Contacts of the helix formed by residues 170 - 192 (chain P) 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 P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56P GLU* 4.2 10.1 - - - -
94P HIS* 2.7 54.5 + + + -
97P LYS* 3.4 21.5 - - + +
98P LEU* 3.2 21.4 + - + +
147P LEU* 3.8 32.9 - - + +
165P PHE* 3.7 30.7 - + - -
166P VAL* 3.0 23.1 + - + +
168P THR 3.5 0.4 - - - -
169P GLU* 1.3 92.4 - - + +
171P LEU* 1.3 59.9 + - - +
172P GLY 3.5 1.6 - - - -
173P GLU* 3.3 5.8 + - - +
174P GLN* 2.9 30.8 + - - +
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Residues in contact with LEU 171 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160K VAL* 3.4 33.7 - - + -
161K GLN* 3.7 19.4 - - + +
164K ASP* 5.5 0.9 - - - +
144P ASN* 4.3 9.8 - - - +
147P LEU* 3.8 29.4 - - + -
148P LEU* 3.9 23.6 - - + -
151P HIS* 4.4 5.8 - - + -
166P VAL* 3.2 19.9 + - + +
167P GLU* 3.4 23.4 + - + +
170P TYR* 1.3 76.1 - - - +
172P GLY* 1.3 63.2 + - - +
174P GLN* 3.3 4.7 + - - +
175P VAL* 3.1 26.2 + - - +
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Residues in contact with GLY 172 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161K GLN* 3.7 23.3 - - - +
164K ASP* 5.3 2.4 + - - -
167P GLU 3.8 5.3 + - - -
170P TYR 3.5 0.2 - - - -
171P LEU* 1.3 77.4 - - - +
173P GLU* 1.3 67.1 + - - +
175P VAL* 3.3 4.5 + - - +
176P GLU* 3.1 29.0 + - - +
215P CA 4.6 5.2 - - - -
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Residues in contact with GLU 173 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94P HIS* 5.9 8.7 - - + +
168P THR 3.5 3.1 - - - +
169P GLU* 3.2 31.6 - - - +
170P TYR* 3.5 9.5 + - - +
172P GLY* 1.3 76.9 + - - +
174P GLN* 1.3 56.6 + - - +
176P GLU* 3.3 11.2 + - - +
177P ALA* 2.9 28.3 + - - +
215P CA 2.6 29.2 - - - -
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Residues in contact with GLN 174 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94P HIS* 5.8 0.9 - - - -
140P GLU* 2.7 56.0 + - - +
143P THR* 3.5 18.1 - - - +
144P ASN* 3.3 39.3 - - + +
147P LEU* 3.6 10.5 - - + +
170P TYR* 2.9 17.6 + - - +
171P LEU* 3.6 6.1 - - - +
172P GLY 3.2 0.2 - - - -
173P GLU* 1.3 75.7 - - - +
175P VAL* 1.3 60.2 + - - +
177P ALA* 3.3 5.4 + - - +
178P ILE* 3.0 35.3 + - + +
214P CA 4.1 6.6 - - - -
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Residues in contact with VAL 175 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101K TYR* 5.2 2.7 - - + -
104K LYS* 3.9 31.4 - - + +
105K ARG* 3.8 28.9 - - - +
161K GLN* 3.6 29.4 - - + +
144P ASN* 5.2 11.4 - - - +
171P LEU 3.1 13.2 + - - +
172P GLY 3.6 8.7 - - - +
174P GLN* 1.3 76.6 - - - +
176P GLU* 1.3 62.1 + - + +
178P ILE* 3.4 8.1 + - + +
179P LYS* 3.0 22.2 + - - +
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Residues in contact with GLU 176 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104K LYS* 2.7 44.5 + - + +
172P GLY 3.1 19.4 + - - +
173P GLU* 3.5 11.0 - - - +
174P GLN 3.3 0.2 - - - -
175P VAL* 1.3 78.1 - - + +
177P ALA* 1.3 56.1 + - - +
179P LYS* 3.4 5.5 + - - +
180P ARG* 3.0 29.3 + - - +
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Residues in contact with ALA 177 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140P GLU* 4.2 21.8 - - + +
173P GLU 2.9 16.5 + - - +
174P GLN* 3.7 7.9 - - - +
175P VAL 3.3 0.2 - - - -
176P GLU* 1.3 75.8 - - - +
178P ILE* 1.3 59.3 + - - +
180P ARG* 3.3 11.6 + - - +
181P ILE* 3.0 37.5 + - + +
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Residues in contact with ILE 178 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37K ALA* 3.6 34.5 - - + +
39K GLN* 3.6 24.0 - - + +
104K LYS 5.7 0.7 - - - +
137P LEU* 3.9 16.6 - - + +
140P GLU* 3.9 35.9 - - + +
141P LYS* 4.1 7.0 - - + +
144P ASN* 3.9 15.0 - - + +
174P GLN* 3.0 22.2 + - - +
175P VAL* 3.7 7.9 - - + +
176P GLU 3.3 0.2 - - - -
177P ALA* 1.3 74.8 - - - +
179P LYS* 1.3 59.4 + - - +
181P ILE* 5.0 0.2 - - - -
182P SER* 2.7 34.0 + - - -
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Residues in contact with LYS 179 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37K ALA* 4.2 4.5 - - + -
100K GLU 5.3 0.4 + - - -
103K ASN* 3.7 18.5 - - - +
104K LYS* 3.9 36.3 - - + +
175P VAL 3.0 15.8 + - - +
176P GLU* 3.9 5.4 - - - +
178P ILE* 1.3 76.9 - - - +
180P ARG* 1.3 63.7 + - - +
182P SER* 3.3 4.7 + - - -
183P GLU* 3.0 51.8 + - - +
71W ASP* 2.9 48.0 + - - -
73W ASP* 3.9 17.9 - - + +
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Residues in contact with ARG 180 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83P PHE* 3.6 31.1 - - - -
86P GLU* 5.4 5.3 + - - -
87P SER* 5.5 0.6 + - - -
90P GLU* 4.8 14.8 + - - -
176P GLU 3.0 17.7 + - - +
177P ALA* 3.5 9.6 - - - +
178P ILE 3.2 0.2 - - - -
179P LYS* 1.3 78.7 - - - +
181P ILE* 1.3 62.9 + - - +
183P GLU* 3.3 15.2 + - - +
184P TYR* 2.9 55.1 + - + +
204P LEU* 5.3 1.2 - - - +
207P GLU* 4.2 6.5 + - - -
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Residues in contact with ILE 181 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63P TYR* 4.2 8.7 - - - +
83P PHE* 4.2 25.6 - - + -
133P MET* 3.4 32.8 - - - +
136P ALA* 4.2 9.9 - - + +
137P LEU* 3.6 18.6 - - + +
140P GLU* 3.5 35.2 - - + +
177P ALA* 3.0 18.2 + - + +
178P ILE 4.2 2.0 - - - +
180P ARG* 1.3 76.4 - - + +
182P SER* 1.3 66.1 + - - +
184P TYR* 3.0 9.1 + - + +
185P VAL* 3.0 21.1 + - - +
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Residues in contact with SER 182 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36K LEU* 3.4 19.0 - - - +
37K ALA* 3.3 22.4 + - - -
137P LEU* 3.4 16.4 - - - +
178P ILE 2.7 23.4 + - - -
179P LYS 3.6 4.5 - - - -
181P ILE* 1.3 78.1 - - - +
183P GLU* 1.3 56.9 - - - +
185P VAL* 3.3 1.8 + - - -
186P ALA* 3.0 24.9 + - - +
73W ASP* 3.5 28.2 - - - +
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Residues in contact with GLU 183 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179P LYS* 3.0 48.7 + - - +
180P ARG* 3.5 15.9 - - - +
181P ILE 3.2 0.2 - - - -
182P SER* 1.3 77.7 - - - +
184P TYR* 1.3 59.1 + - + +
186P ALA* 3.4 1.6 + - - +
187P GLN* 3.0 46.6 + - - +
71W ASP* 4.6 2.8 - - - +
72W ARG 5.2 0.5 - - - +
73W ASP* 3.7 24.9 - - + +
76W ALA* 4.0 12.1 - - + +
78W ARG* 4.9 18.9 - - - +
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Residues in contact with TYR 184 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83P PHE* 3.7 26.2 - + - -
133P MET* 3.4 32.8 - - + -
180P ARG* 2.9 47.4 + - + +
181P ILE* 3.0 12.6 + - - +
183P GLU* 1.3 73.9 - - + +
185P VAL* 1.3 60.9 + - - +
187P GLN* 3.4 11.4 + - - +
188P LEU* 2.9 35.8 + - - +
200P PHE* 3.7 25.7 - + + -
203P MET* 4.9 0.7 - - + -
204P LEU* 3.4 17.3 - - + +
207P GLU* 2.7 37.1 + - - -
78W ARG* 6.2 0.2 - - - -
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Residues in contact with VAL 185 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28K VAL* 5.3 0.2 - - + -
36K LEU* 3.7 17.9 - - + -
130P LEU* 3.9 12.7 - - + +
133P MET* 3.8 34.8 - - + +
134P GLU* 4.0 11.2 - - + +
137P LEU* 4.4 12.1 - - + -
181P ILE 3.0 16.9 + - - +
182P SER 3.3 7.6 + - - +
184P TYR* 1.3 75.7 - - - +
186P ALA* 1.3 62.9 + - - +
188P LEU* 3.3 3.0 + - - +
189P ARG* 3.0 52.4 + - - +
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Residues in contact with ALA 186 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36K LEU* 4.0 6.9 - - + +
182P SER 3.0 9.6 + - - +
183P GLU 3.7 4.0 - - - +
184P TYR 3.3 0.2 - - - -
185P VAL* 1.3 77.5 - - - +
187P GLN* 1.3 57.5 + - - +
189P ARG* 3.2 9.6 + - - +
190P ARG* 3.0 28.2 + - - +
73W ASP 3.4 25.1 - - - +
74W ASN* 3.7 21.8 - - - +
75W VAL 4.8 1.8 - - - +
76W ALA* 3.9 8.1 - - + -
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Residues in contact with GLN 187 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183P GLU* 3.0 38.5 + - - +
184P TYR* 4.0 14.3 - - - +
186P ALA* 1.3 75.0 - - - +
188P LEU* 1.3 63.7 + - - +
190P ARG* 3.1 8.2 + - - +
191P VAL* 3.0 30.4 + - - +
200P PHE* 3.8 16.2 - - + -
203P MET* 3.7 6.4 - - - +
76W ALA* 3.9 22.5 - - + +
78W ARG* 2.9 34.6 + - - +
198W TRP* 2.9 33.3 + - + +
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Residues in contact with LEU 188 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80P LEU* 5.5 0.7 - - + -
129P ALA* 3.8 36.1 - - + +
130P LEU* 4.0 17.4 - - + +
133P MET* 3.6 32.5 - - + -
184P TYR 2.9 20.8 + - - +
185P VAL* 3.7 4.3 - - - +
187P GLN* 1.3 76.4 - - - +
189P ARG* 1.3 62.6 + - - +
191P VAL* 3.6 4.6 - - - +
192P GLY* 3.2 22.3 + - - -
197P VAL* 4.1 20.7 - - + +
200P PHE* 3.6 37.4 - - + -
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Residues in contact with ARG 189 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28K VAL* 3.7 14.5 + - - +
29K PRO 3.0 28.7 + - - -
30K THR* 4.0 22.8 + - - +
31K VAL 5.3 3.4 + - - -
32K PRO* 5.7 2.4 - - - +
36K LEU* 3.5 15.3 - - - +
130P LEU* 3.9 19.2 - - + +
134P GLU* 2.8 28.5 + - - -
185P VAL* 3.0 30.0 + - - +
186P ALA* 3.6 10.5 - - - +
188P LEU* 1.3 78.1 - - - +
190P ARG* 1.3 62.9 + - - +
192P GLY* 3.8 7.4 + - - -
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Residues in contact with ARG 190 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186P ALA 3.0 13.3 + - - +
187P GLN* 3.1 10.8 + - - +
189P ARG* 1.3 80.1 - - - +
191P VAL* 1.3 60.7 + - + +
192P GLY* 3.6 0.3 + - - -
74W ASN 5.0 1.2 + - - -
75W VAL* 3.0 29.7 + - - +
76W ALA 5.2 0.8 + - - -
77W LEU* 3.5 26.8 - - - +
128W ASP* 3.2 38.4 + - - -
194W GLY* 3.3 46.6 - - - +
197W VAL* 3.9 10.1 - - - +
198W TRP* 4.0 19.5 - - + +
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Residues in contact with VAL 191 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187P GLN 3.0 19.6 + - - +
188P LEU* 3.6 11.7 - - + +
190P ARG* 1.3 77.2 - - - +
192P GLY* 1.3 65.3 + - - +
193P LYS 4.9 0.5 - - - +
196P GLY* 3.4 42.1 + - - +
197P VAL* 3.8 4.7 - - - +
200P PHE* 4.4 5.8 - - + -
195W HIS* 3.7 23.0 + - + +
198W TRP* 3.5 49.6 - - + -
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Residues in contact with GLY 192 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188P LEU 3.2 13.9 + - - -
189P ARG 3.8 6.0 + - - -
190P ARG 3.4 2.8 - - - -
191P VAL* 1.3 84.9 - - - +
193P LYS* 1.3 66.5 + - - +
196P GLY* 3.6 0.3 - - - -
197P VAL* 3.1 24.1 + - - +
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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