Contacts of the helix formed by residues 145 - 157 (chain D) in PDB entry 2Q5E
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 TYR 145 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143D ARG 3.4 0.6 + - - -
144D PRO* 1.3 95.6 - - + +
146D VAL* 1.3 57.9 + - - +
147D ASP* 3.3 4.0 + - - -
148D GLU* 3.3 30.9 + - + +
149D PHE* 2.8 29.7 + - - +
240D MET 6.1 0.2 - - - -
241D ALA 5.7 0.2 - - - -
242D ASP 4.1 4.5 - - - -
243D THR* 3.9 18.6 - - + +
245D LEU* 4.5 0.7 - - - -
246D LEU* 3.8 59.4 - - + +
249D ILE* 5.1 0.8 - - + +
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Residues in contact with VAL 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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112D LEU* 3.8 34.1 - - + +
142D LYS* 3.9 29.6 - - + -
143D ARG 3.3 18.4 - - - +
144D PRO 3.2 1.2 - - - -
145D TYR* 1.3 76.3 - - - +
147D ASP* 1.3 70.2 + - - +
149D PHE* 3.7 1.5 - - + +
150D LEU* 3.0 34.8 + - + +
177D LEU* 4.2 15.3 - - + -
245D LEU* 3.7 24.0 - - + -
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Residues in contact with ASP 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 LYS* 2.6 37.0 + - - +
145D TYR* 5.5 0.9 + - - -
146D VAL* 1.3 80.6 + - - +
148D GLU* 1.3 75.2 + - - +
150D LEU* 4.1 4.3 - - - +
151D ARG* 3.1 26.1 + - - +
177D LEU* 4.9 6.6 - - - +
179D ARG* 3.4 31.3 + - + +
180D CYS* 5.5 1.9 - - - -
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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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145D TYR* 3.4 41.0 - - + +
147D ASP* 1.3 87.3 + - - +
149D PHE* 1.3 66.5 + - - +
151D ARG* 3.2 22.1 + - - +
152D ARG* 3.1 24.9 + - - +
246D LEU* 5.6 2.0 - - + -
249D ILE* 4.3 12.1 - - + +
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Residues in contact with PHE 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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106D ILE* 4.6 2.5 - - + -
112D LEU* 3.9 26.0 - - + -
145D TYR 2.8 18.2 + - - +
146D VAL 3.7 4.5 - - - +
147D ASP 3.3 0.2 - - - -
148D GLU* 1.3 78.1 - - - +
150D LEU* 1.3 72.7 + - + +
152D ARG* 3.5 3.6 + - - +
153D MET* 3.0 61.7 + - + +
216D LEU* 3.6 26.0 - - + -
245D LEU* 3.7 37.5 - - + +
248D LEU* 4.0 20.6 - - + -
249D ILE* 3.9 18.4 - - + +
252D PHE* 4.3 4.0 - + - -
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Residues in contact with LEU 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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106D ILE* 4.6 6.1 - - + -
112D LEU* 4.1 9.0 - - + -
146D VAL* 3.0 28.7 + - + +
147D ASP* 4.2 4.3 - - - +
149D PHE* 1.3 95.5 - - + +
151D ARG* 1.3 61.4 + - - +
153D MET* 3.6 3.8 - - + +
154D GLY 2.8 28.4 + - - -
177D LEU* 4.3 31.6 - - + +
178D ASP* 4.5 8.3 - - - +
180D CYS* 6.1 1.6 - - - -
182D VAL* 3.4 21.9 - - + +
183D PHE* 4.0 33.9 - - + -
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Residues in contact with ARG 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 ASP 3.1 20.4 + - - +
148D GLU* 3.2 25.2 + - - +
150D LEU* 1.3 78.5 - - - +
152D ARG* 1.3 61.7 + - - +
154D GLY* 3.5 1.6 + - - -
155D GLU* 3.2 44.6 + - + +
180D CYS* 4.0 29.0 - - - -
182D VAL* 4.7 1.9 - - - +
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Residues in contact with ARG 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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148D GLU 3.1 15.9 + - - +
149D PHE* 3.9 3.6 - - - +
151D ARG* 1.3 77.6 - - - +
153D MET* 1.4 63.0 + - + +
155D GLU* 2.7 73.8 + - - +
156D LEU* 3.2 49.4 + - + +
249D ILE* 4.1 24.0 - - + +
253D GLU* 2.7 30.4 + - + +
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Residues in contact with MET 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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104D VAL* 3.8 21.1 - - + -
106D ILE* 4.5 7.0 - - + -
149D PHE* 3.0 52.2 + - + +
150D LEU* 3.1 8.5 + - + +
152D ARG* 1.4 74.6 - - - +
154D GLY* 1.3 60.6 + - - +
156D LEU* 3.0 2.1 + - - -
157D PHE* 2.8 48.5 + - + +
159D CYS* 3.5 15.9 - - - -
249D ILE* 6.1 0.9 - - - -
252D PHE* 3.7 55.2 - - + -
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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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101D ARG* 3.0 3.1 + - - -
150D LEU 2.8 14.3 + - - -
151D ARG 3.9 1.3 - - - -
153D MET* 1.3 73.0 - - - +
155D GLU* 1.3 62.2 + - - +
159D CYS* 3.9 7.9 - - - -
182D VAL* 3.7 23.1 - - - -
184D ARG* 2.7 32.1 + - - -
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Residues in contact with GLU 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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101D ARG* 2.7 28.3 + - - +
151D ARG* 3.2 29.6 + - + +
152D ARG* 2.7 61.9 + - - +
154D GLY* 1.3 74.1 - - - +
156D LEU* 1.3 57.1 - - + +
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Residues in contact with LEU 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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101D ARG* 3.4 19.7 - - - +
102D ILE 5.0 0.2 + - - -
152D ARG* 3.2 56.2 + - + +
153D MET* 3.0 1.7 + - - -
155D GLU* 1.3 82.6 - - + +
157D PHE* 1.3 84.7 + - + +
252D PHE* 5.9 0.4 - - + -
253D GLU* 3.7 28.7 - - + +
256D SER* 3.7 26.1 - - - +
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Residues in contact with PHE 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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101D ARG* 2.9 23.2 + - - -
102D ILE* 3.2 42.4 - - + +
104D VAL* 3.1 26.7 - - + -
153D MET* 2.8 31.2 + - + +
154D GLY 3.7 0.9 - - - +
156D LEU* 1.3 95.1 - - + +
158D GLU* 1.3 61.1 + - - +
159D CYS* 3.6 8.8 + - - -
184D ARG* 3.0 12.1 + - - -
214D LEU* 4.2 4.0 - - + -
252D PHE* 3.6 37.7 - + + -
255D LEU 4.6 0.7 - - - -
256D SER* 3.5 32.8 - - - -
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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