Contacts of the helix formed by residues 220 - 232 (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 ASP 220 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218L ASP 3.6 2.0 + - - -
219L PHE* 1.3 74.9 - - - +
221L PRO* 1.3 74.8 - - + +
222L ALA* 2.9 25.4 + - - +
223L VAL* 2.8 46.0 + - - +
224L THR* 3.0 9.2 + - - -
265L PRO* 5.5 0.3 - - - +
266L ALA 4.3 16.0 + - - +
267L ASN* 4.6 5.8 - - - +
331L TYR* 4.5 12.3 - - - -
334L HIS* 5.0 1.7 - - - +
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Residues in contact with PRO 221 (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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219L PHE 3.9 2.1 - - - +
220L ASP* 1.3 95.8 - - + +
222L ALA* 1.3 53.2 + - - +
224L THR* 2.9 11.2 + - - +
225L GLU* 2.6 37.8 + - - +
334L HIS* 3.5 30.5 - - + +
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Residues in contact with ALA 222 (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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220L ASP* 2.9 22.4 + - - +
221L PRO* 1.3 72.8 - - - +
223L VAL* 1.3 58.8 + - + +
226L TYR* 3.0 31.2 + - - +
327L PHE* 4.7 3.9 - - + -
330L VAL* 3.4 16.7 - - - +
331L TYR* 3.8 37.7 - - + +
334L HIS* 3.9 15.1 - - + -
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Residues in contact with VAL 223 (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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211L LEU* 4.0 23.3 - - + -
219L PHE* 4.0 25.8 - - + -
220L ASP* 2.8 29.1 + - - +
222L ALA* 1.3 75.9 - - - +
224L THR* 1.3 59.8 + - - +
226L TYR* 3.9 4.9 - - - +
227L ILE* 3.0 33.5 + - + +
263L LEU* 4.2 7.4 - - + -
265L PRO* 3.7 32.1 - - + -
266L ALA 5.3 0.4 - - - +
327L PHE* 4.2 15.9 - - + -
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Residues in contact with THR 224 (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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216L ALA 5.0 3.2 + - - +
219L PHE* 3.4 24.8 + - + +
220L ASP 3.0 14.8 + - - -
221L PRO* 2.9 13.4 + - - +
223L VAL* 1.3 77.3 - - - +
225L GLU* 1.3 61.9 + - - +
227L ILE* 3.4 6.9 + - - +
228L GLN* 3.1 25.8 + - + +
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Residues in contact with GLU 225 (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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221L PRO 2.6 19.8 + - - +
222L ALA 4.1 2.5 - - - +
224L THR* 1.3 70.6 - - - +
226L TYR* 1.3 66.2 + - - +
228L GLN* 3.0 21.3 + - + +
229L ARG* 2.7 57.2 + - + +
330L VAL* 4.1 7.4 - - + +
333L LYS* 3.6 19.9 + - - +
334L HIS* 3.1 27.4 + - + +
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Residues in contact with TYR 226 (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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209L TYR* 5.4 0.7 - - + -
222L ALA 3.0 19.4 + - - +
223L VAL 3.9 3.6 - - - +
224L THR 3.3 0.2 - - - -
225L GLU* 1.3 76.5 - - - +
227L ILE* 1.3 70.6 + - + +
229L ARG* 3.3 13.3 + - + +
230L LYS* 3.2 51.6 + - + +
261L ILE* 3.5 23.7 - - + +
263L LEU* 4.1 29.6 - - + -
323L ASP* 3.4 19.4 + - - +
326L GLU* 4.0 15.0 - - - -
327L PHE* 3.8 49.1 - + + -
330L VAL* 4.1 17.6 - - + +
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Residues in contact with ILE 227 (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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209L TYR* 3.6 23.1 - - + -
211L LEU* 3.6 41.5 - - + -
213L GLU* 4.1 8.5 - - - +
219L PHE* 5.0 7.0 - - + -
223L VAL* 3.0 25.2 + - + +
224L THR* 3.7 6.5 - - - +
225L GLU 3.2 0.2 - - - -
226L TYR* 1.3 86.6 - - + +
228L GLN* 1.3 65.2 + - - +
230L LYS* 3.2 13.3 + - + +
231L LYS* 3.3 39.4 + - + +
263L LEU* 4.9 2.7 - - + -
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Residues in contact with GLN 228 (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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224L THR* 3.1 19.6 + - + +
225L GLU* 3.0 17.6 + - + +
227L ILE* 1.3 76.5 - - - +
229L ARG* 1.3 52.8 + - + +
231L LYS* 3.1 10.6 + - - +
232L PHE* 2.6 77.0 + - + +
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Residues in contact with ARG 229 (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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225L GLU* 2.7 45.2 + - + +
226L TYR* 3.6 8.5 - - + +
227L ILE 3.3 0.4 - - - -
228L GLN* 1.3 78.6 - - + +
230L LYS* 1.3 64.9 + - + +
232L PHE 3.7 8.3 - - - -
233L PRO* 2.8 29.8 - - - +
234L PRO* 3.9 29.0 - - + +
326L GLU* 4.8 14.3 + - - +
329L LYS* 5.0 13.5 - - - +
330L VAL* 4.3 23.4 - - - +
333L LYS* 4.1 15.4 - - - +
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Residues in contact with LYS 230 (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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209L TYR* 4.2 23.6 - - + -
226L TYR* 3.2 48.4 + - + +
227L ILE* 3.8 11.2 - - - +
228L GLN 3.2 0.8 - - - -
229L ARG* 1.3 83.7 + - + +
231L LYS* 1.3 60.3 + - - +
233L PRO* 4.0 0.4 - - - +
239L PRO* 3.2 10.9 - - - +
240L TYR* 3.0 83.1 + - + +
323L ASP* 4.9 0.4 + - - -
326L GLU* 3.3 31.5 + - - -
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Residues in contact with LYS 231 (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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213H GLU* 2.9 56.2 + - - +
214H GLY* 4.5 6.2 - - - +
216H ALA* 4.1 14.8 - - + +
217H LYS* 3.8 8.3 - - - +
231H LYS* 5.7 0.6 - - - +
209L TYR* 3.5 16.2 + - + +
213L GLU* 3.2 21.2 + - - -
227L ILE* 3.5 24.9 - - + +
228L GLN* 3.1 17.9 + - - +
230L LYS* 1.3 79.4 - - - +
232L PHE* 1.3 79.6 + - + +
233L PRO* 3.4 7.5 - - - +
239L PRO* 3.6 16.5 - - - +
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Residues in contact with PHE 232 (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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216H ALA* 4.6 8.1 - - + -
217H LYS* 3.4 52.5 - - + +
228L GLN* 2.6 56.7 + - - +
229L ARG* 3.4 7.9 - - - +
231L LYS* 1.3 88.7 - - + +
233L PRO* 1.3 68.7 - - - +
234L PRO* 3.3 3.3 - - - +
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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