Contacts of the helix formed by residues 147 - 161 (chain D) in PDB entry 1R4N
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 SER 147 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6D ATP 4.5 4.4 + - - -
145D LEU* 3.4 0.9 - - - +
146D ASP* 1.3 85.3 - - - +
148D ILE* 1.3 61.0 + - - +
149D ILE* 4.4 10.6 - - - +
150D ALA* 2.9 33.4 + - - +
151D ARG* 2.7 31.3 + - - +
174J ARG* 4.6 2.7 - - - -
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Residues in contact with ILE 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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147D SER* 1.3 74.6 - - - +
149D ILE* 1.3 74.5 + - + +
151D ARG* 2.8 12.5 + - + +
152D ARG* 2.8 43.5 + - + +
200D ILE* 5.8 0.9 - - + -
204D LEU* 4.7 6.5 - - + -
207D TYR* 3.9 44.9 - - + -
208D PRO 6.0 0.2 - - - +
174J ARG* 3.9 34.5 - - + -
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Residues in contact with ILE 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128D GLN* 5.8 1.8 - - - +
147D SER* 4.5 7.4 - - - +
148D ILE* 1.3 77.8 - - + +
150D ALA* 1.3 53.9 + - - +
152D ARG* 2.8 15.3 + - - +
153D TRP* 2.5 36.1 + - + +
377D LYS* 4.7 24.0 - - + +
907D PRO 4.5 2.9 - - - +
908D GLN* 3.7 35.9 - - + +
909D THR* 4.3 7.0 - - - -
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Residues in contact with ALA 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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6D ATP 3.8 21.8 - - - +
127D ILE* 3.8 7.6 - - + +
128D GLN* 4.6 5.8 + - - +
145D LEU* 3.5 26.5 - - + -
147D SER* 2.9 21.2 + - - +
149D ILE* 1.3 79.0 - - - +
151D ARG* 1.3 64.7 + - - +
153D TRP* 3.0 5.5 + - - +
154D ILE* 2.8 25.5 + - - +
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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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143D CYS* 5.3 1.8 - - + -
145D LEU* 2.8 38.2 + - + +
147D SER 2.7 33.1 + - - +
148D ILE* 2.8 17.1 + - + +
150D ALA* 1.3 75.6 - - - +
152D ARG* 1.3 65.3 + - - +
154D ILE* 3.2 11.6 + - - +
155D ASN* 2.8 24.0 + - - +
179D ASP* 2.6 35.6 + - - +
180D GLY 2.9 20.4 + - - -
181D GLY* 3.8 0.6 - - - -
200D ILE* 4.4 18.8 - - + +
207D TYR* 3.5 20.0 + - - -
173J LEU 3.7 14.0 + - - -
174J ARG* 3.1 24.6 + - - +
175J GLY 3.3 6.3 + - - -
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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 ILE* 2.8 41.6 + - + +
149D ILE* 2.8 13.3 + - - +
151D ARG* 1.3 71.1 - - - +
153D TRP* 1.3 62.1 + - - +
155D ASN* 2.9 25.1 + - - +
156D GLY* 3.0 6.8 + - - -
200D ILE* 4.2 12.3 - - + +
201D GLU* 2.9 42.1 + - - +
204D LEU* 4.1 11.6 - - + +
374D LEU 3.1 28.2 + - - -
375D GLN* 3.9 20.2 + - - +
376D MET* 4.7 8.7 - - - +
909D THR* 3.3 33.7 + - - +
910D VAL* 4.6 3.3 - - - +
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Residues in contact with TRP 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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131B ASN* 5.2 2.0 - - - -
127D ILE* 3.5 30.7 - - + -
128D GLN* 3.5 39.2 - - + +
130D PHE 3.7 16.4 - - - -
135D TYR* 3.6 23.8 - + - -
149D ILE 2.5 13.1 + - - +
150D ALA* 3.3 11.7 - - - +
152D ARG* 1.3 72.8 - - - +
154D ILE* 1.3 90.4 + - + +
156D GLY* 2.8 13.5 + - - -
157D MET* 3.1 31.1 + - + -
908D GLN* 3.2 33.9 - - + +
909D THR 3.2 7.1 + - - -
910D VAL* 4.0 2.4 + - - +
911D LEU* 3.7 33.6 + - + +
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Residues in contact with ILE 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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54D ILE* 3.3 31.0 - - + -
127D ILE* 4.2 4.0 - - + -
135D TYR* 4.5 8.5 - - + -
141D ILE* 4.4 11.4 - - + -
143D CYS* 4.0 20.4 - - - -
145D LEU* 5.0 0.2 - - + -
150D ALA 2.8 15.0 + - - +
151D ARG* 3.2 15.3 - - - +
153D TRP* 1.3 93.5 - - + +
155D ASN* 1.3 67.1 + - - +
157D MET* 4.3 3.4 - - + -
158D LEU* 3.1 43.7 + - + +
177D LEU* 4.2 10.1 - - + -
200D ILE* 6.0 0.2 - - + -
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Residues in contact with ASN 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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151D ARG 2.8 13.7 + - - +
152D ARG 2.9 13.4 + - - +
154D ILE* 1.3 81.7 - - - +
156D GLY* 1.3 64.6 + - - +
158D LEU* 3.6 3.3 + - - +
159D ILE* 3.2 25.4 + - - +
177D LEU* 4.3 11.8 - - - +
192D ILE* 4.6 3.3 - - - +
194D PRO* 5.4 1.0 - - - +
199D CYS* 3.4 16.0 - - - +
200D ILE* 3.3 37.0 + - + +
201D GLU* 3.7 31.7 + - - +
345D ALA* 4.3 4.6 - - - +
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Residues in contact with GLY 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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152D ARG 3.0 8.1 + - - -
153D TRP 2.8 9.1 + - - -
155D ASN* 1.3 74.5 - - - +
157D MET* 1.3 55.0 + - - -
158D LEU 3.0 1.3 - - - -
159D ILE* 2.4 37.1 + - - +
160D SER* 3.1 10.5 + - - -
345D ALA* 6.0 2.7 - - - -
910D VAL* 4.8 8.1 - - - -
911D LEU* 4.6 10.3 - - - -
912D PHE* 4.9 9.6 - - - -
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Residues in contact with MET 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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131D ASN* 4.0 3.6 - - - -
132D ASP* 3.4 46.7 - - + +
135D TYR* 3.5 41.1 - - + -
153D TRP* 3.1 32.2 + - + +
154D ILE* 3.8 9.0 - - + +
156D GLY* 1.3 73.0 - - - +
158D LEU* 1.3 60.0 + - - +
160D SER* 2.7 47.0 + - - +
161D LEU* 3.2 10.4 - - + +
911D LEU* 3.8 16.2 - - + +
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Residues in contact with LEU 158 (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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135D TYR* 4.9 4.3 - - + -
141D ILE* 3.6 23.3 - - + -
154D ILE* 3.1 31.0 + - + +
155D ASN* 4.0 6.1 - - - +
156D GLY 2.7 5.1 + - - -
157D MET* 1.3 75.8 - - + +
159D ILE* 1.3 60.4 + - - +
161D LEU* 3.8 27.2 - - + +
162D LEU* 4.4 3.6 - - - +
173D SER 4.9 0.2 - - - +
175D VAL* 3.4 45.4 + - + +
177D LEU* 3.4 36.6 - - + -
194D PRO* 3.8 17.6 - - + +
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Residues in contact with ILE 159 (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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155D ASN* 3.2 34.5 - - - +
156D GLY* 2.4 22.3 + - - +
158D LEU* 1.3 70.5 - - - +
160D SER* 1.3 53.7 + - - +
161D LEU 2.7 5.3 + - - -
162D LEU* 2.5 55.1 + - + +
194D PRO* 3.6 19.5 - - + -
199D CYS* 4.5 3.1 - - + -
345D ALA* 4.2 16.4 - - + +
346D CYS* 4.1 33.7 - - + +
912D PHE* 6.3 0.9 - - + -
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Residues in contact with SER 160 (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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132D ASP* 5.8 1.8 - - - -
136D ARG* 4.4 6.8 + - - -
156D GLY 3.1 6.1 + - - -
157D MET* 2.7 46.4 + - - +
159D ILE* 1.3 76.0 - - - +
161D LEU* 1.3 61.8 + - - +
162D LEU 3.4 6.7 + - - +
911D LEU* 5.5 1.0 - - - +
912D PHE* 5.2 15.1 - - - +
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Residues in contact with LEU 161 (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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132D ASP* 3.7 33.4 - - + -
135D TYR* 4.2 4.5 - - + -
136D ARG* 3.8 55.3 + - + +
157D MET* 3.2 23.3 - - + +
158D LEU* 3.8 32.5 - - + +
159D ILE 2.7 0.8 + - - -
160D SER* 1.3 78.1 - - - +
162D LEU* 1.3 67.2 + - - +
163D ASN* 3.3 5.0 + - - +
173D SER* 3.6 18.8 - - - +
175D VAL* 4.0 14.8 - - + -
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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