Contacts of the helix formed by residues 215 - 220 (chain A) in PDB entry 2WSC
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 215 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211A LEU 3.6 6.3 - - - -
212A GLY 4.0 0.7 - - - -
214A GLY* 1.3 75.6 - - - -
216A LEU* 1.3 58.4 + - - +
218A TRP* 3.4 21.0 - - - +
219A ALA* 2.8 26.8 + - - +
303A HIS* 2.6 46.5 + - - +
306A ILE* 3.4 13.3 - - - +
307A ALA* 3.6 2.6 + - - -
1774A CLA 3.9 29.5 - - - +
1804A BCR 4.3 0.6 - - - +
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Residues in contact with LEU 216 (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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212A GLY 2.7 28.5 + - - +
213A LEU* 3.8 5.8 - - + -
215A SER* 1.3 68.9 + - - +
217A SER* 1.3 57.3 - - - +
219A ALA* 2.4 38.4 + - + +
220A ARG 3.2 1.9 + - - -
303A HIS 5.0 0.2 - - - -
304A LEU* 4.2 24.7 - - + +
307A ALA* 3.5 9.3 - - + +
311A LEU* 3.8 26.7 - - + -
1771A CLA 3.2 19.5 - - + +
1772A CLA 5.5 0.7 - - + -
1803A BCR 2.9 43.5 - - + -
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Residues in contact with SER 217 (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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213A LEU 3.1 22.8 + - - -
216A LEU* 1.3 77.7 - - - +
218A TRP* 1.3 61.6 + - - +
220A ARG 2.9 30.7 + - - +
1770A CLA 3.4 11.3 - - - +
1771A CLA 4.6 0.2 - - - -
1803A BCR 1.6 73.3 - - - +
1804A BCR 4.1 1.3 - - - -
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Residues in contact with TRP 218 (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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152A ILE* 5.9 5.4 - - + -
155A ALA* 5.0 15.9 - - + -
215A SER* 3.4 22.2 - - - +
216A LEU 2.8 0.8 + - - -
217A SER* 1.3 73.2 - - - +
219A ALA* 1.3 66.0 + - - +
220A ARG 5.0 0.2 - - - -
221A HIS* 3.5 22.2 - + - -
222A GLN* 2.6 66.4 + - + +
226A SER* 6.5 0.9 - - - -
303A HIS* 3.1 20.0 - + - -
1770A CLA 3.1 68.2 - + + +
1774A CLA 3.5 61.1 - + + -
1804A BCR 5.2 0.4 - - + -
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Residues in contact with ALA 219 (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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215A SER 2.8 14.4 + - - +
216A LEU* 2.4 31.4 + - + +
218A TRP* 1.3 65.5 - - - +
220A ARG* 1.3 49.9 + - - +
221A HIS 2.8 2.1 + - - -
222A GLN* 2.5 47.0 + - - +
223A VAL* 3.6 3.5 + - - +
224A HIS 5.0 0.2 + - - -
300A ALA* 4.7 8.8 - - + +
304A LEU* 4.4 23.3 - - + +
1771A CLA 4.0 20.5 - - + +
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Residues in contact with ARG 220 (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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216A LEU 3.2 2.6 + - - -
217A SER* 2.9 16.3 + - - +
219A ALA* 1.3 73.1 - - - +
221A HIS* 1.3 66.9 + - - +
224A HIS* 4.5 9.0 - - - -
1770A CLA 3.5 20.1 - - - +
1771A CLA 3.4 38.8 - - - +
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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