Contacts of the helix formed by residues 213 - 220 (chain A) in PDB entry 3EZZ
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 ARG 213 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209A TYR* 3.3 49.5 + - + +
210A HIS 2.9 9.2 + - - +
211A ALA 3.3 0.4 - - - -
212A ALA* 1.3 83.6 - - - +
214A ARG* 1.3 60.9 + - - +
215A ASP* 2.7 35.0 + - - +
216A MET* 3.5 30.2 - - + +
217A LEU* 2.9 33.9 + - - +
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Residues in contact with ARG 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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212A ALA 3.8 3.8 + - - -
213A ARG* 1.3 69.3 - - - +
215A ASP* 1.3 68.6 + - - +
217A LEU* 3.0 7.9 + - - +
218A ASP* 2.8 33.2 + - - +
236A PHE* 3.2 44.1 - - + -
239A HIS* 6.0 7.8 - - - -
240A TYR* 3.5 28.0 - - + +
507A SO4 2.9 43.2 + - - -
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Residues in contact with ASP 215 (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 ARG* 2.7 49.9 + - - +
214A ARG* 1.3 76.0 - - - +
216A MET* 1.3 76.4 + - - +
218A ASP* 4.0 4.2 - - - +
219A ALA* 3.0 31.1 + - - +
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Residues in contact with MET 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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193A MET* 5.7 0.9 - - - -
194A GLY 4.9 1.6 - - - +
195A GLY* 3.5 26.2 - - - +
196A PRO* 3.6 8.7 - - + -
209A TYR* 4.6 6.5 - - + -
210A HIS* 3.3 40.8 - - + +
213A ARG* 3.5 40.8 - - + +
214A ARG 3.2 0.4 - - - -
215A ASP* 1.3 87.0 + - - +
217A LEU* 1.3 66.0 + - + +
219A ALA* 3.5 6.4 + - - +
220A LEU* 3.3 27.8 + - - +
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Residues in contact with LEU 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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196A PRO* 6.0 2.2 - - + -
210A HIS* 3.9 9.0 - - + +
211A ALA 3.7 17.9 - - - +
213A ARG 2.9 30.1 + - - +
214A ARG* 3.0 9.4 + - - +
216A MET* 1.3 77.8 - - - +
218A ASP* 1.3 59.0 + - - +
220A LEU 3.3 1.7 + - - -
221A GLY 3.0 6.4 + - - -
222A ILE* 2.8 47.9 + - + +
225A LEU* 4.2 15.7 - - + -
236A PHE* 4.5 5.4 - - + -
240A TYR* 4.0 29.8 - - + -
277A LEU* 3.8 28.9 - - + -
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Residues in contact with ASP 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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214A ARG* 2.8 24.5 + - - +
215A ASP* 4.3 3.0 - - - +
217A LEU* 1.3 68.5 - - - +
219A ALA* 1.3 64.5 + - - +
220A LEU 3.1 2.0 - - - -
221A GLY* 3.1 14.5 + - - +
222A ILE 4.7 2.2 - - - +
240A TYR* 2.5 37.5 + - - -
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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 ASP 3.0 21.4 + - - +
216A MET* 3.7 7.2 - - - +
217A LEU 3.3 0.2 - - - -
218A ASP* 1.3 77.8 - - - +
220A LEU* 1.3 62.8 - - + +
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Residues in contact with LEU 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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196A PRO* 3.8 37.7 - - + +
204A TYR* 3.7 40.0 + - + +
216A MET 3.3 14.5 + - - +
217A LEU 3.8 4.3 - - - +
218A ASP 3.1 0.4 - - - -
219A ALA* 1.3 81.2 - - + +
221A GLY* 1.3 63.6 + - - +
222A ILE* 3.9 13.7 - - + -
275A ARG* 3.5 23.1 + - - -
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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