Contacts of the helix formed by residues 146 - 153 (chain B) in PDB entry 1OIZ
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 GLU 146 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107B ARG* 3.2 21.7 + - - +
113B LYS* 2.7 36.0 + - - +
142B LEU 5.3 2.0 - - - +
143B ILE* 3.1 15.9 + - - +
144B VAL 4.2 0.7 - - - -
145B GLN* 1.3 78.0 - - + +
147B VAL* 1.3 66.8 + - - +
148B GLU 3.2 1.1 - - - +
149B THR* 3.0 16.4 + - - +
150B GLN* 3.1 12.5 + - - +
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Residues in contact with VAL 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B PRO* 5.4 1.8 - - + -
19B ASP* 4.1 7.9 - - - +
57B ARG* 3.4 38.6 - - - +
145B GLN 3.6 4.2 + - - -
146B GLU* 1.3 71.2 - - - +
148B GLU* 1.3 62.5 + - + +
150B GLN* 3.2 12.0 + - - +
151B ARG* 2.9 62.8 + - - +
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Residues in contact with GLU 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B ARG* 3.6 31.3 + - - +
111B GLY* 5.6 0.5 - - - -
146B GLU* 3.2 1.6 - - + +
147B VAL* 1.3 82.9 - - + +
149B THR* 1.3 57.3 + - - +
151B ARG* 2.6 39.4 + - - +
152B ASN* 2.8 57.2 + - - +
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Residues in contact with THR 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B ARG* 3.0 28.2 + - - +
113B LYS* 3.7 12.8 - - + +
143B ILE* 3.5 23.4 + - + +
146B GLU* 3.0 11.7 + - - +
148B GLU* 1.3 77.0 - - - +
150B GLN* 1.3 60.0 + - - +
151B ARG 3.2 0.4 - - - -
153B GLY* 2.7 36.3 + - - +
154B ILE* 3.7 29.4 - - + -
189B LEU* 3.9 14.7 - - + +
190B LYS 5.4 0.7 + - - -
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Residues in contact with GLN 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B ASP* 5.4 2.9 - - - +
50B SER 4.6 3.8 - - - +
53B LEU* 3.6 2.4 + - - +
54B ARG* 3.6 35.2 + - - +
57B ARG* 3.0 54.0 + - + +
58B ALA* 4.9 0.9 + - - -
144B VAL* 2.9 38.2 - - + +
145B GLN* 4.2 9.5 - - - +
146B GLU 3.1 5.1 + - - +
147B VAL* 3.2 12.8 + - - +
149B THR* 1.3 75.8 - - - +
151B ARG* 1.3 63.1 + - - +
188B PRO 5.5 2.7 - - - +
189B LEU* 5.4 4.7 - - - +
190B LYS* 3.8 20.8 + - - +
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Residues in contact with ARG 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ASN* 2.9 37.1 + - + +
16B ALA* 3.2 22.5 + - - +
17B LEU 3.1 25.9 + - - -
18B PRO* 3.9 7.5 - - - +
57B ARG* 4.4 5.2 - - - +
147B VAL* 2.9 46.1 + - - +
148B GLU* 2.6 41.2 + - - +
149B THR 3.2 0.2 - - - -
150B GLN* 1.3 80.4 - - - +
152B ASN* 1.3 70.7 + - - +
190B LYS* 4.2 12.5 - - - +
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Residues in contact with ASN 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B THR* 3.4 21.8 + - - +
111B GLY* 3.4 27.9 + - - +
112B SER* 2.7 24.8 + - - -
148B GLU* 2.8 48.0 + - - +
151B ARG* 1.3 83.9 - - - +
153B GLY* 1.3 56.5 - - - +
190B LYS* 5.2 1.1 - - - -
192B ARG* 3.5 15.0 - - - +
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Residues in contact with GLY 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B SER* 3.2 4.9 - - - -
113B LYS 3.1 20.3 + - - -
149B THR* 2.7 27.9 + - - +
150B GLN 4.5 0.8 + - - -
151B ARG 3.6 1.4 - - - -
152B ASN* 1.3 73.6 - - - +
154B ILE* 1.3 66.7 + - - +
189B LEU* 5.6 0.2 - - - -
190B LYS* 3.2 28.2 - - - +
192B ARG* 4.0 1.1 - - - -
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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