Contacts of the helix formed by residues 11 - 17 (chain F) in PDB entry 2W3S
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 SER 11 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9F HIS* 3.1 6.5 + - - -
10F ASP* 1.3 99.5 + - - +
12F ALA* 1.3 54.7 + - - +
13F ARG 3.3 3.4 - - - -
14F ALA* 3.1 11.4 + - - +
15F HIS* 2.7 60.2 + - - -
222F ARG* 3.5 2.6 + - - -
223F ARG* 2.8 29.3 + - - -
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Residues in contact with ALA 12 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96E ILE* 3.9 29.1 - - + +
101E SER* 4.8 7.4 + - - +
8F PRO* 4.5 6.3 - - + -
9F HIS* 3.0 27.8 + - + +
10F ASP 3.5 1.0 - - - -
11F SER* 1.3 77.6 - - - +
13F ARG* 1.3 57.1 + - - +
15F HIS* 3.6 10.0 - - - +
16F VAL* 3.0 30.1 + - - +
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Residues in contact with ARG 13 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86E GLY 4.5 7.9 + - - -
88E LEU* 3.0 44.3 - - + +
96E ILE* 3.7 21.1 - - + +
11F SER 3.3 0.4 - - - -
12F ALA* 1.3 76.6 - - - +
14F ALA* 1.3 57.6 + - - +
16F VAL* 3.4 1.6 - - - +
17F THR* 2.8 44.5 + - + +
19F GLN* 5.3 9.0 - - - +
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Residues in contact with ALA 14 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F SER* 3.1 18.0 + - - +
13F ARG* 1.3 76.8 - - - +
15F HIS* 1.3 64.5 + - - +
17F THR* 3.9 4.7 - - - -
18F GLY 3.3 1.2 + - - -
19F GLN* 2.9 36.3 + - + +
20F ALA* 2.9 28.7 + - + +
223F ARG* 4.9 2.0 - - - +
187H GLU* 5.9 6.3 - - + -
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Residues in contact with HIS 15 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101E SER* 2.9 27.9 + - - +
102E GLN 3.4 24.0 - - - -
103E CYS 3.7 8.0 + - - -
104E GLY* 3.5 25.6 - - - -
107E THR* 4.2 6.7 - - - +
108E PRO* 4.2 11.3 - - - +
9F HIS* 3.7 23.7 + + - -
11F SER* 2.7 38.1 + - - +
12F ALA* 3.6 5.3 - - - +
14F ALA* 1.3 69.8 - - - +
16F VAL* 1.3 58.7 + - - +
18F GLY* 2.9 23.6 + - - -
20F ALA* 3.7 20.2 - - + -
22F TYR* 3.8 2.4 + - - -
223F ARG* 4.0 7.9 + - - -
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Residues in contact with VAL 16 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78E ILE* 3.3 12.7 - - - +
88E LEU* 4.6 3.1 - - + -
92E GLN* 2.9 47.7 + - + +
95E MET* 3.6 13.9 - - + -
96E ILE* 3.8 20.0 - - + -
101E SER* 6.1 0.9 - - - -
107E THR* 3.9 10.5 - - + -
111E ILE* 3.0 35.1 - - + +
12F ALA 3.0 13.8 + - - +
13F ARG* 3.4 11.2 - - - +
15F HIS* 1.3 76.9 - - - +
17F THR* 1.3 63.6 + - + +
18F GLY 3.6 0.2 - - - -
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Residues in contact with THR 17 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78E ILE* 3.7 11.9 - - - +
79E GLU* 4.3 12.8 - - - +
82E ALA* 4.7 8.1 - - + -
88E LEU* 3.8 29.2 - - + -
92E GLN* 3.8 16.6 - - - +
13F ARG* 2.8 26.8 + - + +
14F ALA 3.7 1.0 + - - -
15F HIS 2.9 0.2 + - - -
16F VAL* 1.3 76.9 - - + +
18F GLY* 1.3 63.5 + - - +
19F GLN* 2.7 42.1 + - - +
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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