Contacts of the helix formed by residues 145 - 149 (chain R) in PDB entry 2A3W
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 ASP 145 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16R VAL* 4.3 0.4 - - - -
135R GLN* 3.6 7.8 + - - +
136R GLU 4.0 5.5 + - - +
138R ASP* 5.1 2.8 - - - +
144R PHE* 1.3 75.6 - - - +
146R ARG* 1.3 61.6 + - - +
147R SER* 2.9 32.0 + - - -
148R GLN* 2.9 48.8 + - - +
149R SER 3.1 9.4 + - - -
336R CA 4.2 4.0 - - - -
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Residues in contact with ARG 146 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14R GLU* 3.6 56.6 + - + +
15R SER* 3.6 26.6 - - - +
16R VAL* 3.9 20.9 - - + +
45R ARG* 3.5 5.2 + - - -
145R ASP* 1.3 73.8 + - - +
147R SER* 1.3 58.3 + - - +
148R GLN 3.0 2.8 + - - -
149R SER* 2.6 24.4 + - - -
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Residues in contact with SER 147 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14R GLU* 5.6 1.1 - - - -
45R ARG* 3.3 21.6 + - - +
46R ALA* 3.2 18.0 + - - +
145R ASP* 2.9 25.7 + - - -
146R ARG* 1.3 77.0 - - - +
148R GLN* 1.3 62.1 + - - +
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Residues in contact with GLN 148 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349N CPJ 2.7 37.6 + - - +
45R ARG* 3.8 2.2 - - - +
46R ALA 4.0 4.0 - - - -
47R TYR* 3.5 1.3 - - - +
48R SER* 3.2 24.4 + - - -
64R TYR* 3.0 28.2 + - + +
136R GLU* 3.0 25.7 + - + +
145R ASP* 2.9 29.2 + - + +
147R SER* 1.3 83.0 - - - +
149R SER* 1.3 68.7 + - - +
150R PHE 3.6 0.5 + - - -
336R CA 2.3 25.4 - - - -
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Residues in contact with SER 149 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13R ARG 5.6 0.4 - - - -
14R GLU* 3.6 10.4 - - - +
15R SER 3.3 27.7 + - - -
43R LEU* 3.6 1.4 - - - +
45R ARG* 2.8 42.1 + - - -
47R TYR* 3.5 3.6 - - - +
134R GLY 3.4 7.2 - - - -
135R GLN* 3.6 16.8 - - - +
145R ASP 3.1 3.6 + - - -
146R ARG 2.6 18.8 + - - -
147R SER 3.7 0.2 - - - -
148R GLN* 1.3 78.8 - - - +
150R PHE* 1.3 62.7 + - - +
151R VAL* 4.4 0.4 - - - +
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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