Contacts of the helix formed by residues 145 - 150 (chain A) in PDB entry 1Q8G
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 ASP 145 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A TYR* 3.0 19.4 + - - -
141A GLU* 2.7 29.5 - - - +
142A GLU* 4.0 1.3 - - - +
143A VAL 3.2 4.8 + - - -
144A LYS* 1.3 79.6 - - - +
146A ARG* 1.3 66.2 + - - +
147A CYS* 3.2 6.2 - - + +
148A THR* 2.8 37.3 + - - +
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Residues in contact with ARG 146 (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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66A ASP* 4.8 13.6 + - - +
68A TYR* 3.4 40.9 - - - +
69A ALA* 4.7 6.9 - - - +
144A LYS* 4.1 4.8 + - - +
145A ASP* 1.3 71.4 - - - +
147A CYS* 1.3 63.0 + - - +
148A THR 3.1 0.5 + - - -
149A LEU 3.2 1.9 + - - -
150A ALA 3.1 3.8 + - - -
161A LEU* 2.8 66.4 - - + +
162A GLU* 4.5 7.7 + - - -
165A PRO* 2.9 38.1 + - + +
166A LEU* 4.4 8.7 - - + -
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Residues in contact with CYS 147 (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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145A ASP* 3.2 7.1 - - + +
146A ARG* 1.3 79.2 - - - +
148A THR* 1.3 61.7 - - - +
150A ALA* 3.1 21.6 + - - +
151A GLU* 3.2 14.0 + - - +
166A LEU* 5.6 9.1 - - + +
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Residues in contact with THR 148 (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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68A TYR* 4.2 3.4 - - - +
135A LEU* 3.4 26.0 - - + +
142A GLU* 3.1 24.4 + - + +
145A ASP* 2.8 39.5 + - - +
147A CYS* 1.3 77.9 - - - +
149A LEU* 1.3 48.7 + - - +
151A GLU* 3.1 17.2 + - - +
152A LYS* 2.6 26.5 + - - -
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Residues in contact with LEU 149 (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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68A TYR* 3.8 24.0 - - + +
85A TYR* 4.6 9.2 - - + -
86A ASP 4.9 0.2 - - - -
87A ALA* 3.1 39.7 - - + +
100A VAL* 3.0 30.5 - - + -
102A ILE* 3.7 10.5 - - + -
135A LEU* 3.3 11.4 - - + -
145A ASP 3.5 1.4 + - - -
146A ARG 3.2 2.6 + - - +
148A THR* 1.3 79.3 - - - +
150A ALA* 1.3 54.5 + - - +
151A GLU 3.2 1.6 - - - -
152A LYS* 2.7 37.7 - - - +
153A LEU* 3.2 6.3 - - + +
161A LEU* 3.9 18.8 - - + -
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Residues in contact with ALA 150 (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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146A ARG 3.1 14.1 + - - +
147A CYS* 3.1 16.7 + - - +
148A THR 3.1 1.2 - - - -
149A LEU* 1.3 76.7 - - - +
151A GLU* 1.3 55.2 + - - +
152A LYS 3.3 5.9 + - - -
153A LEU* 3.2 30.2 - - + +
154A GLY 4.2 0.3 + - - -
155A GLY* 3.6 18.2 + - - -
158A VAL* 5.1 0.2 - - + -
161A LEU* 3.6 10.3 - - + -
166A LEU* 4.0 16.8 - - + -
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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