Contacts of the helix formed by residues 145 - 157 (chain D) in PDB entry 3C5C
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 THR 145 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98D TYR* 4.6 0.7 + - - -
142D ARG* 3.7 14.1 - - + +
143D GLN 5.7 1.3 - - - +
144D VAL* 1.3 80.8 - - - +
146D LYS* 1.3 65.7 + - - +
147D ALA* 3.8 10.3 + - - +
148D GLU* 2.9 46.1 + - - +
149D GLY* 3.3 8.1 + - - -
162D GLU* 4.5 0.9 - - - +
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Residues in contact with LYS 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142D ARG* 3.5 10.9 - - - +
145D THR* 1.3 70.5 - - - +
147D ALA* 1.3 62.9 + - + +
149D GLY* 3.0 4.2 + - - +
150D VAL* 2.9 32.8 + - + +
160D PHE* 3.7 6.9 - - + -
162D GLU* 3.4 32.3 - - + +
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Residues in contact with ALA 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145D THR* 3.2 9.1 + - - +
146D LYS* 1.3 80.9 - - + +
148D GLU* 1.3 57.5 + - + +
150D VAL* 3.3 10.6 + - - +
151D ALA* 2.9 30.8 + - - +
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Residues in contact with GLU 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D ARG* 2.9 42.6 + - - -
106D PHE* 3.4 20.3 - - + -
143D GLN 4.2 0.9 - - - +
144D VAL* 3.5 9.2 - - + -
145D THR* 2.9 45.7 + - - +
147D ALA* 1.3 77.7 - - + +
149D GLY* 1.3 57.1 + - - +
151D ALA* 3.6 6.2 + - - +
152D LEU 3.0 22.7 + - - -
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Residues in contact with GLY 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D TYR* 3.4 23.3 + - - -
106D PHE* 4.3 6.7 - - - -
131D LEU* 3.5 7.5 - - - +
145D THR 3.3 4.6 + - - -
146D LYS 3.0 8.2 + - - -
148D GLU* 1.3 75.4 - - - +
150D VAL* 1.3 58.7 + - - +
152D LEU 3.3 0.7 + - - -
153D ALA* 2.9 30.0 + - - +
160D PHE* 3.6 12.8 - - - -
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Residues in contact with VAL 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146D LYS* 2.9 22.8 + - + +
147D ALA* 3.6 9.2 - - - +
149D GLY* 1.3 73.1 - - - +
151D ALA* 1.3 59.5 + - - +
153D ALA* 3.2 7.9 + - - +
154D GLY* 2.9 24.3 + - - -
160D PHE* 3.9 20.8 - - + -
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Residues in contact with ALA 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D ALA 2.9 17.6 + - - +
148D GLU* 3.9 7.0 - - - +
150D VAL* 1.3 76.5 - - - +
152D LEU* 1.3 63.1 + - - +
154D GLY* 3.0 12.9 + - - -
155D ARG* 3.2 16.3 + - - +
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Residues in contact with LEU 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D PHE* 3.4 26.9 - - + +
109D SER* 3.2 27.8 - - - +
110D SER* 3.7 19.1 - - - +
113D LEU* 3.9 10.1 - - + -
131D LEU* 3.7 15.5 - - + -
148D GLU 3.0 19.3 + - - +
149D GLY 3.3 4.2 + - - +
151D ALA* 1.3 73.9 - - - +
153D ALA* 1.3 64.6 + - - +
155D ARG* 3.0 50.4 + - - +
156D PHE* 3.6 19.4 + - + -
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Residues in contact with ALA 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D LEU* 4.1 4.0 - - + +
149D GLY 2.9 13.5 + - - +
150D VAL* 3.3 11.2 - - - +
152D LEU* 1.3 75.2 - - - +
154D GLY* 1.3 56.4 + - - +
156D PHE* 3.3 2.6 + - - -
157D GLY* 2.9 24.6 + - - -
158D CYS* 3.1 43.3 + - - +
160D PHE* 3.7 21.3 - - + -
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Residues in contact with GLY 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150D VAL 2.9 13.1 + - - -
151D ALA* 3.0 6.8 + - - -
153D ALA* 1.3 74.7 - - - +
155D ARG* 1.3 63.3 + - - +
156D PHE 3.3 0.5 + - - -
157D GLY* 3.6 8.6 + - - -
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Residues in contact with ARG 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D PHE* 6.3 1.2 - - - -
110D SER* 3.9 15.0 + - - -
114D GLU* 3.3 24.5 + - - -
151D ALA 3.2 13.8 + - - +
152D LEU* 3.0 34.3 + - - +
154D GLY* 1.3 76.9 - - - +
156D PHE* 1.3 77.9 + - + +
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Residues in contact with PHE 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D SER 3.8 5.4 - - - -
113D LEU* 3.5 38.4 - - + +
114D GLU* 3.4 43.3 - - + -
117D ALA* 4.1 13.9 - - + -
152D LEU* 3.6 33.4 - - + -
153D ALA 3.3 3.6 + - - +
154D GLY 3.2 0.2 - - - -
155D ARG* 1.3 101.1 - - + +
157D GLY* 1.3 64.7 + - - +
158D CYS* 3.3 13.6 + - + +
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Residues in contact with GLY 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153D ALA 2.9 7.0 + - - -
154D GLY* 3.6 9.7 + - - -
156D PHE* 1.3 78.9 - - - +
158D CYS* 1.3 59.2 + - - +
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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