Contacts of the helix formed by residues 144 - 153 (chain D) in PDB entry 3H2U
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 144 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47D ARG* 5.7 7.2 - - - +
142D SER 3.9 8.7 - - - +
143D LEU* 1.3 76.1 - - - +
145D GLN* 1.3 53.3 + - - +
146D GLN* 3.5 8.7 + - - +
147D GLN* 2.6 50.6 + - - +
148D PHE* 2.7 34.0 + - - +
163D LEU* 3.4 2.9 - - - -
165D TYR* 6.5 0.4 - - - -
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Residues in contact with GLN 145 (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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50D HIS* 4.1 30.0 + - + +
51D THR* 4.6 2.6 + - - -
144D THR* 1.3 73.7 - - - +
146D GLN* 1.3 59.9 + - + +
148D PHE* 3.3 3.0 - - - +
149D GLU* 2.9 30.1 + - - +
161D CYS* 3.1 25.3 - - - +
162D PHE* 3.3 10.3 - - - +
163D LEU* 3.0 47.1 - - + +
165D TYR* 3.3 24.1 + - - +
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Residues in contact with GLN 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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144D THR* 3.2 8.5 + - - +
145D GLN* 1.3 81.3 - - + +
147D GLN* 1.3 59.6 + - - +
149D GLU* 3.7 9.1 + - + +
150D GLU* 3.2 48.9 + - - +
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Residues in contact with GLN 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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142D SER 4.1 1.6 - - - +
143D LEU* 3.5 28.4 - - + +
144D THR* 2.6 53.5 + - - +
146D GLN* 1.3 78.8 - - + +
148D PHE* 1.3 67.7 + - - +
150D GLU* 3.1 17.4 + - - +
151D LEU* 3.0 22.7 + - - +
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Residues in contact with PHE 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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136D VAL* 3.9 23.1 - - + -
139D LEU* 3.7 33.7 - - + -
143D LEU* 3.9 9.1 - - + +
144D THR 2.7 11.8 + - - +
145D GLN* 3.3 9.4 - - - +
147D GLN* 1.3 75.2 - - - +
149D GLU* 1.3 62.2 + - - +
151D LEU* 2.9 17.7 + - + +
152D VAL* 3.0 25.3 + - + +
161D CYS* 3.6 23.8 - - - -
162D PHE* 3.9 8.7 - - - -
163D LEU* 3.5 20.4 - - + -
176D GLY* 3.5 25.6 - - - -
177D PHE 3.5 30.1 - - - -
178D ALA* 5.0 0.4 - - + -
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Residues in contact with GLU 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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145D GLN* 2.9 21.0 + - - +
146D GLN* 3.7 10.5 - - + +
147D GLN 3.3 0.2 - - - -
148D PHE* 1.3 76.9 - - - +
150D GLU* 1.3 56.3 + - - +
152D VAL* 4.4 0.6 - - - +
153D ARG* 2.8 60.8 + - - +
158D LEU* 4.4 10.3 - - + -
161D CYS* 3.8 30.3 - - + -
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Residues in contact with GLU 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 GLN* 3.2 38.9 + - + +
147D GLN* 3.1 21.7 + - - +
149D GLU* 1.3 79.1 + - - +
151D LEU* 1.3 58.8 + - - +
153D ARG* 3.7 37.1 + - - +
154D PRO* 3.2 21.8 - - - +
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Residues in contact with LEU 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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136D VAL* 4.6 4.5 - - + -
139D LEU* 4.0 27.1 - - + -
143D LEU* 4.5 2.9 - - + -
147D GLN 3.0 10.9 + - - +
148D PHE* 3.1 22.2 - - + +
150D GLU* 1.3 78.5 - - - +
152D VAL* 1.3 63.6 + - + +
154D PRO* 3.6 8.7 - - - +
155D PHE* 3.5 17.3 - - - -
193D LEU* 3.9 21.5 - - + -
196D LYS* 4.3 18.6 - - + -
198D LEU* 4.2 19.3 - - + -
203D LEU* 4.1 12.6 - - + -
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Residues in contact with VAL 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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134D LEU* 6.4 0.9 - - + -
136D VAL* 4.1 13.7 - - + -
148D PHE* 3.0 19.1 + - + +
149D GLU 4.4 0.4 - - - +
151D LEU* 1.3 80.9 - - + +
153D ARG* 1.3 64.0 + - - +
154D PRO 3.6 0.4 - - - -
155D PHE* 3.3 10.0 - - - -
158D LEU* 3.6 18.6 - - + -
161D CYS* 4.2 14.1 - - - -
178D ALA* 3.5 33.0 - - + -
180D TYR* 2.6 33.2 + - - +
189D ALA* 5.5 0.2 - - + -
193D LEU* 3.8 24.2 - - + -
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Residues in contact with ARG 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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149D GLU* 2.8 38.1 + - - +
150D GLU* 3.7 35.5 + - - +
152D VAL* 1.3 77.8 - - - +
154D PRO* 1.3 69.8 - - + +
155D PHE 2.9 6.9 + - - -
156D GLY 3.0 21.2 + - - +
158D LEU* 3.7 21.5 - - + -
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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