Contacts of the helix formed by residues 170 - 192 (chain S) in PDB entry 3A68
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 TYR 170 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56S GLU* 4.3 6.7 - - - -
94S HIS* 2.7 53.2 + + + -
97S LYS* 3.3 22.2 - - + +
98S LEU* 3.2 24.4 - - + +
147S LEU* 3.7 35.1 - - + +
165S PHE* 3.7 32.5 - + - -
166S VAL* 3.0 16.9 + - + +
168S THR 3.6 0.4 - - - -
169S GLU* 1.3 93.2 - - + +
171S LEU* 1.3 61.3 + - - +
172S GLY 3.5 2.2 - - - -
173S GLU* 3.4 6.0 + - + +
174S GLN* 2.8 32.0 + - - +
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Residues in contact with LEU 171 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160R VAL* 3.5 32.3 - - + -
161R GLN* 3.8 19.7 - - + +
164R ASP* 5.9 0.4 - - + +
144S ASN* 4.4 9.3 - - - +
147S LEU* 3.8 29.2 - - + -
148S LEU* 4.0 22.7 - - + -
151S HIS* 4.3 7.2 - - + -
166S VAL* 3.1 20.3 + - + +
167S GLU* 3.5 24.1 + - + +
170S TYR* 1.3 75.1 - - - +
172S GLY* 1.3 62.6 + - - +
174S GLN* 3.3 5.0 + - - +
175S VAL* 3.1 26.5 + - - +
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Residues in contact with GLY 172 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161R GLN* 3.6 22.7 - - - +
167S GLU 3.9 6.2 + - - -
171S LEU* 1.3 75.2 - - - +
173S GLU* 1.3 70.0 + - - +
175S VAL* 3.2 5.7 + - - +
176S GLU* 3.1 29.8 + - - +
215S CA 4.6 5.4 - - - -
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Residues in contact with GLU 173 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94S HIS* 6.1 5.6 - - + +
168S THR 3.5 3.3 - - - +
169S GLU* 3.3 32.0 - - - +
170S TYR* 3.6 8.2 + - + +
172S GLY* 1.3 76.7 + - - +
174S GLN* 1.3 57.4 + - - +
176S GLU* 3.3 15.6 + - - +
177S ALA* 2.9 27.9 + - - +
215S CA 2.6 29.8 - - - -
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Residues in contact with GLN 174 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56S GLU* 5.4 0.2 - - - +
94S HIS* 5.6 1.6 - - - -
140S GLU* 2.7 56.5 + - - +
143S THR* 3.9 17.9 - - - +
144S ASN* 3.5 36.1 - - + +
147S LEU* 4.0 10.5 - - + +
170S TYR* 2.8 19.3 + - - +
171S LEU 3.6 5.4 - - - +
172S GLY 3.2 0.4 - - - -
173S GLU* 1.3 74.7 - - - +
175S VAL* 1.3 66.2 + - - +
177S ALA* 3.3 5.3 + - - +
178S ILE* 3.0 30.8 + - + +
214S CA 4.1 8.0 - - - -
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Residues in contact with VAL 175 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101R TYR* 5.2 2.5 - - + -
104R LYS* 3.9 36.4 - - + +
105R ARG* 3.8 24.7 - - - +
161R GLN* 3.6 28.0 - - + +
144S ASN* 5.2 11.0 - - - +
171S LEU 3.1 14.4 + - - +
172S GLY* 3.5 9.0 - - - +
174S GLN* 1.3 74.5 - - - +
176S GLU* 1.3 64.0 + - + +
178S ILE* 3.4 8.2 + - + +
179S LYS* 3.1 21.5 + - - +
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Residues in contact with GLU 176 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104R LYS* 3.1 40.3 + - + +
172S GLY 3.1 19.7 + - - +
173S GLU* 3.6 17.8 - - - +
174S GLN 3.2 0.2 - - - -
175S VAL* 1.3 79.4 - - + +
177S ALA* 1.3 56.0 + - - +
179S LYS* 3.3 6.8 + - - +
180S ARG* 3.0 28.5 + - - +
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Residues in contact with ALA 177 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140S GLU* 4.2 22.2 - - - +
173S GLU 2.9 16.3 + - - +
174S GLN* 3.3 9.6 + - - +
176S GLU* 1.3 76.2 - - - +
178S ILE* 1.3 63.7 + - - +
180S ARG* 3.3 10.3 + - - +
181S ILE* 3.1 31.0 + - + +
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Residues in contact with ILE 178 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37R ALA* 3.6 34.8 - - + +
39R GLN* 3.4 24.9 - - + +
137S LEU* 3.8 16.7 - - + +
140S GLU* 3.8 36.6 - - + +
141S LYS* 4.1 7.6 - - + +
144S ASN* 3.8 16.2 - - + +
174S GLN* 3.0 22.8 + - + +
175S VAL* 3.8 6.7 - - - +
177S ALA* 1.3 76.8 - - - +
179S LYS* 1.3 57.9 + - - +
182S SER* 2.8 32.7 + - - -
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Residues in contact with LYS 179 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71N ASP* 3.0 48.4 + - - -
73N ASP* 3.9 17.9 - - + +
37R ALA* 4.3 4.2 - - + +
100R GLU 5.4 0.2 + - - -
103R ASN* 3.9 20.2 - - - +
104R LYS* 3.9 29.5 - - + +
175S VAL 3.1 14.6 + - - +
176S GLU* 3.8 9.0 - - - +
177S ALA 3.3 0.2 - - - -
178S ILE* 1.3 76.3 - - - +
180S ARG* 1.3 64.3 + - - +
182S SER* 3.3 5.6 + - - -
183S GLU* 2.9 52.0 + - - +
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Residues in contact with ARG 180 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83S PHE* 3.7 26.7 - - - -
87S SER* 5.3 1.8 + - - -
90S GLU* 4.7 11.9 + - - -
176S GLU 3.0 17.4 + - - +
177S ALA* 3.5 9.9 - - - +
178S ILE 3.3 0.2 - - - -
179S LYS* 1.3 77.5 - - - +
181S ILE* 1.3 65.5 + - - +
183S GLU* 3.3 17.9 + - - +
184S TYR* 3.0 55.8 + - + +
204S LEU* 5.5 0.4 - - - +
207S GLU* 4.2 6.9 + - - -
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Residues in contact with ILE 181 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63S TYR* 5.5 2.2 - - - +
83S PHE* 3.3 36.8 - - + -
133S MET* 3.5 30.7 - - - +
136S ALA* 4.2 7.9 - - + -
137S LEU* 3.5 23.8 - - + +
140S GLU* 4.4 16.8 - - + +
177S ALA* 3.1 19.5 + - + +
178S ILE* 4.1 2.9 - - - +
180S ARG* 1.3 77.1 - - + +
182S SER* 1.3 66.8 + - - +
184S TYR* 3.1 15.3 + - + +
185S VAL* 3.0 20.7 + - - +
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Residues in contact with SER 182 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73N ASP* 3.5 29.2 - - - -
36R LEU* 3.5 14.9 - - - +
37R ALA* 3.3 22.6 + - - -
137S LEU* 3.4 20.6 - - - +
178S ILE 2.8 23.3 + - - -
179S LYS 3.5 4.7 - - - -
181S ILE* 1.3 76.5 - - - +
183S GLU* 1.3 57.3 + - - +
185S VAL* 3.3 2.5 + - - -
186S ALA* 3.0 25.1 + - - +
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Residues in contact with GLU 183 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71N ASP* 4.6 2.8 - - - +
72N ARG 5.2 0.7 - - - +
73N ASP* 3.7 24.0 - - + +
76N ALA* 3.9 11.9 - - + +
78N ARG* 4.6 21.8 - - - +
179S LYS* 2.9 50.4 + - - +
180S ARG* 3.4 16.3 - - - +
182S SER* 1.3 78.1 - - - +
184S TYR* 1.3 58.5 + - + +
186S ALA* 3.3 2.3 + - - +
187S GLN* 3.0 45.5 + - - +
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Residues in contact with TYR 184 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78N ARG* 6.0 0.4 - - - -
83S PHE* 3.7 23.1 - + - -
133S MET* 3.5 31.0 - - + -
180S ARG* 3.0 44.6 + - + +
181S ILE* 3.1 13.8 + - + +
183S GLU* 1.3 76.9 - - + +
185S VAL* 1.3 60.6 + - - +
187S GLN* 3.3 14.1 + - - +
188S LEU* 2.9 35.7 + - - +
200S PHE* 3.7 24.5 - + + -
203S MET* 4.8 0.7 - - + -
204S LEU* 3.4 18.3 - - + +
207S GLU* 2.5 36.7 + - - -
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Residues in contact with VAL 185 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28R VAL* 5.5 0.2 - - + -
36R LEU* 3.8 16.8 - - + -
130S LEU* 3.9 12.7 - - + +
133S MET* 3.7 34.5 - - + +
134S GLU* 4.0 14.4 - - + +
137S LEU* 4.4 13.5 - - + -
181S ILE 3.0 17.4 + - - +
182S SER* 3.5 7.4 - - - +
184S TYR* 1.3 76.1 - - - +
186S ALA* 1.3 63.7 + - - +
188S LEU* 3.3 3.8 + - - +
189S ARG* 2.9 49.5 + - - +
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Residues in contact with ALA 186 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73N ASP 3.4 25.6 - - - +
74N ASN* 3.8 20.9 - - - +
75N VAL 4.8 2.2 - - - +
76N ALA* 3.8 8.5 - - + -
36R LEU* 4.1 6.3 - - + +
182S SER 3.0 7.9 + - - +
183S GLU 3.6 5.8 - - - +
184S TYR 3.3 0.2 - - - -
185S VAL* 1.3 77.8 - - - +
187S GLN* 1.3 57.3 + - - +
189S ARG* 3.3 9.2 + - - +
190S ARG* 3.0 27.9 + - - +
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Residues in contact with GLN 187 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76N ALA* 3.9 19.8 - - + +
78N ARG* 2.9 37.8 + - - +
198N TRP* 2.9 35.6 + - + +
183S GLU* 3.0 36.0 + - - +
184S TYR* 3.8 19.0 - - - +
185S VAL 3.3 0.2 - - - -
186S ALA* 1.3 72.6 - - - +
188S LEU* 1.3 60.4 + - - +
190S ARG* 3.1 7.9 + - - +
191S VAL* 3.0 35.5 + - - +
200S PHE* 3.8 11.7 - - + -
203S MET* 3.7 6.9 - - - +
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Residues in contact with LEU 188 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80S LEU* 5.5 0.7 - - + -
129S ALA* 3.7 36.1 - - + +
130S LEU* 4.0 17.4 - - + +
133S MET* 3.5 34.5 - - + -
184S TYR 2.9 17.4 + - - +
185S VAL 3.7 3.6 - - - +
187S GLN* 1.3 77.2 - - - +
189S ARG* 1.3 62.6 + - - +
191S VAL* 3.6 4.0 - - + +
192S GLY* 3.3 21.8 + - - -
197S VAL* 4.0 20.5 - - + +
200S PHE* 3.5 38.4 - - + -
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Residues in contact with ARG 189 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28R VAL* 3.8 12.9 - - - +
29R PRO 3.0 30.5 + - - -
30R THR* 4.1 18.7 + - - +
31R VAL 5.6 1.4 + - - -
32R PRO* 6.2 0.8 - - - +
36R LEU* 3.6 14.2 - - - +
130S LEU* 3.9 20.9 - - + +
134S GLU* 2.8 32.3 + - - -
185S VAL* 2.9 30.9 + - - +
186S ALA* 3.6 8.5 - - - +
187S GLN 3.2 0.2 - - - -
188S LEU* 1.3 76.0 - - - +
190S ARG* 1.3 63.8 + - - +
192S GLY* 3.9 6.8 + - - -
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Residues in contact with ARG 190 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74N ASN 5.1 2.0 + - - -
75N VAL* 3.1 27.1 + - - +
76N ALA 5.4 0.4 + - - -
77N LEU* 3.6 27.5 - - - +
128N ASP* 3.1 38.6 + - - -
194N GLY* 3.3 46.8 - - - +
197N VAL* 3.8 11.4 - - - +
198N TRP* 4.1 18.2 - - + +
186S ALA 3.0 17.2 + - - +
187S GLN* 3.1 8.3 + - - +
189S ARG* 1.3 79.9 - - - +
191S VAL* 1.3 61.7 + - + +
192S GLY* 3.5 0.3 + - - -
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Residues in contact with VAL 191 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195N HIS* 3.7 22.4 + - + +
198N TRP* 3.5 49.6 - - + -
187S GLN 3.0 22.6 + - - +
188S LEU* 3.6 13.2 - - + +
190S ARG* 1.3 77.2 - - - +
192S GLY* 1.3 66.7 + - - +
193S LYS 4.8 0.5 - - - +
196S GLY* 3.4 41.0 + - - +
197S VAL* 3.8 4.7 - - - +
200S PHE* 4.4 6.1 - - + -
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Residues in contact with GLY 192 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188S LEU 3.3 11.3 + - - -
189S ARG 3.9 5.4 + - - -
190S ARG 3.4 3.0 - - - -
191S VAL* 1.3 82.4 - - - +
193S LYS* 1.3 67.0 + - - +
196S GLY* 3.6 0.3 - - - -
197S VAL* 3.1 28.4 + - - +
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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