Contacts of the helix formed by residues 142 - 153 (chain I) in PDB entry 5A2Q
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 SER 142 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1912 A 3.2 23.5 + - - -
1922 C 4.4 15.7 + - - -
140I LYS* 5.5 2.6 - - - -
141I ARG* 1.3 76.2 + - - +
143I LYS* 1.3 67.4 + - - +
144I LYS* 3.3 3.1 - - - -
145I ILE* 2.9 33.0 + - - +
146I GLN* 2.9 14.2 + - - +
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Residues in contact with LYS 143 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2012 C 4.4 11.3 + - - -
2022 G 3.2 37.5 + - + +
2032 G 5.3 9.0 + - - +
142I SER* 1.3 72.2 - - - +
144I LYS* 1.3 62.9 + - - +
146I GLN* 3.1 35.9 + - - +
147I LYS* 3.3 10.2 + - - +
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Residues in contact with LYS 144 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2052 G 4.4 24.0 + - - -
2062 G 5.5 13.7 + - - +
142I SER* 3.3 2.5 - - - -
143I LYS* 1.3 78.7 - - - +
145I ILE* 1.3 64.0 + - + +
147I LYS* 3.7 17.9 + - + +
148I LYS* 3.2 20.6 + - - +
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Residues in contact with ILE 145 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1902 G 4.1 12.1 - - - +
1912 A 3.0 43.7 - - - +
139I LYS* 4.1 6.1 - - - +
140I LYS 5.3 0.4 - - - +
141I ARG* 4.0 16.6 - - + -
142I SER* 2.9 29.3 + - - +
144I LYS* 1.3 78.1 - - + +
146I GLN* 1.3 67.2 + - - +
147I LYS 3.0 1.3 - - - -
148I LYS* 2.9 22.2 + - - +
149I TYR* 3.0 40.5 + - + -
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Residues in contact with GLN 146 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2022 G 4.4 18.8 + - - -
2032 G 5.2 6.7 + - - -
141I ARG* 3.2 40.1 + - + +
142I SER 2.9 13.9 + - - +
143I LYS* 3.1 32.0 + - - +
145I ILE* 1.3 74.0 - - - +
147I LYS* 1.3 57.8 + - + +
150I ASP* 2.9 33.5 + - - +
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Residues in contact with LYS 147 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2032 G 4.9 16.8 - - - +
2042 G 2.8 47.3 + - - +
2052 G 4.7 8.9 + - - -
143I LYS 3.3 14.1 + - - +
144I LYS* 3.8 19.0 - - + +
145I ILE 3.0 0.4 - - - -
146I GLN* 1.3 82.2 - - + +
148I LYS* 1.3 59.7 + - - +
150I ASP* 3.8 4.5 - - - +
151I GLU* 2.9 41.5 + - + +
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Residues in contact with LYS 148 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1892 U 3.5 21.9 + - - +
1902 G 2.9 32.3 + - - -
144I LYS 3.2 11.1 + - - +
145I ILE* 2.9 12.2 + - - +
147I LYS* 1.3 78.1 - - - +
149I TYR* 1.3 75.0 + - - +
151I GLU* 2.9 25.7 + - - +
152I ARG* 3.0 52.1 + - + +
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Residues in contact with TYR 149 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1892 U 4.7 0.2 + - - -
1902 G 3.3 31.1 + - - -
115I SER 3.8 16.7 + - - -
116I HIS 3.2 28.0 - - - -
117I TYR 4.3 4.4 - - - +
118I ALA* 4.3 20.0 - - + -
139I LYS* 3.3 25.3 + - + +
141I ARG* 3.9 25.1 - - - +
145I ILE* 3.0 36.6 + - + +
148I LYS* 1.3 87.0 - - - +
150I ASP* 1.3 64.0 + - - +
152I ARG* 3.1 20.1 + - - +
153I LYS* 3.0 28.0 + - - +
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Residues in contact with ASP 150 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141I ARG* 4.4 4.6 + - - +
146I GLN 2.9 22.1 + - - +
147I LYS* 3.9 5.4 - - - +
149I TYR* 1.3 77.0 - - - +
151I GLU* 1.3 62.5 + - - +
153I LYS* 3.2 36.8 + - - +
154I LYS* 3.9 13.4 - - - +
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Residues in contact with GLU 151 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147I LYS* 2.9 29.4 + - + +
148I LYS* 2.9 15.4 + - - +
150I ASP* 1.3 77.2 - - - +
152I ARG* 1.3 60.1 + - + +
154I LYS* 3.4 30.2 + - + +
155I ASN* 4.2 7.6 + - - +
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Residues in contact with ARG 152 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1892 U 2.7 29.7 + - - -
116I HIS* 3.1 59.6 + - - +
117I TYR* 3.5 20.5 - - + -
148I LYS* 3.0 48.1 + - + +
149I TYR* 3.1 19.1 + - - +
151I GLU* 1.3 77.2 - - + +
153I LYS* 1.3 56.7 + - - +
154I LYS 3.0 5.6 - - - -
155I ASN* 2.8 37.7 + - - +
156I ALA 3.4 4.7 + - - -
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Residues in contact with LYS 153 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117I TYR* 4.1 17.9 - - + +
118I ALA 4.6 1.6 - - - -
119I LEU* 4.1 35.7 - - + +
141I ARG* 2.9 43.4 - - - +
149I TYR 3.0 15.0 + - - +
150I ASP* 3.2 30.9 + - - +
152I ARG* 1.3 76.1 - - - +
154I LYS* 1.3 60.9 + - + +
155I ASN 3.2 0.4 + - - -
156I ALA 4.0 13.9 + - - +
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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