Contacts of the helix formed by residues 214 - 221 (chain N) in PDB entry 3J7Y
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 THR 214 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51I THR* 3.7 5.2 - - - +
206N GLU 5.7 2.2 - - - +
209N ASN* 3.8 26.0 - - - +
211N ASN 5.0 0.9 - - - +
212N PRO 3.5 7.1 + - - +
213N TRP* 1.3 75.9 - - - +
215N PHE* 1.3 63.3 + - - +
216N GLU* 3.7 19.7 + - - +
217N ARG* 3.2 29.6 + - - +
218N ILE* 3.5 22.0 + - - +
251N VAL 5.5 8.1 - - - +
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Residues in contact with PHE 215 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44I ARG* 4.6 5.8 - - - -
47I LEU* 3.6 33.0 - - + -
48I MET* 3.8 24.0 - - - -
51I THR* 3.9 20.3 + - - +
214N THR* 1.3 74.1 - - - +
216N GLU* 1.3 61.4 - - + +
218N ILE* 3.2 5.5 + - - +
219N ALA* 2.9 27.1 + - + +
230N LEU* 3.8 32.5 - - + -
234N ASP* 3.6 17.0 - - + -
238N LYS* 3.2 26.7 - - - -
239N GLY* 3.4 24.5 - - - +
250N ARG* 4.6 10.3 - - - +
251N VAL 5.7 4.8 - - - -
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Residues in contact with GLU 216 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206N GLU* 3.3 24.3 - - - +
214N THR* 3.4 17.8 - - - +
215N PHE* 1.3 81.1 - - + +
217N ARG* 1.3 57.1 + - - +
219N ALA* 3.2 5.8 + - - +
220N THR* 2.9 42.1 + - + +
238N LYS* 3.6 41.3 - - + +
251N VAL* 5.5 5.2 - - - +
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Residues in contact with ARG 217 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212N PRO* 4.5 11.4 + - - +
213N TRP* 3.1 40.5 - - + +
214N THR* 3.2 22.4 + - - +
216N GLU* 1.3 81.2 - - - +
218N ILE* 1.3 63.2 + - + +
220N THR* 4.0 4.9 - - - +
221N ALA* 3.1 36.4 + - + +
223N MET* 3.9 12.2 - - - +
43o ALA* 4.3 12.7 - - - +
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Residues in contact with ILE 218 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47I LEU* 3.6 23.3 - - + -
50I VAL* 4.6 0.2 - - + -
51I THR* 3.6 29.8 - - + -
213N TRP* 4.1 10.1 - - + -
214N THR 3.5 6.9 + - - +
215N PHE 3.2 8.3 + - - +
217N ARG* 1.3 77.2 - - + +
219N ALA* 1.3 58.1 + - - +
222N ASN* 3.1 22.3 + - - -
223N MET* 3.1 30.1 + - + +
224N LEU* 4.9 1.3 - - + -
226N ILE* 3.8 23.3 - - + +
35o MET* 5.5 1.1 - - + -
39o LEU* 3.6 40.2 - - + -
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Residues in contact with ALA 219 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215N PHE* 2.9 19.6 + - + +
216N GLU* 3.2 6.5 + - - +
218N ILE* 1.3 76.1 - - - +
220N THR* 1.3 67.2 + - + +
222N ASN* 3.0 18.0 + - - +
226N ILE* 4.9 1.6 - - - -
227N ARG* 4.8 10.0 + - - +
230N LEU* 4.1 27.4 - - + -
234N ASP 4.1 15.3 - - - +
235N LEU* 4.5 14.5 - - + +
238N LYS* 6.1 0.2 - - - -
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Residues in contact with THR 220 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216N GLU* 2.9 26.9 + - + +
217N ARG* 3.7 5.5 + - - +
219N ALA* 1.3 75.9 - - + +
221N ALA* 1.3 68.4 + - - +
222N ASN* 3.1 3.5 + - - +
235N LEU* 4.7 26.7 - - + +
40Z ARG 5.2 0.5 - - - +
41Z ILE* 3.7 6.2 - - - +
42Z PRO* 3.6 35.6 - - + +
45Z VAL* 4.5 6.1 - - - +
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Residues in contact with ALA 221 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217N ARG* 3.1 24.0 + - + +
220N THR* 1.3 78.3 + - - +
222N ASN* 1.3 56.1 + - - +
223N MET* 3.1 19.7 + - - -
41Z ILE* 4.1 3.8 - - - -
45Z VAL* 3.7 31.2 - - + +
114Z LYS* 2.3 31.7 + - - -
46o HIS* 3.7 8.8 + - + +
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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