Contacts of the helix formed by residues 149 - 166 (chain V) in PDB entry 5A0Q
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 LYS 149 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8V PHE 5.5 0.2 - - - +
9V ASP* 2.7 47.1 + - + +
10V GLY* 4.2 11.4 - - - +
11V GLY 5.0 8.3 - - - +
13V VAL* 5.4 8.1 - - + +
148V THR* 1.3 78.1 + - - +
150V GLU* 1.3 63.3 + - + +
152V CYS* 2.9 35.5 - - - -
153V LEU* 4.2 2.3 + - - +
180V ALA* 5.4 7.2 - - - -
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Residues in contact with GLU 150 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148V THR* 3.2 9.7 + - + +
149V LYS* 1.3 82.4 - - + +
151V GLU* 1.4 73.1 + - - +
152V CYS 3.4 0.7 + - - -
153V LEU* 3.4 26.3 + - - +
154V GLN* 3.9 9.0 + - - +
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Residues in contact with GLU 151 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147V MET* 3.7 35.9 - - + +
148V THR* 3.1 48.2 + - + +
150V GLU* 1.4 84.3 - - - +
152V CYS* 1.4 57.1 + - - +
154V GLN* 3.3 10.1 + - - +
155V PHE* 3.0 28.0 + - - +
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Residues in contact with CYS 152 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6V VAL* 3.7 25.6 - - + -
7V GLN 5.2 1.6 - - - +
8V PHE* 5.0 14.8 - - + -
13V VAL* 3.8 28.7 - - + +
147V MET* 6.4 0.2 - - - -
148V THR 4.1 2.1 + - - +
149V LYS* 2.9 34.1 - - - -
151V GLU* 1.4 75.5 - - - +
153V LEU* 1.3 60.2 + - - +
155V PHE* 3.8 10.5 - - + -
156V THR* 2.9 34.2 + - - +
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Residues in contact with LEU 153 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13V VAL* 4.2 9.9 - - + -
149V LYS 5.0 2.5 - - - +
150V GLU* 3.4 21.0 + - - +
151V GLU 3.2 0.4 - - - -
152V CYS* 1.3 80.3 - - - +
154V GLN* 1.4 82.8 + - - +
156V THR* 3.4 5.8 + - - -
157V ALA* 3.1 33.9 + - + +
176V LEU* 4.3 15.2 - - + +
187V GLN* 4.2 29.6 - - - +
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Residues in contact with GLN 154 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150V GLU 4.1 11.4 - - - +
151V GLU* 3.3 9.1 + - - +
153V LEU* 1.4 102.7 - - - +
155V PHE* 1.3 57.0 + - - +
157V ALA* 4.6 2.2 - - - +
158V ASN* 2.9 51.6 + - - +
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Residues in contact with PHE 155 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4V MET* 3.9 2.7 - - + -
6V VAL* 3.6 32.1 - - + -
138V TYR* 3.6 36.1 - + - -
139V VAL* 3.8 37.9 - - + -
142V THR* 3.6 32.5 - - + -
143V TYR* 4.1 18.6 - + - -
147V MET* 5.9 4.7 - - - -
151V GLU* 3.0 18.6 + - + +
152V CYS* 3.7 12.3 - - + +
153V LEU 3.3 0.2 - - - -
154V GLN* 1.3 73.5 - - - +
156V THR* 1.3 60.2 + - + +
159V ALA* 2.9 29.3 + - - +
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Residues in contact with THR 156 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4V MET* 4.2 21.8 - - + +
6V VAL* 3.6 37.2 - - + -
13V VAL* 3.6 10.7 - - + +
14V LEU* 4.6 0.2 - - - -
15V GLY 5.1 2.7 - - - -
152V CYS 2.9 21.0 + - - +
153V LEU 3.4 0.5 + - - -
155V PHE* 1.3 75.7 - - + +
157V ALA* 1.4 62.1 + - - +
159V ALA* 3.5 5.6 - - - +
160V LEU* 3.1 33.3 + - - +
176V LEU* 3.1 28.0 - - - +
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Residues in contact with ALA 157 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153V LEU* 3.1 22.6 + - + +
154V GLN* 4.1 4.5 - - - +
156V THR* 1.4 78.6 + - - +
158V ASN* 1.4 63.7 + - - +
161V ALA* 3.9 5.4 + - - +
174V ILE* 3.6 36.6 - - + +
176V LEU* 4.9 2.2 - - + -
187V GLN* 4.3 19.1 - - - +
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Residues in contact with ASN 158 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138V TYR* 3.9 17.4 + - + +
154V GLN* 2.9 35.4 + - - +
157V ALA* 1.4 80.1 - - - +
159V ALA* 1.3 66.8 + - - +
160V LEU 3.3 0.2 - - - -
161V ALA* 3.6 6.5 + - - +
162V LEU* 3.3 28.3 + - + +
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Residues in contact with ALA 159 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4V MET* 4.3 15.7 - - + -
135V ILE* 3.9 19.5 - - + +
138V TYR* 3.6 27.1 - - + -
155V PHE* 2.9 20.8 + - + +
156V THR* 3.2 8.5 + - - +
158V ASN* 1.3 79.3 - - - +
160V LEU* 1.3 64.0 + - - +
162V LEU* 3.4 5.8 + - - +
163V ALA* 3.3 17.3 + - - +
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Residues in contact with LEU 160 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2V THR* 3.6 25.4 - - + -
4V MET* 2.8 36.8 - - + +
15V GLY* 3.8 9.9 - - - +
16V ALA* 3.8 27.4 - - - +
17V ASP* 5.5 0.9 - - + +
135V ILE* 4.2 1.3 - - + -
156V THR* 3.1 18.6 + - - +
159V ALA* 1.3 81.8 - - - +
161V ALA* 1.3 57.3 + - - +
163V ALA* 3.0 8.7 + - - +
164V MET* 2.9 33.3 + - - +
174V ILE* 3.7 38.4 - - + -
176V LEU* 6.1 0.9 - - + -
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Residues in contact with ALA 161 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157V ALA 3.9 6.6 + - - +
158V ASN* 3.6 10.3 + - - +
159V ALA 3.3 0.6 - - - -
160V LEU* 1.3 79.8 - - - +
162V LEU* 1.3 61.9 + - + +
164V MET* 3.2 12.5 + - + +
165V GLU* 3.2 24.9 + - - +
174V ILE* 3.6 20.0 - - + +
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Residues in contact with LEU 162 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136H TYR* 5.8 1.0 - - - +
137H GLY* 4.0 20.6 + - - +
140H ASP* 4.8 12.8 - - + +
141H ALA* 3.9 28.3 - - + +
134V TYR* 5.0 2.3 - - - +
135V ILE* 6.3 1.3 - - - -
138V TYR* 3.7 37.5 - - + -
158V ASN* 3.3 19.7 - - + +
159V ALA 3.6 5.2 - - - +
160V LEU 3.3 0.2 - - - -
161V ALA* 1.3 73.7 - - + +
163V ALA* 1.3 64.7 + - - +
164V MET 3.6 0.2 + - - -
165V GLU* 3.7 17.2 + - + +
166V ARG* 4.1 10.6 + - - +
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Residues in contact with ALA 163 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2V THR* 3.8 13.2 - - + +
131V GLY 4.0 7.0 - - - +
134V TYR* 3.6 14.9 - - - -
135V ILE* 3.3 40.4 - - + +
159V ALA 3.3 2.0 + - - -
160V LEU 3.0 12.9 + - - +
162V LEU* 1.3 80.6 - - - +
164V MET* 1.4 57.1 + - - +
165V GLU 3.5 0.2 + - - -
166V ARG 3.6 0.9 + - - -
167V ASP* 3.1 28.1 + - - +
170V SER* 4.5 0.2 - - - -
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Residues in contact with MET 164 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2V THR* 4.5 2.5 - - - +
17V ASP* 3.8 10.5 - - + -
160V LEU* 2.9 17.4 + - + +
161V ALA* 3.2 12.5 + - + +
163V ALA* 1.4 73.9 - - - +
165V GLU* 1.3 60.1 + - - +
166V ARG 3.2 1.1 - - - -
167V ASP 2.8 22.1 - - - +
170V SER* 3.4 31.1 - - - +
171V GLY* 3.3 38.4 - - - +
172V GLY 4.0 6.5 - - - +
174V ILE* 3.7 35.0 - - + -
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Residues in contact with GLU 165 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140H ASP* 6.4 2.0 - - + -
27N LEU* 6.0 0.2 - - - +
34N ALA* 4.4 2.9 - - - +
37N ARG* 3.3 54.9 + - - +
184N TYR* 4.0 38.2 + - - -
161V ALA 3.2 12.5 + - - +
162V LEU* 3.7 15.5 - - + +
163V ALA 3.3 0.8 - - - -
164V MET* 1.3 76.8 - - - +
166V ARG* 1.3 63.0 + - + +
167V ASP 4.8 0.3 - - - +
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Residues in contact with ARG 166 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123H GLN* 6.0 1.4 - - - +
125H PHE* 4.3 14.8 - - - -
136H TYR* 3.5 46.5 - - + -
139H VAL* 6.0 0.2 - - - +
140H ASP* 3.4 29.1 + - - +
33N LEU* 3.6 16.2 - - + -
34N ALA* 2.9 48.7 + - - +
35N ARG* 3.0 29.1 + - - +
37N ARG* 3.6 26.0 - - - +
134V TYR* 3.8 22.2 - - + -
162V LEU 4.1 8.9 + - - +
163V ALA 3.6 2.4 + - - +
165V GLU* 1.3 80.7 - - + +
167V ASP* 1.3 61.3 + - - +
168V GLY 3.6 0.9 + - - -
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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