Contacts of the helix formed by residues 209 - 214 (chain A) 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 209 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A CYS 4.3 5.7 + - - -
64A LEU* 3.1 38.3 + - - +
66A MET* 3.5 21.5 - - - -
205A GLY 2.7 22.1 + - - -
208A VAL* 1.3 74.6 - - - +
210A LEU* 1.3 60.9 + - - +
211A TRP 3.2 0.2 - - - -
212A VAL* 3.1 11.7 + - - +
213A THR* 2.9 33.7 + - - +
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Residues in contact with LEU 210 (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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40A ASN 4.5 3.8 - - - +
41A GLU* 3.9 36.6 - - + +
64A LEU* 3.9 22.4 - - + -
206A THR 3.7 22.9 - - - +
207A ASP* 3.8 12.1 - - - +
208A VAL 3.2 0.6 - - - -
209A SER* 1.3 76.5 - - - +
211A TRP* 1.3 61.8 + - + +
212A VAL 3.2 0.2 - - - -
213A THR* 3.8 7.4 - - + +
214A LYS* 3.0 16.0 + - + +
215A ALA* 3.0 21.7 + - - +
1465A FAD 4.3 7.2 - - + -
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Residues in contact with TRP 211 (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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200A THR* 4.3 15.3 - - + -
207A ASP* 3.2 22.1 + - - +
208A VAL* 3.1 29.3 + - + +
210A LEU* 1.3 80.9 - - + +
212A VAL* 1.3 52.4 + - + +
215A ALA* 3.1 13.0 - - + +
216A LEU 3.0 7.3 + - - -
217A ARG* 2.7 82.2 + - + +
219A LEU* 3.8 14.4 - - + -
287A ASN* 4.8 8.1 + - - -
1465A FAD 3.4 37.7 - - - -
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Residues in contact with VAL 212 (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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20A THR* 4.1 28.5 - - + +
66A MET* 3.8 15.3 - - + -
208A VAL 3.7 5.6 - - - +
209A SER* 3.3 25.8 - - - +
211A TRP* 1.3 78.1 - - - +
213A THR* 1.3 67.7 + - + +
216A LEU* 3.3 7.8 - - - -
217A ARG 3.8 17.9 - - - +
219A LEU* 4.8 10.1 - - + -
107B ARG* 2.5 42.2 + - - +
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Residues in contact with THR 213 (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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22A SER* 5.6 5.2 - - - -
25A GLU* 5.9 1.1 - - - +
40A ASN* 2.8 54.5 + - - +
63A CYS 4.4 13.5 - - - +
209A SER* 2.9 29.0 + - - +
210A LEU* 3.8 4.1 - - + -
212A VAL* 1.3 81.9 - - + +
214A LYS* 1.3 77.3 + - - +
216A LEU* 3.3 17.8 - - - +
107B ARG* 4.4 2.4 + - - +
110B ARG* 3.8 7.8 + - - -
258B ASP* 5.4 0.9 - - - +
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Residues in contact with LYS 214 (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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39A CYS 2.9 28.9 + - - -
40A ASN* 3.6 12.5 - - - +
41A GLU* 3.5 38.0 + - + +
210A LEU* 3.0 17.0 + - + +
213A THR* 1.3 89.7 + - - +
215A ALA* 1.3 62.8 + - - +
216A LEU* 3.2 2.3 + - - +
110B ARG* 4.7 3.4 - - - +
114B ARG* 3.1 28.6 + - - -
258B ASP* 3.2 34.3 + - - +
259B ARG* 4.6 1.0 - - - +
260B ASP* 3.5 21.7 + - - +
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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