Contacts of the helix formed by residues 170 - 192 (chain L) in PDB entry 3A9Q
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 L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56L GLU* 4.3 6.3 - - - -
94L HIS* 2.6 54.5 + + + -
97L LYS* 3.3 23.6 - - - +
98L LEU* 3.3 22.3 - - + +
147L LEU* 3.8 34.4 - - + +
165L PHE* 3.7 33.9 - + - -
166L VAL* 2.9 20.9 + - + +
168L THR 3.5 0.6 - - - -
169L GLU* 1.3 91.6 - - + +
171L LEU* 1.3 59.3 + - - +
172L GLY 3.4 2.2 - - - -
173L ALA* 3.4 5.9 + - - +
174L GLN* 2.9 31.2 + - - +
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Residues in contact with LEU 171 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144L ASN* 4.3 8.4 - - - +
147L LEU* 3.8 28.5 - - + -
148L LEU* 3.8 27.4 - - + -
151L HIS* 4.2 8.3 - - + -
166L VAL* 3.1 21.4 + - + +
167L GLU* 3.6 25.1 + - + +
170L TYR* 1.3 76.3 - - - +
172L GLY* 1.3 62.5 + - - +
174L GLN* 3.4 4.7 + - - +
175L VAL* 3.1 27.0 + - - +
160T VAL* 3.5 31.6 - - + -
161T GLN* 3.7 18.8 - - + +
164T ASP* 6.1 0.4 - - + -
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Residues in contact with GLY 172 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167L GLU 3.9 8.2 + - - -
168L THR 5.6 1.4 + - - -
170L TYR 3.4 0.2 - - - -
171L LEU* 1.3 74.1 - - - +
173L ALA* 1.3 66.0 + - - +
175L VAL* 3.1 5.8 + - - +
176L GLU* 3.0 27.5 + - - +
161T GLN* 3.6 22.0 - - - +
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Residues in contact with ALA 173 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94L HIS* 5.7 9.2 - - + +
168L THR 5.9 0.6 + - - -
169L GLU 4.3 13.8 + - - +
170L TYR* 3.4 8.8 + - - +
171L LEU 3.4 0.4 - - - -
172L GLY* 1.3 75.9 - - - +
174L GLN* 1.3 56.4 + - - +
176L GLU* 3.2 10.5 + - - +
177L ALA* 2.8 30.4 + - - +
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Residues in contact with GLN 174 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94L HIS* 6.0 0.2 - - - -
140L GLU* 2.7 51.6 + - - +
143L THR* 3.4 23.6 - - - +
144L ASN* 3.4 35.9 - - + +
147L LEU* 3.5 11.4 - - + +
170L TYR 2.9 17.9 + - - +
171L LEU* 3.6 5.8 - - - +
172L GLY 3.2 0.2 - - - -
173L ALA* 1.3 78.0 - - - +
175L VAL* 1.3 62.2 + - - +
177L ALA* 3.3 5.1 + - - +
178L ILE* 3.0 30.5 + - + +
214L CA 4.1 6.1 - - - -
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Residues in contact with VAL 175 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144L ASN* 5.3 10.5 - - - +
171L LEU 3.1 14.7 + - - +
172L GLY* 3.1 9.2 + - - +
174L GLN* 1.3 76.4 - - - +
176L GLU* 1.3 64.2 + - + +
178L ILE* 3.3 8.9 + - + +
179L LYS* 3.0 22.0 + - - +
101T TYR* 5.2 2.7 - - + -
104T LYS* 3.9 31.3 - - + +
105T ARG* 3.8 30.7 - - - +
161T GLN* 3.7 26.7 - - + +
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Residues in contact with GLU 176 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172L GLY 3.0 19.8 + - - +
173L ALA* 3.2 8.7 + - - +
175L VAL* 1.3 76.6 - - + +
177L ALA* 1.3 62.9 + - - +
179L LYS* 3.3 6.3 + - - +
180L ARG* 3.0 24.8 + - - +
104T LYS* 2.7 45.4 + - - +
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Residues in contact with ALA 177 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140L GLU* 4.0 22.2 - - - +
173L ALA 2.8 17.5 + - - +
174L GLN* 3.7 7.2 - - - +
175L VAL 3.3 0.2 - - - -
176L GLU* 1.3 76.3 - - - +
178L ILE* 1.3 63.0 + - - +
180L ARG* 3.3 10.5 + - - +
181L ILE* 3.0 34.3 + - + +
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Residues in contact with ILE 178 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137L LEU* 3.8 16.6 - - + +
140L GLU* 3.9 20.6 - - + +
141L LYS* 4.1 7.0 - - + +
144L ASN* 3.8 24.0 - - + +
174L GLN* 3.0 30.7 + - - +
175L VAL* 3.7 7.4 - - + +
176L GLU 3.3 0.2 - - - -
177L ALA* 1.3 77.5 - - - +
179L LYS* 1.3 62.1 + - - +
181L ILE 3.5 0.2 + - - -
182L SER* 2.8 28.9 + - - -
37T ALA* 3.5 34.5 - - + +
39T GLN* 3.6 23.6 - - + +
104T LYS 5.7 0.7 - - - +
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Residues in contact with LYS 179 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175L VAL 3.0 15.9 + - - +
176L GLU* 3.3 6.9 + - - +
178L ILE* 1.3 76.4 - - - +
180L ARG* 1.3 63.8 + - - +
182L SER* 3.3 1.4 + - - -
183L GLU* 2.9 53.6 + - - +
71P ASP* 2.9 47.6 + - - -
73P ASP* 3.9 18.4 - - + +
37T ALA* 4.2 8.5 - - + +
103T ASN* 3.8 22.1 - - - +
104T LYS* 4.0 30.6 - - + +
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Residues in contact with ARG 180 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83L PHE* 3.7 30.1 - - - -
86L GLU* 5.6 3.8 + - - -
87L SER* 5.5 0.8 + - - -
176L GLU 3.0 16.9 + - - +
177L ALA* 3.5 9.9 - - - +
179L LYS* 1.3 76.5 - - - +
181L ILE* 1.3 63.7 + - - +
183L GLU* 3.3 16.8 + - - +
184L TYR* 3.0 50.7 + - + +
207L GLU* 3.3 23.6 + - - +
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Residues in contact with ILE 181 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63L TYR* 4.3 7.6 - - - +
83L PHE* 4.2 24.5 - - + -
133L MET* 3.5 37.0 - - + +
136L ALA* 4.3 7.0 - - + +
137L LEU* 3.6 17.5 - - + +
140L GLU* 3.5 33.9 - - + -
177L ALA* 3.0 19.0 + - + +
178L ILE 4.2 2.0 - - - +
180L ARG* 1.3 78.4 - - + +
182L SER* 1.3 65.6 + - - +
184L TYR* 3.1 9.1 + - + +
185L VAL* 2.9 22.2 + - - +
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Residues in contact with SER 182 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137L LEU* 3.4 16.4 - - - +
178L ILE 2.8 24.0 + - - -
179L LYS 3.5 4.9 - - - -
181L ILE* 1.3 78.6 - - - +
183L GLU* 1.3 56.1 + - - +
185L VAL* 3.3 1.1 + - - -
186L ALA* 2.9 25.5 + - - +
73P ASP* 3.5 26.9 - - - -
36T LEU* 3.4 18.9 - - - +
37T ALA* 3.2 23.0 + - - -
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Residues in contact with GLU 183 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179L LYS* 2.9 50.2 + - - +
180L ARG* 3.4 16.1 - - - +
182L SER* 1.3 74.5 - - - +
184L TYR* 1.3 65.4 + - + +
186L ALA* 3.3 2.1 + - - +
187L GLN* 3.0 40.6 + - - +
71P ASP* 4.5 3.5 - - - +
72P ARG 5.1 0.5 - - - +
73P ASP* 3.7 24.2 - - + +
76P ALA* 3.9 11.7 - - + +
78P ARG* 4.7 20.4 - - - +
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Residues in contact with TYR 184 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83L PHE* 3.8 23.8 - + - -
133L MET* 3.5 34.8 - - + -
180L ARG* 3.0 43.6 + - + +
181L ILE* 3.1 12.4 + - - +
183L GLU* 1.3 77.5 - - + +
185L VAL* 1.3 62.2 + - - +
187L GLN* 3.3 12.3 + - - +
188L LEU* 3.0 28.8 + - - +
200L PHE* 3.7 25.3 - + + -
203L MET* 5.0 4.5 - - + -
204L LEU* 3.3 18.8 - - + +
207L GLU* 2.5 34.1 + - - -
78P ARG* 6.1 2.7 - - - -
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Residues in contact with VAL 185 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130L LEU* 3.9 8.0 - - + +
133L MET* 3.8 33.7 - - + +
134L GLU* 3.9 20.6 - - + +
137L LEU* 4.3 12.6 - - + -
181L ILE 2.9 18.0 + - - +
182L SER 3.5 7.6 - - - +
184L TYR* 1.3 75.0 - - - +
186L ALA* 1.3 64.6 + - - +
188L LEU* 3.3 2.7 + - - +
189L ARG* 3.0 49.7 + - - +
28T VAL* 5.3 0.2 - - + -
36T LEU* 3.7 16.8 - - + -
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Residues in contact with ALA 186 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182L SER 2.9 9.9 + - - +
183L GLU 3.6 4.3 - - - +
185L VAL* 1.3 78.8 - - - +
187L GLN* 1.3 56.6 + - - +
189L ARG* 3.3 9.1 + - - +
190L ARG* 3.0 27.3 + - - +
73P ASP 3.4 25.4 - - - +
74P ASN* 3.8 18.2 - - - +
75P VAL 4.8 1.8 - - - +
76P ALA* 3.7 11.0 - - + -
36T LEU* 4.2 7.0 - - + -
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Residues in contact with GLN 187 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183L GLU* 3.0 36.3 + - - +
184L TYR* 3.8 17.8 - - - +
186L ALA* 1.3 73.4 - - - +
188L LEU* 1.3 62.0 + - - +
190L ARG* 3.0 8.7 + - - +
191L VAL* 2.9 35.3 + - - +
200L PHE* 3.9 12.8 - - + -
203L MET* 3.6 7.3 - - - +
76P ALA* 3.9 20.1 - - + +
78P ARG* 2.9 37.4 + - - +
198P TRP* 2.8 33.7 + - + +
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Residues in contact with LEU 188 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80L LEU* 5.5 0.2 - - + -
129L ALA* 3.8 37.5 - - + +
130L LEU* 4.0 17.7 - - + +
133L MET* 3.9 19.1 - - + -
184L TYR 3.0 20.4 + - - +
185L VAL 3.7 3.8 - - - +
186L ALA 3.3 0.2 - - - -
187L GLN* 1.3 78.2 - - - +
189L ARG* 1.3 60.3 + - - +
191L VAL* 3.7 4.5 - - - +
192L GLY* 3.4 21.1 + - - -
197L VAL* 4.0 28.8 - - + +
200L PHE* 3.4 42.4 - - + -
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Residues in contact with ARG 189 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126L LYS* 4.9 2.6 - - - +
130L LEU* 4.0 20.5 - - + +
134L GLU* 2.9 28.1 + - - -
185L VAL* 3.0 29.8 + - - +
186L ALA* 3.6 10.5 - - - +
188L LEU* 1.3 76.8 - - - +
190L ARG* 1.3 64.1 + - - +
191L VAL 3.6 0.2 + - - -
192L GLY* 3.8 7.0 + - - -
28T VAL* 3.6 16.2 + - - +
29T PRO 3.0 28.9 + - - -
30T THR* 4.0 21.1 + - - +
31T VAL 5.4 1.8 + - - -
32T PRO* 5.9 1.8 - - - +
36T LEU* 3.6 13.6 - - - +
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Residues in contact with ARG 190 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186L ALA 3.0 14.6 + - - +
187L GLN* 3.0 11.9 + - - +
189L ARG* 1.3 79.4 - - - +
191L VAL* 1.3 61.6 + - + +
192L GLY 3.5 0.3 + - - -
74P ASN 5.1 1.6 + - - -
75P VAL* 3.2 27.1 + - - +
76P ALA 5.4 0.8 + - - -
77P LEU* 3.5 26.9 - - - +
128P ASP* 3.4 36.0 + - - -
194P GLY* 3.2 48.5 - - - +
195P HIS 3.6 0.2 + - - -
197P VAL* 3.9 11.5 - - - +
198P TRP* 4.0 19.3 - - + +
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Residues in contact with VAL 191 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187L GLN 2.9 21.4 + - - +
188L LEU* 3.7 11.9 - - + +
190L ARG* 1.3 76.3 - - - +
192L GLY* 1.3 66.0 + - - +
193L LYS 4.8 0.5 - - - +
196L GLY* 3.3 42.9 + - - +
197L VAL* 3.7 4.7 - - + +
200L PHE* 4.4 5.6 - - + -
195P HIS* 3.6 24.5 + - + +
198P TRP* 3.4 49.4 - - + -
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Residues in contact with GLY 192 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188L LEU 3.4 9.4 + - - -
189L ARG 3.8 5.1 + - - -
190L ARG 3.4 3.8 - - - -
191L VAL* 1.3 84.4 - - - +
193L LYS* 1.3 67.8 + - - +
196L GLY* 3.6 0.3 - - - -
197L 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