Contacts of the helix formed by residues 159 - 183 (chain R) in PDB entry 1HI0
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 159 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157R SER* 3.3 4.0 + - - +
158R ASN* 1.3 74.3 - - - +
160R MET* 1.3 67.9 + - - +
161R GLY* 2.9 16.3 + - - -
162R THR* 3.0 28.0 + - - +
163R LYS* 2.8 23.9 + - - +
541R LYS* 4.8 5.8 - - - +
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Residues in contact with MET 160 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145R ILE* 3.6 27.8 - - + +
146R ARG 3.8 5.2 - - - +
147R LYS* 3.6 35.4 - - + -
148R GLY 6.1 0.2 - - - +
158R ASN 3.3 5.4 + - - +
159R ASP* 1.3 74.3 + - - +
161R GLY* 1.3 63.9 + - - +
163R LYS* 4.0 11.4 - - - +
164R ILE* 2.9 51.2 + - + +
541R LYS* 5.4 4.6 - - - +
647R HIS* 3.4 40.8 - - + -
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Residues in contact with GLY 161 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159R ASP* 2.9 13.7 + - - -
160R MET* 1.3 81.0 - - - +
162R THR* 1.3 59.7 - - - +
164R ILE* 3.3 6.3 + - - +
165R GLU* 3.2 32.4 + - - +
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Residues in contact with THR 162 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155R TYR* 5.9 2.2 - - + -
157R SER* 3.4 26.3 + - - +
159R ASP* 3.0 22.7 + - - +
161R GLY* 1.3 72.6 - - - +
163R LYS* 1.3 66.6 + - - +
165R GLU* 3.2 15.6 + - + +
166R ILE* 2.8 39.4 + - + +
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Residues in contact with LYS 163 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145R ILE* 3.4 23.3 - - + -
146R ARG 3.5 9.9 + - - -
148R GLY 3.5 9.3 - - - +
149R SER* 3.0 40.9 + - - +
150R SER 5.0 0.2 - - - -
151R THR* 3.6 28.3 - - + +
157R SER* 4.3 2.7 - - - +
158R ASN 3.2 22.3 + - - -
159R ASP 2.8 17.5 + - - +
160R MET* 3.3 21.7 + - - +
162R THR* 1.3 77.7 - - - +
164R ILE* 1.3 63.2 + - - +
166R ILE* 3.1 8.2 + - - +
167R ALA* 2.9 23.0 + - - +
277R PHE* 3.8 12.1 - - + -
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Residues in contact with ILE 164 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145R ILE* 3.9 13.2 - - + -
160R MET* 2.9 44.0 + - + +
161R GLY* 3.5 8.3 - - - +
163R LYS* 1.3 77.1 - - - +
165R GLU* 1.3 63.9 + - + +
167R ALA* 3.3 4.7 + - - +
168R GLU* 2.9 50.0 + - + +
647R HIS* 3.7 17.7 - - + +
648R GLY 3.5 24.5 - - - +
649R VAL* 4.5 5.8 - - + -
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Residues in contact with GLU 165 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161R GLY* 3.2 19.7 + - - +
162R THR* 3.2 15.5 + - + +
164R ILE* 1.3 80.3 - - + +
166R ILE* 1.3 65.4 + - + +
168R GLU* 3.7 7.6 - - - +
169R ARG* 2.8 27.9 + - - +
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Residues in contact with ILE 166 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151R THR* 4.0 25.6 - - + +
155R TYR* 3.8 33.9 - - + -
157R SER* 5.1 0.4 - - - -
162R THR* 2.8 28.7 + - + +
163R LYS 3.3 7.6 - - - +
165R GLU* 1.3 76.9 - - + +
167R ALA* 1.3 58.4 + - - +
169R ARG* 3.4 6.6 + - - +
170R ALA* 2.9 27.2 + - - +
277R PHE* 3.3 30.3 - - + -
278R ALA* 4.4 14.7 - - + +
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Residues in contact with ALA 167 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143R LEU* 4.2 22.2 - - + -
145R ILE* 4.4 2.9 - - + -
163R LYS 2.9 15.0 + - - +
164R ILE 3.6 7.0 - - - +
166R ILE* 1.3 72.8 - - - +
168R GLU* 1.3 68.1 + - - +
170R ALA* 2.9 13.7 + - - +
171R LEU* 2.9 18.4 + - - +
277R PHE* 4.0 15.3 - - + -
281R ALA* 4.2 11.0 - - + -
649R VAL* 4.4 11.4 - - + -
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Residues in contact with GLU 168 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164R ILE* 2.9 38.9 + - + +
165R GLU* 3.7 6.8 - - - +
167R ALA* 1.3 72.8 - - - +
169R ARG* 1.3 62.8 + - - +
171R LEU* 3.4 9.1 + - - +
172R GLU* 3.1 29.2 + - - +
649R VAL* 3.2 33.4 - - + +
650R SER* 3.8 6.9 + - - -
653R LYS* 3.2 42.5 + - + +
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Residues in contact with ARG 169 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466P VAL* 6.1 0.8 - - - +
470P ARG* 4.3 26.6 - - - +
165R GLU 2.8 20.8 + - - +
166R ILE* 3.5 7.9 - - - +
168R GLU* 1.3 71.4 - - - +
170R ALA* 1.3 65.3 + - - +
172R GLU* 2.9 23.0 + - - +
173R LYS* 2.8 63.0 + - + +
192R LEU 5.3 3.4 + - - -
193R HIS* 4.7 12.6 + - + +
194R GLN* 5.8 4.3 - - - +
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Residues in contact with ALA 170 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166R ILE 2.9 13.4 + - - +
167R ALA 2.9 10.0 + - - +
169R ARG* 1.3 75.6 - - - +
171R LEU* 1.3 57.2 + - - +
172R GLU 2.9 0.5 + - - -
173R LYS* 3.0 1.4 + - - +
174R ALA* 2.6 36.1 + - - +
193R HIS 6.0 0.2 - - - -
195R MET* 3.6 12.1 - - + -
278R ALA* 3.3 31.9 - - + +
281R ALA* 3.9 14.8 - - + -
282R PRO* 4.1 1.6 - - + -
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Residues in contact with LEU 171 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143R LEU* 4.7 9.2 - - + -
167R ALA 2.9 20.9 + - - +
168R GLU* 3.8 9.6 - - - +
170R ALA* 1.3 72.4 - - - +
172R GLU* 1.3 59.9 + - + +
174R ALA* 4.3 2.1 + - - +
175R GLU* 5.2 0.9 + - - +
281R ALA* 4.2 4.0 - - + +
282R PRO* 3.7 28.0 - - + -
285R ALA* 4.1 6.7 - - + -
649R VAL* 5.4 3.1 - - + -
653R LYS* 4.0 10.5 - - + +
654R THR* 3.8 41.3 - - + +
657R PHE* 3.2 54.1 - - + +
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Residues in contact with GLU 172 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168R GLU* 3.1 16.6 + - - +
169R ARG* 2.9 23.8 + - - +
171R LEU* 1.3 81.4 - - + +
173R LYS* 1.3 70.4 + - + +
174R ALA 3.5 0.4 + - - -
175R GLU* 4.8 6.1 + - - +
653R LYS* 3.6 26.9 + - - +
656R ARG* 5.1 16.5 + - - +
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Residues in contact with LYS 173 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169R ARG* 2.8 57.3 + - + +
170R ALA* 3.5 0.9 - - - -
172R GLU* 1.3 83.5 - - + +
174R ALA* 1.3 66.0 + - - +
175R GLU 3.2 2.7 - - - -
176R GLU* 3.1 36.2 + - + +
177R ALA* 2.9 22.7 + - - +
193R HIS* 3.3 28.3 - - + +
195R MET* 4.2 3.6 - - + -
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Residues in contact with ALA 174 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170R ALA 2.6 22.8 + - - +
171R LEU 4.4 1.1 - - - +
172R GLU 3.5 1.4 - - - -
173R LYS* 1.3 71.1 - - - +
175R GLU* 1.3 59.0 + - - +
177R ALA* 3.1 3.3 + - - +
178R GLY* 2.8 26.0 + - - -
195R MET* 3.4 14.6 - - + -
282R PRO* 3.8 18.4 - - + -
352R TRP* 3.9 2.5 - - + -
356R LEU* 3.7 13.4 - - + +
657R PHE* 3.8 26.2 - - + -
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Residues in contact with GLU 175 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171R LEU 5.2 1.4 + - - +
172R GLU 4.8 4.9 + - - +
173R LYS 3.2 1.1 - - - -
174R ALA* 1.3 78.8 - - - +
176R GLU* 1.3 63.0 + - - +
177R ALA 3.2 0.2 + - - -
178R GLY 3.2 1.2 + - - -
179R ASN* 3.1 40.8 + - - +
352R TRP* 3.2 53.5 + - + +
660R SER* 4.0 13.0 + - - -
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Residues in contact with GLU 176 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172R GLU 5.4 0.4 + - - +
173R LYS* 3.1 40.5 + - + +
175R GLU* 1.3 80.9 - - - +
177R ALA* 1.3 60.3 + - - +
179R ASN* 3.7 9.5 + - - +
180R LEU* 3.2 28.6 + - + +
192R LEU* 4.2 10.9 - - - +
193R HIS* 3.1 28.0 + - - +
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Residues in contact with ALA 177 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173R LYS 2.9 12.9 + - - +
174R ALA 3.3 8.1 - - - +
176R GLU* 1.3 75.2 - - - +
178R GLY* 1.3 66.0 + - - +
180R LEU* 2.9 28.2 - - - +
181R MET* 3.0 14.4 + - + +
189R ALA* 4.0 4.3 - - + +
193R HIS* 4.0 16.1 - - + -
195R MET* 3.5 31.2 - - + -
356R LEU* 4.5 1.1 - - + -
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Residues in contact with GLY 178 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174R ALA 2.8 13.6 + - - -
175R GLU 3.7 2.9 - - - -
177R ALA* 1.3 76.5 - - - +
179R ASN* 1.3 57.4 + - - +
181R MET* 2.9 9.2 + - - +
182R LEU* 2.8 30.0 + - - +
352R TRP* 3.6 28.3 - - - -
355R LYS* 4.1 1.6 - - - +
356R LEU* 3.9 10.7 - - - +
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Residues in contact with ASN 179 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175R GLU* 3.1 38.5 + - - +
176R GLU* 4.0 8.4 - - - +
178R GLY* 1.3 74.3 - - - +
180R LEU* 1.3 63.3 + - - +
182R LEU* 3.1 27.6 + - - +
183R GLN* 3.1 24.2 + - - +
351R PRO* 5.7 0.2 - - - +
352R TRP* 3.5 17.3 + - - +
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Residues in contact with LEU 180 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176R GLU* 3.2 22.6 + - + +
177R ALA* 2.9 17.0 + - - +
179R ASN* 1.3 79.5 - - - +
181R MET* 1.3 56.6 - - - +
183R GLN* 3.2 18.1 + - - +
185R LYS* 2.9 64.9 + - + +
188R ASP* 4.1 13.7 - - + +
189R ALA* 4.0 22.2 - - + +
192R LEU* 4.4 12.6 - - + -
193R HIS* 4.3 11.9 - - + +
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Residues in contact with MET 181 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177R ALA 3.0 15.2 + - - +
178R GLY 2.9 8.8 + - - +
180R LEU* 1.3 73.4 - - - +
182R LEU* 1.3 59.8 + - - +
183R GLN 3.1 0.2 - - - -
184R GLY* 2.7 23.1 + - - +
185R LYS 4.3 3.6 - - - +
186R PHE* 3.5 31.8 - - + -
189R ALA* 3.9 10.3 - - + -
195R MET* 4.1 25.6 - - + +
279R LEU* 4.5 5.2 - - + -
355R LYS* 3.6 21.4 - - + +
356R LEU* 2.9 42.2 - - + -
359R THR* 3.5 31.4 - - + -
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Residues in contact with LEU 182 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178R GLY 2.8 14.6 + - - +
179R ASN* 3.1 29.4 + - - +
181R MET* 1.3 75.0 - - - +
183R GLN* 1.3 60.1 + - + +
184R GLY* 2.9 4.0 + - - -
351R PRO* 4.0 16.4 - - + +
352R TRP* 3.7 21.5 - - - +
355R LYS* 3.5 33.7 - - + +
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Residues in contact with GLN 183 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179R ASN* 3.1 22.0 + - - +
180R LEU* 3.5 26.0 - - - +
181R MET 3.1 0.4 - - - -
182R LEU* 1.3 76.6 - - + +
184R GLY* 1.3 61.9 + - - +
185R LYS* 3.2 37.8 + - + +
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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