Contacts of the helix formed by residues 146 - 162 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58D GLY* 5.8 0.9 - - - -
59D ASN* 4.5 6.5 - - + +
138D GLY* 3.2 22.2 + - - +
139D ARG 4.1 2.7 - - - +
140D ASP* 3.8 32.3 - - + +
144D GLN 3.6 0.4 + - - -
145D LEU* 1.3 68.9 - - - +
147D SER* 1.3 67.7 + - - +
148D GLU* 3.0 21.1 - - - +
149D GLN* 3.1 40.3 + - + +
150D VAL* 3.0 21.8 + - - +
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Residues in contact with SER 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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145D LEU 3.1 8.1 + - - -
146D LEU* 1.3 70.9 - - - +
148D GLU* 1.3 74.9 + - - +
150D VAL* 3.2 8.8 + - - +
151D SER* 2.9 25.2 + - - -
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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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146D LEU* 3.0 35.0 - - - +
147D SER* 1.3 85.1 + - - +
149D GLN* 1.3 60.8 + - + +
151D SER* 2.9 21.5 + - - -
152D ALA* 3.1 11.6 + - - +
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Residues in contact with GLN 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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57D TRP* 3.9 23.8 - - + -
58D GLY 3.3 20.2 + - - +
59D ASN 3.0 20.2 + - - +
60D VAL* 4.0 4.2 - - - +
137D LEU* 3.6 22.9 - - + +
138D GLY 3.1 31.3 + - - +
146D LEU* 3.1 33.4 + - + +
148D GLU* 1.3 77.4 + - + +
150D VAL* 1.3 56.9 + - - +
152D ALA* 3.1 8.3 + - - +
153D PHE* 2.7 35.7 + - - +
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Residues in contact with VAL 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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111D GLU* 4.5 5.6 - - - +
120D ALA* 5.3 0.4 - - + -
137D LEU* 3.8 13.0 - - + -
145D LEU* 3.5 37.2 - - + +
146D LEU 3.0 18.3 + - - +
147D SER* 3.2 10.7 + - - +
149D GLN* 1.3 73.6 - - - +
151D SER* 1.3 66.1 + - - +
153D PHE* 3.4 3.0 + - + +
154D HIS* 3.0 43.1 + - + +
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Residues in contact with SER 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 SER 2.9 13.0 + - - -
148D GLU* 2.9 23.0 + - - -
150D VAL* 1.3 77.1 - - - +
152D ALA* 1.3 57.6 + - - +
154D HIS* 3.1 7.3 + - - +
155D THR* 2.9 34.2 + - - -
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Residues in contact with ALA 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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53D THR* 5.4 1.1 - - + +
57D TRP* 3.7 31.4 + - + +
148D GLU 3.1 14.6 + - - +
149D GLN* 3.4 10.1 - - - +
151D SER* 1.3 77.7 + - - +
153D PHE* 1.3 56.8 + - - +
155D THR* 3.2 9.1 + - - -
156D LEU* 2.9 30.1 + - - +
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Residues in contact with PHE 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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57D TRP* 3.7 21.0 - + + -
109D LEU* 3.5 35.0 - - + +
110D ILE 3.5 22.7 - - - -
111D GLU* 4.0 20.0 - - + -
120D ALA* 4.3 3.4 - - + -
121D SER 3.6 28.3 - - - -
122D ILE* 4.3 2.0 - - + -
137D LEU* 3.9 28.0 - - + -
149D GLN 2.7 18.9 + - - +
150D VAL* 3.4 6.7 - - - +
151D SER 3.3 0.2 - - - -
152D ALA* 1.3 72.5 - - - +
154D HIS* 1.3 81.1 + + - +
156D LEU* 3.2 3.6 + - - +
157D ALA* 2.9 28.3 + - + +
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Residues in contact with HIS 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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111D GLU* 2.9 46.5 + - - +
150D VAL* 3.0 35.6 + - + +
151D SER* 3.8 4.9 - - - +
153D PHE* 1.3 91.1 - + - +
155D THR* 1.3 60.6 + - - +
157D ALA* 3.7 7.8 - - + +
158D ALA* 2.8 31.6 + - - +
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Residues in contact with THR 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 SER* 2.9 16.9 + - - -
152D ALA* 3.4 12.2 - - - -
154D HIS* 1.3 75.8 - - - +
156D LEU* 1.3 58.7 + - - +
158D ALA* 3.4 5.5 + - - +
159D SER* 2.8 32.6 + - - -
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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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49D THR* 4.5 11.7 - - + +
50D VAL* 4.5 20.4 - - + -
53D THR* 4.0 28.9 - - + +
54D VAL* 4.8 0.9 - - + -
57D TRP* 3.8 26.0 - - + -
109D LEU* 3.8 22.7 - - + -
122D ILE* 4.8 0.4 - - + -
152D ALA 2.9 16.5 + - - +
153D PHE 3.2 3.1 + - - +
155D THR* 1.3 75.8 - - - +
157D ALA* 1.3 61.9 + - - +
159D SER* 3.1 9.2 + - - +
160D LEU* 2.7 53.4 + - + +
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Residues in contact with ALA 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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40D THR* 3.7 31.4 - - + +
109D LEU* 3.5 20.1 - - + +
153D PHE* 2.9 21.8 + - + +
154D HIS* 3.7 12.6 - - + +
156D LEU* 1.3 76.6 - - - +
158D ALA* 1.3 64.5 + - - +
160D LEU* 3.3 5.5 + - - +
161D LYS* 3.2 19.8 + - - +
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Residues in contact with ALA 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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154D HIS 2.8 19.1 + - - +
155D THR* 3.7 6.1 - - - +
157D ALA* 1.3 76.1 - - - +
159D SER* 1.3 53.3 + - - +
161D LYS* 3.0 7.7 + - - +
162D GLU* 2.8 34.8 + - - +
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Residues in contact with SER 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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49D THR* 6.0 2.4 - - - +
155D THR* 2.8 22.3 + - - -
156D LEU* 3.1 12.9 + - - +
158D ALA* 1.3 77.4 - - - +
160D LEU* 1.3 60.0 + - - +
162D GLU* 3.2 22.9 - - - +
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Residues in contact with LEU 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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40D THR* 4.7 5.2 - - - +
42D VAL* 3.9 35.9 - - + +
46D LYS* 3.6 38.0 + - + +
49D THR* 4.6 9.0 - - + -
50D VAL* 5.7 5.2 - - + +
107D ILE* 6.0 0.2 - - + -
109D LEU* 3.9 34.3 - - + -
156D LEU* 2.7 39.3 + - + +
157D ALA* 3.7 6.1 - - - +
158D ALA 3.1 0.2 - - - -
159D SER* 1.3 75.2 - - - +
161D LYS* 1.3 61.6 + - - +
162D GLU 4.8 0.9 - - - -
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Residues in contact with LYS 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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40D THR* 6.0 4.7 - - + -
42D VAL* 5.9 1.1 - - - -
157D ALA 3.2 7.9 + - - +
158D ALA* 3.0 9.0 + - - +
160D LEU* 1.3 78.8 - - - +
162D GLU* 1.3 67.7 + - - +
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Residues in contact with GLU 162 (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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158D ALA 2.8 13.0 + - - +
159D SER* 3.2 22.9 - - - +
160D LEU 3.3 1.7 - - - -
161D LYS* 1.3 82.8 - - - +
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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