Contacts of the helix formed by residues 145 - 154 (chain D) in PDB entry 2EHO
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 ARG 145 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104D PRO* 3.2 31.2 + - + -
105D ASN* 3.3 23.9 + - - +
107D VAL* 3.1 30.7 + - - +
109D LEU* 3.0 32.1 - - - +
141D THR* 2.8 23.3 + - - +
142D PHE 2.6 10.7 + - - +
144D GLY* 1.3 72.8 - - - +
146D PHE* 1.3 64.2 + - - +
147D ARG 2.9 5.5 + - - -
148D ARG* 3.4 4.1 + - + +
149D ILE* 3.2 32.4 + - + +
167D ARG* 3.6 9.3 + - - +
168D LEU* 3.9 7.7 - - - +
172D GLU* 2.5 40.8 + - - +
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Residues in contact with PHE 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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132C ALA* 3.9 9.6 - - + -
133C ASP* 3.7 37.0 - - - +
136C VAL* 3.4 38.1 - - + -
137C ARG* 5.9 0.2 - - + -
159C PHE* 3.8 23.0 - + - -
160C LEU* 4.5 4.9 - - + -
163C ALA* 3.4 33.0 - - + -
164C LEU* 5.7 0.2 - - + -
142D PHE* 2.8 26.3 + + + +
143D ILE* 4.0 12.6 - - - +
144D GLY 3.5 0.6 - - - -
145D ARG* 1.3 75.2 - - - +
147D ARG* 1.3 66.5 + - - +
149D ILE* 3.7 8.9 + - - +
150D MSE 3.2 34.0 + - + +
175D LEU* 4.9 3.4 - - + -
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Residues in contact with ARG 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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133C ASP* 2.8 43.9 + - + +
137C ARG* 4.8 5.5 - - - +
105D ASN* 5.1 3.6 - - - +
144D GLY 4.9 3.1 + - - +
145D ARG 2.9 2.6 + - - -
146D PHE* 1.3 75.8 - - - +
148D ARG* 1.3 59.7 + - + +
149D ILE 2.5 17.1 + - - -
150D MSE 2.7 20.6 + - + +
151D ASP* 2.9 36.1 + - - +
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Residues in contact with ARG 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 ASP* 5.4 0.8 + - - -
105D ASN* 2.6 61.8 + - - +
106D VAL* 4.9 1.0 - - - +
145D ARG* 3.4 4.0 + - + +
147D ARG* 1.3 84.2 - - + +
149D ILE* 1.3 60.7 + - + +
151D ASP* 4.3 7.7 - - - +
152D SER* 3.4 20.3 + - - -
164D LEU* 4.2 27.9 - - + +
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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
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159C PHE* 5.0 1.3 - - + -
142D PHE* 4.7 9.6 - - + -
145D ARG* 3.2 26.9 - - + +
146D PHE* 3.8 7.6 - - - +
147D ARG 2.5 6.5 + - - -
148D ARG* 1.3 75.7 - - + +
150D MSE 1.3 65.9 + - - +
152D SER* 3.2 5.9 + - - -
153D SER* 3.1 20.6 + - - -
164D LEU* 5.1 2.2 - - + -
168D LEU* 3.4 34.8 - - + -
172D GLU* 3.5 37.2 - - + +
175D LEU* 4.2 27.8 - - + -
176D PHE* 4.4 8.0 - - + +
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Residues in contact with MSE 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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129C ARG* 3.3 48.9 - - + +
132C ALA* 4.1 6.3 - - + -
133C ASP* 4.9 3.4 - - + +
159C PHE* 3.4 23.8 - - + -
160C LEU* 4.1 24.2 - - - -
146D PHE* 3.2 29.9 + - + +
147D ARG* 2.7 13.9 + - + +
149D ILE* 1.3 72.5 - - - +
151D ASP* 1.3 72.5 + - - +
153D SER* 2.7 22.3 + - - -
154D GLN* 2.8 34.1 + - + +
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Residues in contact with ASP 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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129C ARG* 4.0 21.5 + - - +
147D ARG* 2.9 39.4 + - - +
148D ARG* 4.6 5.0 + - - +
150D MSE 1.3 93.5 - - - +
152D SER* 1.3 59.1 + - - +
154D GLN* 4.2 1.9 - - - +
155D ASN* 3.6 22.3 + - - +
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Residues in contact with SER 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 ARG 3.4 19.3 + - - -
149D ILE* 3.2 6.7 + - - -
150D MSE 3.0 0.6 - - - -
151D ASP* 1.3 79.4 - - - +
153D SER* 1.3 63.6 + - - +
155D ASN* 3.1 25.4 - - - +
161D THR* 3.0 32.9 - - - +
164D LEU* 4.4 10.9 - - - +
176D PHE* 3.3 20.5 - - - -
180D GLN* 4.3 1.2 + - - -
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Residues in contact with SER 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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159C PHE* 3.3 22.4 - - - -
149D ILE 3.1 9.5 + - - -
150D MSE 2.7 19.2 + - - -
152D SER* 1.3 73.4 - - - +
154D GLN* 1.3 54.6 + - - +
155D ASN 2.8 16.5 + - - +
176D PHE* 3.5 30.3 - - - -
179D GLY* 3.6 22.7 - - - +
180D GLN* 3.1 24.3 + - - +
183D LEU* 3.8 4.5 - - - +
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Residues in contact with GLN 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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125C ILE* 5.2 6.9 - - + +
129C ARG* 3.7 41.9 + - - +
155C THR 4.3 7.8 + - - +
156C SER* 2.9 36.7 + - - +
159C PHE* 5.7 5.4 - - + +
160C LEU* 6.1 1.6 - - - +
150D MSE 2.8 31.6 + - + +
151D ASP 4.3 2.5 - - - +
153D SER* 1.3 72.7 + - - +
155D ASN* 1.3 58.8 + - - +
179D GLY* 3.4 20.2 - - - +
183D LEU* 3.5 30.0 - - + +
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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