Contacts of the helix formed by residues 153 - 162 (chain A) in PDB entry 2Q53
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 PRO 153 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A VAL* 4.4 0.4 - - + -
80A TRP* 3.5 57.7 - - + +
115A GLN* 4.0 20.2 - - - +
151A GLY 3.7 0.4 - - - +
152A LEU* 1.3 87.6 - - + +
154A LEU* 1.3 66.8 + - - +
155A GLU* 3.1 4.5 - - + +
156A TYR* 2.9 25.9 + - + +
157A GLN* 3.0 10.0 + - - +
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Residues in contact with LEU 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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151A GLY* 6.1 1.1 - - - -
152A LEU 3.2 3.7 + - - +
153A PRO* 1.3 71.7 - - - +
155A GLU* 1.3 62.1 + - - +
157A GLN* 3.4 29.8 + - - +
158A GLU* 3.2 22.8 + - - +
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Residues in contact with GLU 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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78A GLU* 5.5 2.8 - - - +
153A PRO* 3.1 4.6 - - + +
154A LEU* 1.3 76.4 - - - +
156A TYR* 1.3 71.3 + - - +
158A GLU* 2.9 26.0 + - + +
159A LYS* 3.4 23.9 + - - +
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Residues in contact with TYR 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 TYR 5.2 2.8 + - - -
26A LEU* 5.8 0.7 - - + -
51A LEU* 3.9 22.7 - - + +
78A GLU* 3.6 21.1 - - + +
79A VAL* 3.7 13.9 - - - +
80A TRP* 3.4 72.8 + + + -
152A LEU* 3.9 11.7 - - + -
153A PRO* 2.9 16.5 + - + +
155A GLU* 1.3 84.6 + - - +
157A GLN* 1.3 63.9 + - - +
159A LYS* 2.9 32.6 + - + +
160A LEU* 3.2 35.7 + - + +
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Residues in contact with GLN 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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144A CYS 4.7 0.9 - - - +
147A ALA* 3.7 30.9 + - + +
148A LYS* 3.1 32.8 + - - +
151A GLY* 4.7 1.4 - - - -
152A LEU* 3.1 24.8 + - + +
153A PRO 3.0 12.1 + - - +
154A LEU* 3.4 32.2 - - - +
155A GLU 3.1 0.2 - - - -
156A TYR* 1.3 76.3 - - - +
158A GLU* 1.3 57.2 + - + +
160A LEU* 3.1 12.4 + - - +
161A LYS* 2.8 46.7 + - + +
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Residues in contact with GLU 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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154A LEU 3.2 13.6 + - - +
155A GLU* 2.9 25.2 + - + +
157A GLN* 1.3 80.1 - - - +
159A LYS* 1.3 60.2 + - + +
161A LYS* 3.5 29.4 + - - +
162A ALA* 3.2 24.1 + - - +
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Residues in contact with LYS 159 (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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50A LYS* 5.4 5.5 - - - +
77A ASP* 5.2 9.5 + - - +
78A GLU* 5.4 12.5 + - + +
155A GLU* 3.8 30.1 - - - +
156A TYR* 2.9 27.6 + - + +
158A GLU* 1.3 78.4 - - - +
160A LEU* 1.3 61.9 + - + +
162A ALA* 3.4 13.7 + - - +
163A ILE* 3.4 14.0 + - - +
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Residues in contact with LEU 160 (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 TYR 5.6 1.6 - - - +
26A LEU* 4.5 2.9 - - + -
51A LEU* 3.8 29.6 - - + -
53A PHE* 5.4 0.2 - - + -
140A LYS* 3.4 7.3 - - - -
143A ILE* 3.7 28.0 - - + +
144A CYS* 4.0 14.1 - - - -
147A ALA* 3.4 33.2 - - + -
156A TYR* 3.2 37.3 + - + +
157A GLN* 3.1 7.9 + - - +
159A LYS* 1.3 78.1 - - + +
161A LYS* 1.3 60.9 + - + +
163A ILE* 3.1 35.1 + - + +
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Residues in contact with LYS 161 (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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140A LYS* 2.7 28.3 + - - +
144A CYS* 4.3 16.8 - - + -
157A GLN* 2.8 37.7 + - + +
158A GLU* 3.7 28.6 + - - +
160A LEU* 1.3 73.3 - - + +
162A ALA* 1.3 54.4 + - - +
163A ILE 3.2 1.1 - - - -
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Residues in contact with ALA 162 (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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158A GLU* 3.2 18.0 + - - +
159A LYS* 3.7 8.7 - - - +
160A LEU 3.1 1.2 - - - -
161A LYS* 1.3 75.3 - - - +
163A ILE* 1.3 63.2 + - - +
164A GLU* 3.4 10.4 + - - +
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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