 1.3 71.6 + - + +
167D GLN* 3.3 5.0 + - - +
168D ASP* 2.8 56.5 + - - +
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Residues in contact with MET 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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161D TRP* 2.8 59.4 + - + +
162D LYS 3.3 5.1 + - - +
164D LYS* 1.3 92.3 - - + +
166D LEU* 1.3 54.0 + - - +
168D ASP* 3.9 19.8 - - + +
169D THR* 2.7 38.7 + - - -
254D ILE* 3.6 22.9 - - + +
255D LEU* 4.7 9.6 - - - -
258D ARG* 4.1 25.9 - - + +
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Residues in contact with LEU 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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162D LYS* 3.0 46.8 + - + +
163D GLU* 3.7 7.9 - - - +
164D LYS 3.3 0.2 - - - -
165D MET* 1.3 81.1 - - + +
167D GLN* 1.3 60.0 + - - +
169D THR* 3.5 6.7 + - - +
170D GLU* 3.2 28.7 + - - +
254D ILE* 4.9 10.1 - - + -
257D ARG* 6.0 4.0 - - - +
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Residues in contact with GLN 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163D GLU* 3.0 18.4 + - + +
164D LYS* 3.8 5.6 - - - +
166D LEU* 1.3 74.8 - - - +
168D ASP* 1.3 63.5 + - - +
170D GLU* 3.4 10.9 + - - +
171D ASP* 2.9 65.2 + - - +
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Residues in contact with ASP 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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164D LYS* 2.8 54.8 + - - +
165D MET* 3.9 9.5 - - + +
167D GLN* 1.3 73.8 - - - +
169D THR* 1.3 63.7 + - - +
171D ASP* 3.4 11.3 + - - +
172D LYS* 3.1 24.3 + - - +
258D ARG* 3.6 28.0 + - - +
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Residues in contact with THR 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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165D MET 2.7 22.2 + - - -
166D LEU* 3.6 9.0 - - - +
168D ASP* 1.3 75.7 - - - +
170D GLU* 1.3 58.4 + - - +
172D LYS* 3.4 4.5 + - - +
173D ARG* 3.0 45.2 + - - +
257D ARG* 4.4 9.0 - - + +
258D ARG* 3.5 27.5 + - - +
261D VAL* 3.6 30.4 - - + +
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Residues in contact with GLU 170 (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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166D LEU 3.2 17.2 + - - +
167D GLN* 3.9 13.0 - - - +
168D ASP 3.4 0.2 - - - -
169D THR* 1.3 78.2 - - - +
171D ASP* 1.3 59.9 + - - +
173D ARG* 2.8 35.0 + - - -
174D LYS* 3.1 64.3 + - + +
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Residues in contact with ASP 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167D GLN* 2.9 45.7 + - - +
168D ASP* 3.7 11.5 - - - +
169D THR 3.3 0.2 - - - -
170D GLU* 1.3 78.1 - - - +
172D LYS* 1.3 56.3 + - - +
174D LYS* 3.7 4.6 - - - +
175D GLU* 3.3 23.7 + - - +
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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 ASP 3.1 17.1 + - - +
169D THR 3.9 2.5 - - - +
171D ASP* 1.3 73.7 - - - +
173D ARG* 1.3 65.5 + - - +
174D LYS 3.2 0.2 - - - -
175D GLU* 3.1 16.0 + - + +
176D LYS* 3.1 34.4 + - + +
258D ARG* 3.8 20.1 - - - +
261D VAL* 4.4 10.1 - - + -
262D GLU* 3.1 46.4 + - + +
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Residues in contact with ARG 173 (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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169D THR* 3.0 38.4 + - - +
170D GLU* 2.8 32.5 + - - +
172D LYS* 1.3 78.1 - - - +
174D LYS* 1.3 80.9 + - - +
175D GLU 3.4 2.8 + - - -
176D LYS* 3.7 6.6 + - - +
177D ARG* 3.4 26.8 + - - +
261D VAL* 4.0 26.2 - - + +
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Residues in contact with LYS 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170D GLU* 3.1 41.4 + - + +
171D ASP* 3.7 5.5 - - - +
172D LYS 3.2 0.2 - - - -
173D ARG* 1.3 103.0 - - - +
175D GLU* 1.3 60.0 + - - +
177D ARG* 3.8 31.2 - - + +
178D LYS* 3.4 27.9 - - + +
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Residues in contact with GLU 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171D ASP 3.3 16.8 - - - +
172D LYS* 3.1 20.8 + - + +
174D LYS* 1.3 77.4 - - - +
176D LYS* 1.3 63.5 + - - +
177D ARG 3.3 1.3 - - - -
178D LYS* 3.6 15.4 - - - +
179D GLN* 3.1 31.4 + - - +
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Residues in contact with LYS 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172D LYS* 3.1 25.8 + - + +
173D ARG* 4.0 7.2 - - - +
175D GLU* 1.3 78.7 - - + +
177D ARG* 1.3 56.7 + - + +
179D GLN* 3.5 6.6 + - - +
180D LYS* 3.0 30.4 + - - +
261D VAL* 3.3 28.7 - - + +
262D GLU* 4.0 21.1 + - - +
263D TYR 4.4 4.6 + - - +
264D SER 4.4 15.8 + - - +
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Residues in contact with ARG 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173D ARG* 3.4 21.2 + - - +
174D LYS* 3.8 32.0 - - + +
175D GLU 3.3 0.4 - - - -
176D LYS* 1.3 77.7 - - + +
178D LYS* 1.3 60.2 + - + +
180D LYS* 4.1 6.1 - - - +
181D GLN* 3.1 31.2 + - - +
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Residues in contact with LYS 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174D LYS* 3.4 22.4 - - + +
175D GLU* 3.4 27.4 + - - +
176D LYS 3.3 0.4 - - - -
177D ARG* 1.3 81.0 - - + +
179D GLN* 1.3 58.3 + - - +
181D GLN* 4.4 2.1 - - - +
182D LYS* 3.5 35.2 + - + +
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Residues in contact with GLN 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175D GLU* 3.1 21.7 + - - +
176D LYS* 4.0 6.4 - - - +
178D LYS* 1.3 75.0 - - - +
180D LYS* 1.3 63.9 + - - +
181D GLN 3.6 0.2 + - - -
182D LYS* 3.8 7.7 - - - +
183D ASN* 3.2 22.8 - - + +
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Residues in contact with LYS 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176D LYS 3.0 18.7 + - - +
177D ARG* 4.1 7.4 - - - +
179D GLN* 1.3 78.1 - - - +
181D GLN* 1.3 59.5 + - - +
183D ASN* 3.9 5.4 - - - +
184D LEU* 3.6 23.9 + - - +
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Residues in contact with GLN 181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177D ARG 3.1 20.8 + - - +
178D LYS* 4.4 3.8 - - - +
180D LYS* 1.3 74.9 - - - +
182D LYS* 1.3 60.5 + - + +
183D ASN 3.1 10.2 + - - -
184D LEU 3.7 15.2 + - - +
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Residues in contact with LYS 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178D LYS* 3.5 22.9 + - + +
179D GLN* 3.8 5.9 + - - +
181D GLN* 1.3 79.1 - - + +
183D ASN* 1.3 61.7 + - - +
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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