Contacts of the helix formed by residues 146 - 161 (chain A) in PDB entry 2OVI
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 LEU 146 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A TRP 5.5 1.1 - - - +
59A ASN* 4.7 9.4 - - + +
138A GLY* 3.2 10.9 + - - +
139A ARG 3.1 25.8 - - - +
140A ASP* 3.3 20.2 - - - +
145A LEU* 1.3 69.0 - - - +
147A SER* 1.3 62.3 + - - +
148A GLU* 3.3 10.5 - - + +
149A GLN* 3.0 39.7 + - + +
150A VAL* 3.0 28.4 + - - +
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Residues in contact with SER 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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145A LEU 3.4 6.0 + - - -
146A LEU* 1.3 68.0 - - - +
148A GLU* 1.3 77.8 + - - +
150A VAL* 3.4 8.2 + - - +
151A SER* 3.0 24.3 + - - -
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Residues in contact with GLU 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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146A LEU* 4.0 9.1 - - + +
147A SER* 1.3 90.0 + - - +
149A GLN* 1.3 59.0 + - + +
151A SER* 3.2 8.3 + - - -
152A ALA* 3.0 29.5 + - - +
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Residues in contact with GLN 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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57A TRP* 2.8 43.2 - - + +
58A GLY 4.0 0.5 - - - -
59A ASN 2.7 20.2 + - - +
60A VAL* 3.7 8.1 - - - +
137A LEU* 3.5 20.5 - - + +
138A GLY* 2.7 41.6 + - - +
146A LEU* 3.0 27.2 + - + +
148A GLU* 1.3 75.6 - - + +
150A VAL* 1.3 55.2 + - - +
152A ALA* 3.2 5.1 + - - +
153A PHE* 2.7 37.4 + - - +
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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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111A GLU* 4.6 4.7 - - - +
137A LEU* 3.7 13.0 - - + -
145A LEU* 3.7 34.1 - - + +
146A LEU 3.0 20.7 + - - +
147A SER* 3.7 9.6 - - - +
148A GLU 3.3 0.2 - - - -
149A GLN* 1.3 76.1 - - - +
151A SER* 1.3 58.4 + - - +
153A PHE* 3.3 3.2 - - + +
154A HIS* 2.9 60.3 + - + +
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Residues in contact with SER 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 SER 3.0 14.1 + - - -
148A GLU* 3.2 12.5 + - - -
150A VAL* 1.3 79.3 - - - +
152A ALA* 1.3 59.9 + - - +
154A HIS* 3.2 13.1 + - - +
155A THR* 2.8 32.5 + - - -
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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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53A THR* 5.5 1.6 - - + +
57A TRP* 3.4 33.8 - - + +
148A GLU 3.0 17.4 + - - +
149A GLN* 3.9 1.8 - - - +
151A SER* 1.3 74.5 + - - +
153A PHE* 1.3 56.7 + - - +
155A THR* 2.9 9.8 + - - -
156A LEU* 2.6 37.1 + - - +
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Residues in contact with PHE 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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57A TRP* 3.5 15.8 - + + -
109A LEU* 3.5 34.7 - - + +
110A ILE 3.5 21.3 - - - -
111A GLU* 3.7 26.0 - - + -
120A ALA* 4.1 5.4 - - + -
121A SER 3.5 22.4 - - - -
122A ILE* 3.9 15.5 - - + -
137A LEU* 3.8 27.8 - - + -
149A GLN 2.7 21.8 + - - +
150A VAL* 3.3 5.2 - - + +
152A ALA* 1.3 73.5 - - - +
154A HIS* 1.3 70.2 + + - +
156A LEU* 3.1 4.3 + - - +
157A ALA* 2.8 33.8 + - + +
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Residues in contact with HIS 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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111A GLU* 2.6 40.1 + - - -
150A VAL* 2.9 41.7 + - + +
151A SER* 3.5 11.6 - - - +
152A ALA 3.2 0.2 - - - -
153A PHE* 1.3 80.6 - + - +
155A THR* 1.3 53.5 + - - +
157A ALA* 3.2 7.8 + - + +
158A ALA* 2.7 36.4 + - - +
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Residues in contact with THR 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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151A SER* 2.8 22.9 + - - -
152A ALA* 2.9 12.8 + - - -
154A HIS* 1.3 78.1 - - - +
156A LEU* 1.3 61.1 - - - +
158A ALA* 3.7 6.2 - - + +
159A SER* 3.0 26.8 + - - +
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Residues in contact with LEU 156 (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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49A THR* 4.3 16.6 - - + +
50A VAL* 4.4 22.0 - - + +
53A THR* 4.1 31.9 - - + +
54A VAL* 4.6 1.3 - - + -
57A TRP* 4.1 21.5 - - + -
109A LEU* 3.9 14.4 - - + -
122A ILE* 5.5 0.9 - - + -
152A ALA 2.6 16.0 + - - +
153A PHE* 3.4 9.2 - - - +
155A THR* 1.3 72.7 - - - +
157A ALA* 1.3 58.3 + - - +
159A SER* 3.1 10.8 + - - +
160A LEU* 2.9 56.8 + - + +
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Residues in contact with ALA 157 (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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40A THR* 4.0 24.4 + - - +
109A LEU* 4.0 17.9 - - + +
111A GLU* 5.9 0.7 - - - +
153A PHE* 2.8 22.0 + - + +
154A HIS* 3.5 10.5 - - + +
156A LEU* 1.3 77.0 - - - +
158A ALA* 1.3 63.1 + - - +
160A LEU* 3.3 5.9 + - - +
161A LYS* 3.2 21.7 + - - +
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Residues in contact with ALA 158 (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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154A HIS 2.7 20.9 + - - +
155A THR* 3.3 7.6 + - - +
157A ALA* 1.3 74.1 - - - +
159A SER* 1.3 63.0 + - - +
161A LYS 3.5 18.9 - - - +
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Residues in contact with SER 159 (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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46A LYS* 6.0 0.9 - - - -
155A THR* 3.0 20.7 + - - +
156A LEU* 3.1 19.6 + - - +
158A ALA* 1.3 77.2 - - - +
160A LEU* 1.3 64.1 + - - +
161A LYS 4.5 1.6 - - - -
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Residues in contact with LEU 160 (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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40A THR* 4.2 4.3 - - + -
42A VAL* 3.7 28.4 - - + +
46A LYS* 4.1 45.2 + - + +
49A THR* 4.6 7.6 - - + -
50A VAL* 4.0 11.9 - - + -
109A LEU* 3.7 25.4 - - + -
156A LEU* 2.9 53.8 + - + +
157A ALA* 3.8 5.2 - - - +
158A ALA 3.3 0.4 - - - -
159A SER* 1.3 79.8 - - - +
161A LYS* 1.3 59.8 + - - +
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Residues in contact with LYS 161 (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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40A THR* 3.5 27.4 - - + +
41A VAL 5.7 1.8 - - - +
42A VAL* 5.1 2.5 - - + -
157A ALA 3.2 7.4 + - - +
158A ALA* 3.5 17.4 - - - +
159A SER 4.5 1.8 - - - -
160A LEU* 1.3 80.7 - - - +
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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