Contacts of the strand formed by residues 143 - 150 (chain Q) 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 TYR 143 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108Q GLU* 5.3 8.7 - - + -
140Q ASP* 3.0 29.8 + - - +
142Q HIS* 1.3 89.5 - - + +
144Q GLY* 1.3 61.6 + - - +
145Q PHE 3.9 5.2 + - - +
146Q GLN* 3.1 15.0 - - - +
148Q TYR* 5.1 6.3 - - - -
71Y ASN 4.9 1.4 + - - -
72Y GLY* 5.1 2.3 + - - -
73Y TYR* 3.7 37.3 - + - -
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Residues in contact with GLY 144 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139Q TRP* 2.9 28.7 - - - -
140Q ASP* 3.0 32.4 + - - +
141Q LYS 4.4 2.4 + - - -
142Q HIS 3.9 0.6 - - - -
143Q TYR* 1.3 80.0 - - - +
145Q PHE* 1.4 62.6 + - - -
146Q GLN* 3.7 1.2 - - - +
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Residues in contact with PHE 145 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38Q LEU* 3.6 12.6 - - + +
39Q ALA 4.4 14.6 - - - +
40Q ASN 4.8 2.9 - - - -
41Q ASP* 2.7 42.6 - - - -
42Q GLY* 3.3 6.7 - - - +
43Q VAL* 3.6 16.2 - - + -
138Q GLY 3.3 14.4 - - - -
139Q TRP* 2.8 37.8 - + + -
143Q TYR* 3.9 5.6 + - - +
144Q GLY* 1.4 71.7 - - - -
146Q GLN* 1.3 60.4 + - - +
216Q LEU* 3.6 25.6 - - + -
217Q THR 4.0 1.1 - - - -
218Q ARG* 3.6 34.8 - - + -
223Q THR* 4.4 1.8 - - + -
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Residues in contact with GLN 146 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38Q LEU* 3.7 9.4 - - - +
43Q VAL* 4.2 3.9 - - - +
107Q CYS* 3.6 8.8 - - + +
108Q GLU* 3.5 24.9 - - - +
136Q TYR 4.1 0.2 - - - -
137Q ILE* 3.6 1.6 - - - -
138Q GLY 2.9 40.8 + - - +
140Q ASP* 2.7 43.5 + - - +
143Q TYR* 3.1 19.8 - - + +
144Q GLY 3.7 3.9 - - - +
145Q PHE* 1.3 74.6 - - - +
147Q LEU* 1.3 61.3 + - - +
148Q TYR* 3.5 29.1 + - + +
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Residues in contact with LEU 147 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36Q GLY* 3.8 25.4 - - - +
37Q ILE 4.5 0.2 - - - +
38Q LEU* 4.1 9.6 - - + +
43Q VAL* 4.1 10.8 - - + -
135Q LEU* 4.2 16.4 - - + -
136Q TYR 2.8 19.1 - - - +
137Q ILE* 4.0 17.3 - - + -
146Q GLN* 1.3 73.2 - - - +
148Q TYR* 1.3 78.6 + - - +
158Q GLY* 3.4 3.1 - - - -
159Q TRP* 2.7 53.1 + - + +
160Q LYS 3.8 12.1 - - - +
161Q ALA* 3.9 2.7 - - - +
162Q THR* 4.3 14.1 - - + -
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Residues in contact with TYR 148 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107Q CYS* 5.4 2.2 - - - -
108Q GLU* 3.2 40.0 - - + +
111Q VAL* 4.2 11.7 - - + -
135Q LEU* 3.0 6.4 - - - +
136Q TYR* 2.5 58.1 + - + -
143Q TYR* 5.1 5.5 - - - -
146Q GLN* 3.5 41.5 + - + +
147Q LEU* 1.3 82.1 - - - +
149Q GLN* 1.3 59.3 + - - +
156Q TYR* 4.5 12.6 - + + -
157Q GLY 3.5 10.8 - - - +
158Q GLY* 3.5 28.7 - - - -
159Q TRP* 4.6 0.4 - - - +
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Residues in contact with GLN 149 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133Q SER* 4.9 4.2 + - - -
134Q LEU 3.3 11.9 - - - +
135Q LEU* 3.7 15.9 - - + -
136Q TYR* 4.7 0.9 - - - -
148Q TYR* 1.3 75.6 - - - +
150Q SER* 1.3 66.5 + - - +
151Q ASP* 3.9 6.2 + - - +
155Q ASN* 5.8 0.2 + - - -
156Q TYR* 3.2 23.7 - - - -
157Q GLY 3.2 13.1 + - - +
159Q TRP* 4.3 17.9 + - + +
162Q THR* 2.9 27.6 + - + -
163Q CYS 4.5 4.2 + - - -
164Q ILE* 3.7 29.1 - - + +
168Q SER* 5.6 0.4 + - - -
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Residues in contact with SER 150 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115Q CYS* 3.1 25.2 - - - -
118Q LYS* 3.1 20.4 + - - -
133Q SER* 3.2 7.6 - - - -
134Q LEU* 2.8 33.0 + - - -
136Q TYR* 3.8 28.1 + - - -
149Q GLN* 1.3 72.7 - - - +
151Q ASP* 1.3 65.9 + - - +
155Q ASN 4.0 6.1 - - - -
156Q TYR* 4.6 0.2 - - - +
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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