Contacts of the helix formed by residues 148 - 156 (chain A) in PDB entry 3RLE
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 ASP 148 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A TRP* 3.8 16.2 + - + +
143A MSE 4.0 4.4 - - - +
144A ASN 2.8 16.8 - - - +
145A GLU* 3.7 15.3 - - - +
146A SER 3.2 1.9 + - - +
147A GLU* 1.3 77.8 - - - +
149A LEU* 1.3 65.3 + - - +
150A PHE* 3.2 31.8 + - - +
151A SER* 2.8 39.6 + - - -
152A LEU* 3.2 21.5 + - - +
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Residues in contact with LEU 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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113A TRP* 3.8 35.1 - - + +
136A ILE* 3.8 26.7 - - + -
143A MSE 3.8 12.1 - - - -
148A ASP* 1.3 77.8 - - - +
150A PHE* 1.3 60.3 + - + +
152A LEU* 3.2 4.4 + - + +
153A ILE* 2.9 54.5 + - + +
161A LEU* 5.5 0.7 - - + -
163A LEU* 4.2 26.7 - - + -
190A LEU* 4.6 2.9 - - + -
194A ILE* 3.7 37.0 - - + -
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Residues in contact with PHE 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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113A TRP* 5.0 4.7 - + - -
148A ASP* 3.2 23.9 + - - +
149A LEU* 1.3 77.0 - - + +
151A SER* 1.3 61.1 + - - +
153A ILE* 3.3 14.4 + - + +
154A GLU* 2.9 34.6 + - + +
190A LEU* 4.2 21.8 - - + -
192A CYS 5.7 1.3 - - - -
194A ILE* 3.7 39.5 - - + -
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Residues in contact with SER 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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146A SER 3.3 12.3 + - - -
147A GLU* 4.2 16.2 - - - -
148A ASP* 2.8 31.3 + - - -
150A PHE* 1.3 77.2 - - - +
152A LEU* 1.3 62.8 + - - +
154A GLU* 3.2 16.0 + - - +
155A THR* 3.2 29.1 + - - +
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Residues in contact with LEU 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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139A ALA* 3.6 31.0 - - + -
141A THR* 3.5 21.3 - - + +
143A MSE 3.8 19.1 - - + -
147A GLU 6.0 0.4 - - - -
148A ASP 3.2 11.0 + - - +
149A LEU* 3.2 9.1 + - + +
151A SER* 1.3 81.4 - - - +
153A ILE* 1.3 62.6 + - - +
155A THR* 3.0 11.3 + - + +
156A HIS* 3.0 46.0 + - + -
161A LEU* 3.7 25.6 - - + -
163A LEU* 4.5 3.4 - - + -
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Residues in contact with ILE 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 LEU* 2.9 43.9 + - + +
150A PHE* 3.7 13.9 - - + +
152A LEU* 1.3 74.6 - - - +
154A GLU* 1.3 64.3 + - + +
156A HIS 3.1 11.1 + - - -
157A GLU* 3.3 11.1 + - - +
161A LEU* 4.1 18.8 - - + -
163A LEU* 6.1 0.9 - - + -
178A ILE* 5.8 2.0 - - + -
180A PRO* 3.7 29.1 - - + +
189A SER* 4.0 20.4 - - - +
190A LEU* 4.0 34.5 - - + -
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Residues in contact with GLU 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 PHE* 2.9 17.4 + - + +
151A SER* 3.4 16.2 - - - +
152A LEU 3.2 0.2 - - - -
153A ILE* 1.3 78.7 - - + +
155A THR* 1.3 64.6 + - + +
156A HIS 3.2 0.3 + - - -
157A GLU* 3.3 18.9 + - - +
159A LYS* 5.0 0.5 + - - -
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Residues in contact with THR 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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147A GLU* 6.2 0.2 - - - +
151A SER* 3.2 16.5 + - - +
152A LEU* 3.0 11.3 + - + +
154A GLU* 1.3 76.9 - - + +
156A HIS* 1.3 81.5 + - - +
157A GLU 3.4 0.7 - - - -
159A LYS* 3.0 22.8 + - - +
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Residues in contact with HIS 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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141A THR* 6.5 0.4 - - + -
152A LEU* 3.0 33.4 + - + +
153A ILE 3.1 6.9 + - - +
154A GLU 3.1 1.2 - - - -
155A THR* 1.3 104.0 + - - +
157A GLU* 1.3 66.2 + - - +
158A ALA 3.1 0.7 + - - -
159A LYS* 3.0 37.0 + - + +
160A PRO 3.7 21.8 - - - -
161A LEU* 3.8 29.8 - - + +
180A PRO* 3.3 11.5 - - + +
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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