Contacts of the helix formed by residues 163 - 174 (chain b) 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 THR 163 (chain b).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161b SER* 3.1 6.7 + - - -
162b GLN* 1.3 88.1 + - - +
164b GLU* 1.3 65.1 + - + +
166b ARG* 3.3 16.4 + - - +
167b ASP* 3.0 49.3 + - - +
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Residues in contact with GLU 164 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153b VAL* 4.4 8.5 - - + +
157b GLN* 2.8 45.9 + - - +
160b LEU* 3.7 21.3 - - + +
161b SER* 3.0 34.5 + - - +
163b THR* 1.3 78.6 - - + +
165b ALA* 1.3 57.6 + - - +
167b ASP* 3.6 3.2 + - - +
168b LEU* 3.0 27.9 + - - +
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Residues in contact with ALA 165 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14b VAL* 4.0 13.5 - - + -
15b LYS 3.1 22.2 - - - +
16b PHE* 2.1 44.2 - - + -
160b LEU* 4.1 13.8 - - + +
161b SER 3.4 0.8 + - - -
164b GLU* 1.3 74.1 - - - +
166b ARG* 1.4 52.2 + - - +
168b LEU* 3.4 7.7 - - - +
169b VAL* 3.1 32.2 + - - +
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Residues in contact with ARG 166 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16b PHE* 1.7 31.9 - - + -
21b VAL* 4.4 9.8 - - + +
162b GLN* 3.0 59.4 + - - +
163b THR* 3.3 22.5 + - - +
165b ALA* 1.4 65.6 - - - +
167b ASP* 1.3 65.2 + - - +
169b VAL* 3.4 2.9 + - - +
170b GLU* 3.0 50.4 + - + +
189b ILE* 6.2 0.3 - - - +
191b THR* 5.8 5.8 - - - +
200b GLU* 5.1 8.5 + - - -
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Residues in contact with ASP 167 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163b THR* 3.0 38.0 + - - +
164b GLU* 4.2 2.4 - - - +
166b ARG* 1.3 81.6 - - - +
168b LEU* 1.3 63.5 + - - +
170b GLU* 3.1 22.7 - - - +
171b ARG* 3.1 32.9 + - + +
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Residues in contact with LEU 168 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14b VAL* 5.4 0.7 - - + -
149b LEU* 3.9 16.4 - - + +
150b LEU* 3.6 41.5 - - + +
153b VAL* 3.7 35.9 - - + -
160b LEU* 4.1 20.0 - - + -
164b GLU 3.0 18.3 + - - +
165b ALA* 3.4 7.9 - - - +
166b ARG 3.2 0.2 - - - -
167b ASP* 1.3 76.6 - - - +
169b VAL* 1.4 54.1 + - + +
171b ARG* 3.4 4.2 + - - +
172b CYS* 2.8 46.1 + - + +
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Residues in contact with VAL 169 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12b LEU* 4.4 16.6 - - + -
13b GLY 5.4 0.2 - - - -
14b VAL* 3.4 26.9 - - + +
21b VAL* 3.5 19.7 - - + -
23b ALA* 3.3 35.4 - - + +
150b LEU* 5.1 3.4 - - + -
165b ALA 3.1 16.4 + - - +
166b ARG 3.9 2.5 - - - +
168b LEU* 1.4 73.6 - - + +
170b GLU* 1.3 64.4 + - + +
172b CYS* 4.1 5.6 - - - -
173b MET* 3.0 28.8 + - + +
187b PHE* 6.0 0.2 - - + -
189b ILE* 5.2 4.5 - - + -
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Residues in contact with GLU 170 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166b ARG* 3.0 44.6 + - - +
167b ASP* 3.1 23.2 + - - +
169b VAL* 1.3 75.9 - - + +
171b ARG* 1.3 61.1 + - + +
174b ARG* 4.1 12.0 + - - +
187b PHE* 4.3 16.6 - - + -
189b ILE* 4.2 25.0 - - + +
200b GLU* 5.6 2.3 - - - +
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Residues in contact with ARG 171 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140I ASP* 3.2 49.7 + - - +
141I LYS* 4.7 11.3 - - - +
167b ASP* 3.1 22.9 + - + +
168b LEU* 3.9 3.4 - - - +
170b GLU* 1.3 78.9 - - + +
172b CYS* 1.3 58.3 + - - +
173b MET 3.2 0.4 - - - -
174b ARG* 3.0 43.2 + - - +
175b VAL* 3.1 14.4 + - - +
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Residues in contact with CYS 172 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12b LEU* 4.1 11.6 - - + +
145b LEU* 5.1 2.0 - - - +
146b ALA* 3.4 46.8 - - - +
149b LEU* 4.0 17.9 - - + -
150b LEU* 5.1 0.9 - - - -
168b LEU* 2.8 30.4 + - + +
169b VAL* 3.3 6.7 + - - +
171b ARG* 1.3 76.0 - - - +
173b MET* 1.3 61.9 + - - +
175b VAL* 3.1 26.9 + - - +
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Residues in contact with MET 173 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10b SER* 4.0 14.8 - - - +
12b LEU* 3.6 29.6 - - + -
23b ALA* 4.0 20.0 - - + +
24b ALA 4.1 0.9 - - - -
25b ASP* 3.6 36.6 - - + +
169b VAL* 3.0 22.7 + - + +
172b CYS* 1.3 74.9 - - - +
174b ARG* 1.3 61.9 + - - +
175b VAL 3.6 3.1 + - - -
183b SER* 6.0 1.6 - - - -
185b ASN* 5.7 1.2 + - - +
187b PHE* 2.9 49.7 - - + -
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Residues in contact with ARG 174 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139I GLU* 4.6 2.9 - - - +
140I ASP* 5.6 2.4 + - - +
170b GLU 4.1 8.4 + - - +
171b ARG* 3.0 36.2 + - - +
173b MET* 1.3 73.8 - - - +
175b VAL* 1.3 70.6 + - - +
185b ASN* 5.0 17.3 - - - +
187b PHE* 4.4 1.2 - - - -
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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