Contacts of the helix formed by residues 214 - 219 (chain L) 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 GLY 214 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209H TYR* 4.7 3.1 - - - -
231H LYS* 4.3 6.0 - - - +
239H PRO* 4.0 19.2 - - - +
240H TYR 3.5 22.7 - - - -
241H GLY* 4.6 0.4 - - - -
242H ALA* 4.2 5.1 - - - +
212L ASN* 2.8 16.8 + - - -
213L GLU* 1.3 76.2 - - - +
215L TYR* 1.3 58.5 + - - +
216L ALA* 2.7 18.0 + - - +
217L LYS 4.1 2.3 + - - -
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Residues in contact with TYR 215 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239H PRO* 5.9 0.9 - - - -
240H TYR 5.9 0.4 - - - -
212L ASN* 3.8 28.4 + - + +
214L GLY* 1.3 75.4 - - - +
216L ALA* 1.3 52.3 + - - -
217L LYS* 3.1 4.5 - - - -
218L ASP* 2.5 39.9 + - + +
219L PHE* 3.1 27.6 + + + -
264L TYR* 4.0 19.8 + + - -
267L ASN* 4.5 14.4 - - - +
269L LYS* 3.0 40.3 + - + -
274L LYS* 4.2 5.9 + - - -
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Residues in contact with ALA 216 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231H LYS* 3.6 40.4 - - + +
232H PHE* 4.2 13.7 - - + -
213L GLU 3.7 7.5 + - - +
214L GLY 2.7 10.1 + - - +
215L TYR* 1.3 72.1 - - - +
217L LYS* 1.3 61.6 + - - +
218L ASP 3.0 0.9 + - - -
219L PHE* 3.1 34.0 + - + +
224L THR* 5.0 3.1 + - - +
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Residues in contact with LYS 217 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231H LYS 3.8 9.8 + - - +
232H PHE* 3.3 41.2 - - + +
233H PRO* 4.0 24.4 + - - +
236H ASN* 3.6 24.2 + - - +
237H SER 4.9 1.6 + - - -
239H PRO* 4.5 16.0 - - + +
214L GLY 4.1 1.4 + - - -
215L TYR* 3.0 2.4 + - - -
216L ALA* 1.3 76.9 - - - +
218L ASP* 1.3 72.6 + - - +
219L PHE 3.6 1.4 - - - +
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Residues in contact with ASP 218 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215L TYR* 2.5 26.7 + - + +
217L LYS* 1.3 87.0 - - - +
219L PHE* 1.3 61.4 + - - +
267L ASN* 2.8 38.8 - - - +
268L LYS* 3.5 38.6 + - + +
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Residues in contact with PHE 219 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231H LYS* 5.6 0.2 - - - -
211L LEU* 3.7 28.5 - - + -
212L ASN 3.1 27.6 - - - -
213L GLU* 4.2 13.2 - - + -
215L TYR* 3.1 21.8 + + + -
216L ALA* 3.1 32.5 + - + +
217L LYS 4.7 2.1 - - - +
218L ASP* 1.3 82.8 - - - +
220L ASP* 1.3 65.0 + - - +
221L PRO* 3.9 1.4 - - - +
223L VAL* 4.0 18.8 - - + -
224L THR* 3.4 25.8 + - + +
227L ILE* 5.0 5.8 - - + -
265L PRO* 4.9 10.8 - - + -
267L ASN* 4.6 8.5 - - - -
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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