Contacts of the helix formed by residues 145 - 155 (chain A) in PDB entry 2WOE
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 ASP 145 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139A THR* 3.7 10.1 - - + -
142A HIS* 2.6 45.4 + - - +
144A ALA* 1.3 82.2 - - - +
146A LEU* 1.3 64.0 + - - +
147A GLU 3.4 1.3 - - - -
148A PRO* 3.6 9.0 - - - +
149A TRP* 3.0 47.9 + - - +
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Residues in contact with LEU 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A ALA 4.3 0.4 - - - +
136A ALA* 3.8 15.7 - - - -
139A THR* 3.6 25.8 - - - +
143A PRO 3.0 16.3 + - - +
145A ASP* 1.3 77.8 - - - +
147A GLU* 1.3 60.5 + - - +
150A VAL* 2.9 63.9 + - + +
168A LEU* 4.7 5.6 - - + +
171A GLY* 3.6 32.1 - - - +
172A ARG* 3.6 22.2 - - + +
175A HIS* 3.7 19.3 - - + +
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Residues in contact with GLU 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A PRO 4.5 0.6 + - - -
144A ALA 4.4 1.9 + - - +
146A LEU* 1.3 79.5 - - - +
148A PRO* 1.3 80.7 - - + +
150A VAL* 4.9 0.2 - - - -
151A LEU* 3.1 50.7 + - + +
168A LEU* 3.8 38.1 - - + +
172A ARG* 4.8 7.9 - - - +
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Residues in contact with PRO 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A LEU* 4.3 2.5 - - + +
144A ALA 3.4 20.2 - - - +
145A ASP* 3.4 16.4 - - - +
147A GLU* 1.3 105.8 - - + +
149A TRP* 1.3 62.9 + - + +
151A LEU* 4.4 1.9 - - + +
152A ALA* 2.9 31.4 + - - +
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Residues in contact with TRP 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A LEU* 3.9 24.2 - - + -
76A GLY 4.8 1.3 - - - -
77A THR* 3.6 27.1 - - - -
78A LEU* 3.5 48.3 - - + +
135A ALA* 4.3 10.7 - - + +
138A ALA* 3.8 24.9 - - + -
139A THR* 3.4 21.1 - - + -
142A HIS* 3.9 19.5 - + - -
145A ASP* 3.0 41.3 + - + +
146A LEU 4.1 1.1 - - - +
148A PRO* 1.3 81.1 - - + +
150A VAL* 1.3 66.2 + - - +
152A ALA 3.4 0.2 + - - -
153A GLN* 3.2 22.0 + - - +
290A LEU* 4.5 7.4 - - + -
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Residues in contact with VAL 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A CYS* 3.7 16.4 - - + -
135A ALA* 3.7 21.1 - - + -
136A ALA 4.5 2.2 - - - +
146A LEU* 2.9 45.1 + - + +
147A GLU* 4.2 3.1 - - - +
149A TRP* 1.3 75.6 - - - +
151A LEU* 1.3 61.9 + - + +
153A GLN* 3.2 7.5 - - - +
154A ALA* 2.9 26.5 + - - +
167A CYS* 3.6 41.5 - - + +
168A LEU* 4.3 4.7 - - - +
171A GLY* 5.0 2.5 - - - -
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Residues in contact with LEU 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A GLU* 3.1 45.8 + - + +
148A PRO* 4.4 2.0 - - + +
150A VAL* 1.3 84.4 - - + +
152A ALA* 1.3 65.8 + - - +
154A ALA* 4.2 4.0 - - + -
155A ARG* 2.8 55.7 + - + +
164A ASP* 3.7 42.0 - - + +
167A CYS* 4.5 3.1 - - + -
168A LEU* 4.9 9.4 - - + -
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Residues in contact with ALA 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A LEU* 3.4 29.6 - - + -
80A VAL* 3.9 16.8 - - + +
115A THR 4.8 0.7 - - - +
116A THR* 5.5 0.2 + - - -
148A PRO 2.9 21.5 + - - +
149A TRP 3.8 2.0 - - - +
150A VAL 3.4 0.2 - - - -
151A LEU* 1.3 77.4 - - - +
153A GLN* 1.3 63.0 + - - +
155A ARG* 4.0 4.4 - - - +
156A ILE* 3.6 18.5 + - - +
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Residues in contact with GLN 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A LEU* 3.8 40.1 - - + +
78A LEU* 4.8 0.4 - - - +
83A ILE* 4.3 9.9 - - + -
87A PHE* 4.1 2.3 - - - -
128A ALA 3.4 21.4 + - - -
131A ARG* 2.7 48.5 + - - +
132A CYS* 3.4 24.2 + - - -
135A ALA* 4.6 3.6 - - + -
149A TRP 3.2 12.8 + - - +
150A VAL* 3.2 16.4 + - - +
152A ALA* 1.3 76.6 - - - +
154A ALA* 1.3 79.3 + - - +
156A ILE* 3.3 25.7 + - + +
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Residues in contact with ALA 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A ALA* 3.6 19.8 - - + +
131A ARG* 3.3 10.6 + - - +
150A VAL 2.9 18.5 + - - +
151A LEU* 3.3 9.8 + - + +
153A GLN* 1.3 88.5 - - - +
155A ARG* 1.3 58.7 + - + +
157A THR* 3.1 7.1 + - - -
158A HIS* 2.9 27.7 + - - +
163A SER* 5.2 1.3 - - - +
164A ASP* 5.4 2.7 - - - +
167A CYS* 3.9 14.8 - - + -
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Residues in contact with ARG 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A THR* 3.4 20.0 + - - +
117A ALA* 2.8 32.3 + - - +
151A LEU* 2.8 46.5 + - + +
152A ALA* 4.0 5.4 - - - +
154A ALA* 1.3 71.8 - - + +
156A ILE* 1.3 62.2 + - - +
157A THR 3.0 2.1 + - - -
158A HIS 3.3 16.2 - - - +
159A ASN* 3.6 33.3 + - - +
164A ASP* 3.1 35.7 + - - +
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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