Contacts of the helix formed by residues 146 - 154 (chain A) in PDB entry 1Q8K
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 146 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A LYS* 4.6 24.1 - - - +
99A ASP* 3.0 46.9 + - + +
100A LYS* 3.7 22.0 - - + -
103A LYS* 3.9 37.5 + - + +
104A SER* 4.6 0.2 + - - -
143A ARG* 4.6 19.1 - - + +
144A PRO* 3.0 14.6 + - + +
145A GLY* 1.3 75.2 - - - +
147A GLY* 1.3 65.7 + - - +
149A TYR* 3.5 1.7 + - - +
150A ASP* 3.2 21.3 + - - +
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Residues in contact with GLY 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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141A TYR* 3.2 18.7 - - - -
143A ARG* 3.1 32.5 - - - +
145A GLY 3.1 0.4 - - - -
146A TYR* 1.3 79.8 - - - +
148A ALA* 1.3 64.0 + - - +
149A TYR 3.0 0.9 + - - -
150A ASP* 3.1 5.1 + - - +
151A ALA* 2.9 22.2 + - - +
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Residues in contact with ALA 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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107A VAL* 5.0 4.5 - - + -
134A ALA* 2.8 28.0 - - + +
135A TRP* 4.9 1.1 - - + -
137A PHE* 4.0 7.4 - - + -
138A ASP* 2.7 37.9 + - - +
141A TYR* 3.4 11.9 - - - -
145A GLY 3.7 0.9 - - - +
147A GLY* 1.3 70.0 - - - -
149A TYR* 1.3 52.7 + - - +
151A ALA 3.5 0.2 - - - -
152A PHE* 2.6 43.9 + - + +
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Residues in contact with TYR 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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102A THR* 6.1 0.2 - - + -
103A LYS* 3.0 76.3 - - + +
106A THR* 3.7 29.0 + - + +
107A VAL* 4.7 7.7 - - + +
110A ILE* 5.7 1.1 - - + -
145A GLY 3.1 11.3 + - - +
146A TYR 3.5 9.0 - - - +
148A ALA* 1.3 76.4 - - - +
150A ASP* 1.3 59.8 + - - +
152A PHE* 2.7 30.2 + - + +
153A LYS* 2.9 34.8 + - + -
183A LEU* 4.4 14.3 - - + +
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Residues in contact with ASP 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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103A LYS* 4.7 10.6 + - - +
146A TYR 3.2 8.8 + - - +
147A GLY* 3.1 9.5 + - - +
149A TYR* 1.3 82.7 - - - +
151A ALA* 1.3 63.2 + - - +
153A LYS* 3.0 10.3 + - - +
154A HIS* 2.9 36.6 + - - +
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Residues in contact with ALA 151 (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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137A PHE* 4.5 4.3 - - + -
141A TYR* 2.6 41.5 - - + +
147A GLY 2.9 9.5 + - - +
148A ALA* 3.6 3.1 - - - +
150A ASP* 1.3 77.5 - - - +
152A PHE* 1.3 59.7 + - - +
154A HIS* 4.2 6.0 - - - +
155A ALA* 2.8 32.3 + - - +
161A ILE* 4.2 15.1 - - + +
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Residues in contact with PHE 152 (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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107A VAL* 3.1 38.8 - - + -
110A ILE* 5.2 9.9 - - + -
111A LEU* 3.7 11.7 - - + -
133A THR* 3.6 20.2 - - + -
134A ALA* 3.5 24.0 - - + -
137A PHE* 3.8 29.4 - + + -
148A ALA 2.6 26.1 + - - +
149A TYR* 2.7 12.8 + - + +
151A ALA* 1.3 75.6 - - - +
153A LYS* 1.3 56.2 + - - -
155A ALA* 4.1 6.3 + - + -
156A VAL* 4.0 0.7 - - - +
162A LEU* 5.7 1.3 - - + -
175A LEU* 5.5 2.7 - - + -
179A ILE* 2.7 54.4 - - + +
183A LEU* 2.8 9.6 - - + +
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Residues in contact with LYS 153 (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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149A TYR* 2.9 24.4 + - + +
150A ASP* 3.4 13.7 - - - +
152A PHE* 1.3 79.0 - - - +
154A HIS* 1.3 66.4 + - + +
155A ALA 3.3 0.4 - - - -
156A VAL* 3.2 24.9 - - - +
183A LEU* 3.6 41.3 - - + +
184A THR* 4.1 3.2 + - - +
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Residues in contact with HIS 154 (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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150A ASP* 2.9 25.9 + - - +
151A ALA* 4.2 5.6 - - - +
153A LYS* 1.3 82.4 - - + +
155A ALA* 1.3 57.8 + - - +
156A VAL* 3.0 8.4 + - + -
157A SER* 3.3 9.8 + - - -
158A ASP* 2.8 41.3 + - + +
161A ILE* 5.1 4.7 - - + -
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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