Contacts of the helix formed by residues 146 - 152 (chain A) in PDB entry 3A2C
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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144A GLY 3.8 0.6 + - - -
145A GLU* 1.3 73.3 - - - +
147A PHE* 1.3 89.8 + - + +
149A ARG* 3.5 10.7 + - - +
150A ILE* 3.6 25.2 + - + +
166A ILE* 4.1 24.2 - - + -
170A ILE* 4.6 5.4 - - + -
189A PRO* 4.5 4.5 + - + +
192A LEU* 2.7 46.9 + - + +
193A LEU* 4.5 0.2 - - - +
194A TYR* 3.8 31.6 - - + +
203A LEU* 4.1 6.7 - - + -
252A ILE* 4.6 5.2 - - + -
256A LEU* 4.6 1.6 - - + -
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Residues in contact with PHE 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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2A PDY 4.6 13.7 - - + -
145A GLU* 3.2 3.0 - - + +
146A LEU* 1.3 88.8 - - + +
148A SER* 1.3 64.4 + - - +
149A ARG 3.3 0.7 - - - -
150A ILE* 4.0 15.1 - - + +
151A GLN* 3.1 24.9 + - - +
189A PRO* 3.7 40.5 - - + +
252A ILE* 4.0 11.9 - - + -
255A ILE* 3.5 43.1 - - + -
256A LEU* 3.5 34.8 - - + -
338A THR* 5.3 0.2 - - + -
342A LEU* 4.4 23.1 - - + +
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Residues in contact with SER 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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144A GLY* 5.3 2.0 - - - -
145A GLU* 2.8 38.7 + - - +
147A PHE* 1.3 75.1 - - - +
149A ARG* 1.3 62.5 + - - +
151A GLN* 3.4 11.9 + - - +
152A ASP* 2.9 37.7 + - - +
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Residues in contact with ARG 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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143A GLY 3.4 17.4 + - - +
144A GLY* 4.8 0.9 - - - -
145A GLU 3.3 6.6 + - - +
146A LEU 3.7 6.7 - - - +
148A SER* 1.3 74.3 - - - +
150A ILE* 1.3 68.7 + - + +
151A GLN 3.0 2.4 + - - -
152A ASP* 3.1 20.9 + - - +
153A ARG* 3.8 4.7 + - - +
194A TYR* 3.5 54.5 - - + +
196A SER 2.7 30.1 + - - -
197A LYS* 3.5 24.4 - - - +
198A ARG 4.3 6.6 + - - -
199A PRO 5.6 2.0 + - - -
201A ALA* 3.8 8.5 + - - +
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Residues in contact with ILE 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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146A LEU* 3.6 25.4 + - + +
147A PHE* 3.7 16.1 + - + +
148A SER 3.4 0.2 - - - -
149A ARG* 1.3 77.4 - - + +
151A GLN* 1.3 57.1 + - - +
153A ARG* 2.9 24.6 - - - +
158A PHE* 3.5 43.7 - - + -
162A GLU* 5.5 0.2 - - - +
166A ILE* 4.0 4.7 - - + -
194A TYR* 5.8 1.1 - - + +
256A LEU* 3.3 33.7 - - + -
338A THR* 4.4 6.5 - - + -
339A SER* 2.8 34.6 + - - +
342A LEU* 4.8 2.5 - - + -
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Residues in contact with GLN 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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2A PDY 6.2 0.8 - - - -
147A PHE 3.1 19.9 + - - +
148A SER* 3.6 13.0 - - - +
149A ARG 3.0 0.6 - - - -
150A ILE* 1.3 74.6 - - - +
152A ASP* 1.3 67.7 + - - +
153A ARG 3.1 4.5 - - - -
339A SER* 4.0 3.4 - - - -
342A LEU* 2.7 51.1 + - + +
343A LYS* 3.0 45.2 + - + +
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Residues in contact with ASP 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 SER* 2.9 24.6 + - - +
149A ARG* 3.1 10.7 + - - +
151A GLN* 1.3 87.0 - - - +
153A ARG* 1.3 57.4 + - - +
343A LYS* 5.0 2.0 - - - +
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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