Contacts of the strand formed by residues 150 - 158 (chain A) in PDB entry 1QAO
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 VAL 150 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A VAL* 4.0 24.5 - - + -
123A ILE* 5.7 2.5 - - + -
146A LEU* 2.8 32.9 + - + +
147A MET* 3.4 13.9 - - - +
149A GLU* 1.3 86.9 - - + +
151A ASP* 1.3 62.4 + - - +
152A ILE* 4.0 17.8 + - + +
176A LEU* 4.4 18.4 - - + -
177A ASN 3.2 17.7 - - - +
178A ARG* 3.9 16.4 - - + +
179A LYS* 3.3 19.5 + - - +
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Residues in contact with ASP 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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150A VAL* 1.3 72.4 - - - +
152A ILE* 1.3 61.8 + - - +
153A SER* 4.9 4.1 + - - +
175A ARG 3.5 1.2 - - - +
176A LEU* 3.3 7.3 - - - -
177A ASN* 2.8 44.3 + - + +
179A LYS* 2.8 41.5 + - - +
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Residues in contact with ILE 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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132A ALA 5.6 1.1 - - - +
135A LEU* 3.5 40.8 - - + +
136A LEU* 3.3 36.2 - - + +
146A LEU* 4.3 26.7 - - + -
147A MET* 4.5 12.0 - - + +
150A VAL* 4.2 10.5 - - + +
151A ASP* 1.3 75.2 - - - +
153A SER* 1.3 73.8 + - - +
154A ILE* 5.5 2.0 - - + -
174A ILE* 5.2 4.7 - - + -
175A ARG 3.6 2.2 - - - +
176A LEU* 3.5 25.1 - - + -
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Residues in contact with SER 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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136A LEU* 5.2 0.9 - - - -
151A ASP* 4.9 4.2 + - - +
152A ILE* 1.3 80.4 + - - +
154A ILE* 1.3 64.6 + - - +
155A LEU* 3.6 19.4 + - - -
174A ILE* 3.2 6.4 - - - +
175A ARG* 2.8 60.6 + - - -
177A ASN* 5.3 0.9 + - - -
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Residues in contact with ILE 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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129A TYR* 6.2 2.7 - - + -
132A ALA* 4.2 20.4 - - + +
133A LYS* 4.0 25.4 - - + +
136A LEU* 3.9 28.5 - - + +
152A ILE* 5.5 1.6 - - + -
153A SER* 1.3 73.7 - - - +
155A LEU* 1.3 64.9 + - - +
156A SER 4.1 10.8 - - - +
172A SER* 4.0 25.1 - - - +
173A LEU 3.9 2.9 - - - +
174A ILE* 4.1 11.9 - - + -
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Residues in contact with LEU 155 (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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25A ASN* 3.8 28.4 + - + +
27A ARG* 5.1 2.7 - - - +
124A TYR* 3.7 33.4 - - + -
153A SER* 3.9 18.4 - - - +
154A ILE* 1.3 77.5 - - - +
156A SER* 1.3 65.7 + - - +
173A LEU* 2.9 28.3 + - + +
175A ARG* 3.7 38.6 - - + +
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Residues in contact with SER 156 (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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22A ILE* 6.0 0.7 - - - +
25A ASN* 4.0 20.3 + - - -
154A ILE* 3.6 7.3 - - - +
155A LEU* 1.3 82.3 - - - +
157A MET* 1.3 67.0 + - - +
158A VAL* 5.0 1.7 - - - +
172A SER* 3.4 8.8 + - - -
173A LEU* 3.0 39.3 + - - +
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Residues in contact with MET 157 (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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129A TYR* 4.3 23.6 - - + -
156A SER* 1.3 81.3 + - - +
158A VAL* 1.3 70.5 + - - +
159A PRO* 3.4 37.3 - - + +
162A TYR* 5.6 0.5 - - - -
170A ASN* 3.7 26.9 - - + +
171A SER 3.7 8.1 - - - +
172A SER* 4.5 2.2 - - - +
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Residues in contact with VAL 158 (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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13A ILE* 4.2 3.1 - - + -
22A ILE* 3.9 33.9 - - + -
126A ILE* 4.3 9.4 - - + -
156A SER* 5.0 2.0 - - - +
157A MET* 1.3 79.2 - - - +
159A PRO* 1.3 71.2 - - - +
162A TYR* 4.2 10.1 - - + -
163A PHE* 3.7 25.9 - - + -
171A SER* 2.7 38.9 + - - +
172A SER 4.2 2.2 - - - -
173A LEU* 4.1 30.3 - - + +
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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