Contacts of the helix formed by residues 174 - 192 (chain A) in PDB entry 1BQ2
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 LEU 174 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A TYR* 4.0 13.7 - - + -
7A LEU* 3.7 29.4 - - + -
34A MET* 4.0 12.6 - - + -
168A CYS* 3.6 21.5 - - - -
169A ASP 2.9 9.1 + - - -
170A VAL* 3.5 15.5 - - + +
173A GLY* 1.3 73.4 - - - +
175A PRO* 1.4 64.5 - - + +
177A ALA* 3.0 16.4 + - + +
178A ILE* 3.2 30.1 + - + +
201A TRP* 3.4 37.9 - - + +
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Residues in contact with PRO 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET* 6.1 0.2 - - + -
4A TYR* 3.7 10.3 - - + +
43A PRO 5.0 2.5 - - - +
44A LEU* 5.3 2.3 - - - +
45A VAL* 3.7 23.0 + - + +
48A LYS* 3.8 16.4 - - - +
50A CYS* 3.7 24.7 - - - -
55A ILE* 5.6 0.7 - - - -
170A VAL 3.6 7.0 - - - +
171A PHE 3.4 18.4 - - - +
172A LEU 3.4 15.3 - - - +
174A LEU* 1.4 86.2 - - + +
176A PHE* 1.3 59.7 + - + +
178A ILE* 3.5 10.0 + - + +
179A ALA* 3.2 24.0 + - - +
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Residues in contact with PHE 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A CYS* 5.5 0.4 - - - -
51A HIS 5.0 2.9 - - - -
54A SER* 4.1 11.0 - - - -
55A ILE* 3.5 48.8 - - + +
58A GLU* 3.3 25.6 - - - -
79A ILE* 3.6 30.7 - - + -
147A HIS* 6.3 1.1 - - - -
172A LEU 4.4 6.7 - - - +
173A GLY* 3.5 13.2 + - - +
174A LEU 3.1 0.2 - - - -
175A PRO* 1.3 77.9 - - - +
177A ALA* 1.3 64.4 + - - +
179A ALA* 4.1 0.3 - - - +
180A SER* 3.0 30.1 + - - -
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Residues in contact with ALA 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A HIS* 3.7 20.9 - - + +
163A LEU* 4.8 4.9 - - + -
165A GLN* 3.2 28.5 - - - +
173A GLY 3.2 10.6 + - - +
174A LEU* 3.0 13.8 + - + +
176A PHE* 1.3 76.5 - - - +
178A ILE* 1.3 65.0 + - - +
180A SER* 3.4 3.8 + - - -
181A TYR* 3.1 30.2 + - - +
199A PHE* 5.3 1.3 - - - -
201A TRP* 4.8 1.6 - - - +
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Residues in contact with ILE 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET* 4.0 13.9 - - + -
4A TYR* 4.8 5.8 - - + -
34A MET* 4.1 12.8 - - + -
36A PHE* 3.7 30.5 - - + -
43A PRO* 3.7 32.3 - - + +
174A LEU* 3.2 31.1 + - + +
175A PRO* 3.9 7.4 - - + +
177A ALA* 1.3 76.6 - - - +
179A ALA* 1.3 56.7 + - - +
181A TYR* 4.0 0.5 - - - +
182A ALA* 2.9 32.8 + - + +
199A PHE* 3.9 29.9 - - + -
201A TRP* 4.9 2.5 - - + -
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Residues in contact with ALA 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A PHE* 3.8 16.0 - - + -
43A PRO 4.7 5.3 + - - +
44A LEU* 4.2 13.7 - - + -
52A LEU* 4.2 12.3 - - + -
55A ILE* 3.8 26.6 - - + +
175A PRO 3.2 17.1 + - - +
176A PHE 4.1 0.2 - - - +
178A ILE* 1.3 75.7 - - - +
180A SER* 1.3 62.8 + - - +
182A ALA* 4.4 1.6 - - - -
183A LEU* 3.1 24.1 + - - +
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Residues in contact with SER 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A ILE* 3.7 18.8 + - - +
58A GLU* 4.3 10.8 + - - -
59A LEU* 3.7 25.3 - - - +
62A PHE* 5.0 6.2 - - - -
176A PHE* 3.0 25.7 + - - -
177A ALA* 3.7 5.4 - - - -
179A ALA* 1.3 79.1 - - - +
181A TYR* 1.3 71.3 + - - +
183A LEU* 3.3 11.2 + - - +
184A LEU* 3.3 8.8 + - - +
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Residues in contact with TYR 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A LEU* 6.3 0.7 - - + -
62A PHE* 5.4 3.4 - + - -
94A TYR* 4.7 2.8 - - - -
98A TRP* 3.2 25.5 - + - -
147A HIS* 3.9 30.4 + + + +
150A PHE* 3.6 41.8 - + - -
161A CYS* 4.9 7.2 - - - -
163A LEU* 3.5 33.7 - - + -
177A ALA* 3.1 18.8 + - - +
180A SER* 1.3 80.5 - - - +
182A ALA* 1.3 66.6 + - - +
184A LEU* 3.0 22.6 + - + +
185A VAL* 3.0 27.0 + - - +
199A PHE* 3.6 24.9 - + + -
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Residues in contact with ALA 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A LEU* 4.2 23.7 - - + +
42A PHE* 4.2 13.0 - - + -
43A PRO* 4.2 9.2 - - + -
178A ILE* 2.9 21.7 + - + +
179A ALA* 4.0 3.6 - - - +
181A TYR* 1.3 77.9 - - - +
183A LEU* 1.3 61.1 + - - +
185A VAL* 3.3 16.8 + - - +
186A HIS* 3.1 22.8 + - - -
199A PHE* 4.8 8.2 - - + -
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Residues in contact with LEU 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A PHE* 4.1 11.0 - - + -
52A LEU* 5.9 2.2 - - + -
55A ILE* 4.9 5.8 - - + -
56A ILE* 4.3 32.3 - - + -
59A LEU* 3.5 22.4 - - + -
60A LEU* 6.1 0.9 - - + -
179A ALA 3.1 19.5 + - - +
180A SER 3.4 5.2 - - - +
181A TYR 3.1 0.2 - - - -
182A ALA* 1.3 77.4 - - - +
184A LEU* 1.3 56.4 + - - +
186A HIS* 3.1 8.3 + - - +
187A MET* 3.0 28.3 + - - +
230A LEU* 4.1 24.2 - - + -
247A PHE* 3.7 39.5 - - + -
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Residues in contact with LEU 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A LEU* 4.0 22.4 - - + +
63A LEU* 4.5 20.0 - - + -
98A TRP* 4.1 19.1 - - + -
112A ILE* 5.6 1.6 - - + -
150A PHE* 4.1 26.2 - - + -
152A PHE* 4.8 4.0 - - + -
180A SER 3.3 9.1 + - - +
181A TYR* 3.0 23.9 + - + +
183A LEU* 1.3 76.4 - - - +
185A VAL* 1.3 58.8 + - + +
187A MET* 3.3 11.8 + - - -
188A MET* 2.9 55.9 + - + +
239A ILE* 4.8 3.6 - - + -
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Residues in contact with VAL 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A LEU* 3.6 25.8 - - + -
152A PHE* 4.7 4.0 - - + -
159A LEU* 3.8 31.5 - - + +
160A SER* 5.0 0.9 - - - -
161A CYS* 3.7 31.2 - - + +
181A TYR 3.0 16.9 + - - +
182A ALA* 3.3 10.7 + - - +
184A LEU* 1.3 74.7 - - + +
186A HIS* 1.3 58.0 + - - +
188A MET* 3.7 6.0 - - - +
189A ALA* 2.9 32.2 + - - +
196A VAL* 4.3 6.7 - - + -
198A ASP 5.1 0.2 - - - +
199A PHE* 4.6 5.6 - - + -
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Residues in contact with HIS 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A LEU* 4.2 22.5 + - + +
42A PHE* 4.3 23.3 - + - -
182A ALA* 3.1 25.3 + - + -
183A LEU* 3.1 9.1 + - + +
185A VAL* 1.3 79.8 - - - +
187A MET* 1.3 63.7 + - - +
189A ALA* 3.5 1.7 - - - +
190A GLN* 3.0 23.2 + - - +
196A VAL* 3.4 36.6 - - + +
230A LEU* 4.2 25.5 + - + +
232A ILE* 4.2 18.6 - - + +
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Residues in contact with MET 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A LEU* 3.9 26.7 - - - -
60A LEU* 3.7 18.2 - - + -
63A LEU* 3.9 20.0 - - + -
183A LEU* 3.0 17.6 + - - +
184A LEU* 3.3 8.7 + - - +
186A HIS* 1.3 72.8 - - + +
188A MET* 1.4 62.2 + - - +
190A GLN* 3.1 7.0 + - - +
191A GLN* 3.0 25.1 + - - +
232A ILE* 4.6 2.9 - - + +
239A ILE* 3.7 15.0 - - + +
242A TYR* 3.5 53.4 - - + -
247A PHE* 4.0 26.0 - - + -
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Residues in contact with MET 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A ILE* 3.9 34.3 - - + +
115A VAL* 4.1 22.2 - - + -
116A LEU* 3.9 22.4 - - + -
119A LEU* 4.8 5.4 - - + -
150A PHE* 6.1 0.2 - - + -
152A PHE* 3.8 26.0 - - + -
159A LEU* 3.8 15.9 - - + -
184A LEU* 2.9 36.2 + - + +
185A VAL* 3.7 4.7 - - - +
187A MET* 1.4 69.1 - - - +
189A ALA* 1.3 58.5 + - - +
191A GLN* 2.9 21.0 + - - +
192A CYS* 3.0 17.8 + - - -
239A ILE* 3.8 15.2 - - + +
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Residues in contact with ALA 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A LEU* 3.7 14.3 - - + +
185A VAL 2.9 22.7 + - - +
186A HIS 3.5 4.5 - - - +
188A MET* 1.3 70.9 - - - +
190A GLN* 1.3 63.8 + - - +
192A CYS* 3.1 2.4 + - - -
193A ASP* 3.0 5.0 + - - -
194A LEU* 2.9 49.0 + - - +
195A GLU 4.4 2.5 - - - +
196A VAL* 3.8 19.5 - - + -
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Residues in contact with GLN 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A HIS 3.0 13.1 + - - +
187A MET 3.3 8.3 - - - +
189A ALA* 1.3 74.6 - - - +
191A GLN* 1.3 63.6 + - - +
192A CYS 3.2 0.5 + - - -
193A ASP* 3.4 8.5 + - - +
194A LEU 5.0 0.4 - - - -
232A ILE* 3.4 32.5 - - + +
234A ARG 3.3 17.1 + - - +
235A LYS* 3.2 47.2 + - + +
242A TYR* 2.6 41.6 + - - +
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Residues in contact with GLN 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A LEU* 4.2 18.2 - - + +
120A LYS* 3.7 16.6 + - - +
187A MET 3.0 13.7 + - - +
188A MET* 2.9 11.0 + - - +
190A GLN* 1.3 77.3 - - - +
192A CYS* 1.3 60.6 + - - +
193A ASP* 3.9 1.7 + - - +
235A LYS* 4.1 17.9 + - - +
236A PRO* 3.2 25.3 + - - +
237A GLU 4.3 1.9 - - - +
238A SER* 3.2 10.5 - - - -
239A ILE* 3.1 37.0 + - + +
242A TYR* 3.0 26.3 + - - +
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Residues in contact with CYS 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A LEU* 3.2 34.3 - - - -
119A LEU* 4.2 23.1 - - + +
120A LYS* 4.3 18.4 - - + +
188A MET 3.0 14.3 + - - +
189A ALA 3.1 0.8 + - - +
191A GLN* 1.3 79.9 - - - +
193A ASP* 1.3 70.3 + - - +
194A LEU* 3.2 28.7 + - + +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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