Contacts of the helix formed by residues 147 - 152 (chain A) in PDB entry 2O2C
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 147 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132A VAL 3.4 22.9 - - - +
133A PHE 3.8 8.1 - - - +
135A GLY* 3.9 15.0 - - - +
145A PRO* 3.9 7.8 - - + -
146A VAL* 1.3 75.1 - - - +
148A HIS* 1.3 64.1 + - - +
149A ILE* 3.1 14.1 - - + +
150A ALA* 3.1 12.5 + - + +
151A LEU 3.9 0.9 + - - -
159A ILE* 3.7 32.3 - - + -
161A VAL* 3.6 31.6 - - + -
166A VAL* 4.8 3.6 - - + -
322A TRP* 3.1 46.5 + - + -
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Residues in contact with HIS 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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132A VAL* 5.4 4.6 - - + +
146A VAL* 3.6 30.7 + - + +
147A LEU* 1.3 76.3 + - - +
149A ILE* 1.3 71.5 + - + +
151A LEU* 3.2 30.9 + - + +
152A ARG* 3.4 23.9 + - - +
322A TRP 4.1 4.8 + - - +
323A VAL* 5.4 2.7 - - - -
324A GLY 5.5 1.6 + - - -
327A TYR* 3.5 62.4 - + + +
547A GLU* 3.5 27.8 + - - +
548A HIS* 4.6 6.1 + - - -
551A LEU* 5.6 2.8 - - + +
562A TYR* 4.2 6.7 - + - -
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Residues in contact with ILE 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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132A VAL* 5.1 3.1 - - + +
133A PHE* 3.7 60.1 - - + +
146A VAL 5.0 2.5 - - - +
147A LEU* 3.1 12.5 - - + -
148A HIS* 1.3 85.4 - - + +
150A ALA* 1.3 60.4 + - - +
151A LEU 3.3 0.4 - - - -
152A ARG* 3.5 21.8 + - - +
153A ASN* 3.3 20.6 + - - +
157A ARG* 4.2 6.5 - - - +
159A ILE* 3.8 15.9 - - + -
354A HIS* 5.2 0.3 + - - -
357A ASP* 3.8 30.1 - - + +
548A HIS* 3.8 13.9 - - + -
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Residues in contact with ALA 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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147A LEU* 3.1 24.2 + - + +
149A ILE* 1.3 77.9 - - - +
151A LEU* 1.3 63.0 + - - +
152A ARG 3.2 1.5 + - - -
153A ASN* 3.3 9.4 + - - -
159A ILE* 3.9 19.3 - - + -
166A VAL* 4.1 22.7 - - + -
167A MET* 3.3 28.0 - - - +
170A VAL* 3.7 4.2 - - + +
322A TRP* 4.2 6.3 - - + -
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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 LEU 4.2 2.2 - - - +
148A HIS* 3.2 25.7 + - - +
150A ALA* 1.3 75.8 - - - +
152A ARG* 1.3 58.7 + - - +
153A ASN 3.6 0.4 - - - -
154A ARG* 5.4 0.3 + - - -
170A VAL* 3.8 21.1 - - + +
174A LEU* 4.1 11.1 - - - +
320A TRP* 3.9 25.4 - - + -
322A TRP* 4.1 5.4 - - + -
323A VAL* 3.9 26.0 - - + -
327A TYR 4.1 5.6 - - - +
330A TRP* 3.9 21.6 - - + +
331A SER* 3.8 38.8 - - - +
350A LEU* 3.9 11.9 - - - +
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Residues in contact with ARG 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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148A HIS* 3.4 28.5 + - - -
149A ILE* 3.7 16.0 - - - +
150A ALA 3.2 0.2 - - - -
151A LEU* 1.3 78.7 - - - +
153A ASN* 1.3 57.3 + - - +
154A ARG* 2.9 17.9 + - - +
330A TRP* 3.0 33.6 - - - +
350A LEU* 3.4 34.3 - - + +
353A ALA* 3.7 20.8 - - + +
354A HIS* 3.2 19.8 - - - +
357A ASP* 2.8 42.3 + - - +
544A ALA* 3.8 6.8 - - - +
547A GLU* 2.8 30.5 + - - -
548A HIS* 3.8 8.1 + - - -
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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