Contacts of the helix formed by residues 212 - 219 (chain D) in PDB entry 2FIE
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 ASN 212 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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241A GLY* 4.6 5.1 - - - -
242A ALA* 3.1 22.0 + - - +
243A ARG* 3.4 25.0 - - - +
211D LEU* 1.3 73.3 - - - +
213D GLU* 1.3 57.6 + - - +
214D GLY* 2.8 28.4 + - - -
215D TYR* 3.5 34.9 + - + +
219D PHE* 3.5 16.8 - - - -
244D TYR* 3.6 28.2 + - + +
263D LEU 4.9 0.6 + - - -
264D TYR* 5.5 6.7 + - + +
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Residues in contact with GLU 213 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A TYR* 3.4 7.0 + - - +
213A GLU* 3.1 34.2 - - - +
231A LYS* 3.3 27.9 + - - +
242A ALA* 3.8 6.4 - - + +
209D TYR* 2.9 32.7 + - - -
211D LEU* 3.2 24.5 + - + +
212D ASN* 1.3 70.2 + - - +
214D GLY* 1.3 60.2 + - - +
215D TYR 3.4 0.7 - - - -
216D ALA* 3.4 14.1 - - + +
219D PHE* 4.3 11.9 - - + -
227D ILE* 4.1 5.7 - - + +
231D LYS* 3.1 20.8 + - - -
242D ALA* 4.5 3.8 - - - +
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Residues in contact with GLY 214 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A TYR* 4.3 6.3 - - - -
231A LYS* 4.4 7.9 - - - -
239A PRO* 3.7 21.4 - - - +
240A TYR 3.5 22.7 - - - -
241A GLY* 4.7 0.2 - - - -
242A ALA* 3.9 2.3 - - - +
212D ASN* 2.8 16.4 + - - -
213D GLU* 1.3 75.9 - - - +
215D TYR* 1.3 62.6 + - - +
216D ALA* 2.9 12.0 + - - +
217D LYS 4.5 1.7 + - - -
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Residues in contact with TYR 215 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A PRO* 5.8 3.1 - - + -
212D ASN* 3.5 31.2 + - + +
213D GLU 3.4 0.8 - - - -
214D GLY* 1.3 77.1 - - - +
216D ALA* 1.3 62.8 + - - +
217D LYS 3.4 2.0 - - - -
218D ASP* 3.1 28.2 + - + +
219D PHE* 3.3 26.1 + + + -
264D TYR* 4.2 19.1 + + - -
267D ASN* 4.3 19.3 - - - +
269D LYS* 3.4 38.3 + - + -
274D LYS* 5.0 4.3 + - - -
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Residues in contact with ALA 216 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A LYS* 3.8 25.4 - - + +
232A PHE* 4.4 8.2 - - + -
213D GLU* 3.4 18.9 + - + +
214D GLY 2.9 3.6 + - - -
215D TYR* 1.3 73.3 - - - +
217D LYS* 1.3 59.5 + - - +
218D ASP 2.9 10.2 + - - -
219D PHE* 3.2 34.7 + - + +
224D THR* 4.6 3.3 + - - +
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Residues in contact with LYS 217 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A LYS 3.4 21.7 + - - +
232A PHE* 3.1 48.2 - - + +
233A PRO* 4.2 8.7 + - - +
236A ASN* 4.3 18.4 + - - +
237A SER 5.3 0.4 + - - -
239A PRO* 4.2 16.8 - - + -
214D GLY 4.5 1.6 + - - -
215D TYR 3.4 0.6 - - - -
216D ALA* 1.3 76.4 - - - +
218D ASP* 1.3 76.0 + - - +
219D PHE 3.7 0.8 - - - +
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Residues in contact with ASP 218 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A PRO* 5.4 5.2 - - - +
215D TYR* 3.1 22.6 + - + +
216D ALA 2.9 1.0 - - - -
217D LYS* 1.3 100.7 - - - +
219D PHE* 1.3 63.7 + - - +
220D ASP* 3.7 0.3 + - - -
267D ASN* 3.1 29.3 - - + +
268D LYS* 4.0 38.5 + - + +
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Residues in contact with PHE 219 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211D LEU* 3.3 32.5 - - + -
212D ASN 3.5 21.1 - - - -
213D GLU* 4.3 9.0 - - + -
215D TYR* 3.6 17.9 - + + -
216D ALA* 3.2 36.7 + - + +
217D LYS 3.7 0.7 - - - +
218D ASP* 1.3 81.2 - - - +
220D ASP* 1.3 66.1 + - - +
221D PRO* 3.8 1.4 - - - +
223D VAL* 3.7 20.2 - - + -
224D THR* 3.3 26.7 + - + +
227D ILE* 5.3 4.7 - - + -
265D PRO* 4.6 15.0 - - + -
266D ALA 5.3 1.3 - - - -
267D ASN* 4.9 8.1 - - - -
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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