Contacts of the helix formed by residues 221 - 232 (chain C) in PDB entry 1FTA
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 PRO 221 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219C PHE 4.0 4.3 - - - +
220C ASP* 1.3 84.4 - - + +
222C ALA* 1.3 57.3 + - - +
224C THR* 3.4 10.7 - - - +
225C GLU* 2.9 31.7 + - - +
334C HIS* 3.8 28.2 + - + +
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Residues in contact with ALA 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220C ASP* 2.9 17.9 + - - +
221C PRO* 1.3 74.3 - - - +
223C VAL* 1.3 59.6 + - - +
225C GLU* 3.7 0.7 - - - +
226C TYR* 2.9 28.4 + - - +
327C PHE* 4.4 2.0 - - + -
330C VAL* 3.5 10.9 - - + +
331C TYR* 3.6 44.6 - - + +
334C HIS* 4.0 18.6 + - + +
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Residues in contact with VAL 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211C LEU* 4.3 7.9 - - + -
219C PHE* 3.6 28.9 - - + -
220C ASP* 2.9 36.5 + - - +
222C ALA* 1.3 75.6 - - - +
224C THR* 1.3 58.7 + - - +
226C TYR* 3.1 2.7 + - - +
227C ILE* 2.9 50.5 + - + +
263C LEU* 4.9 5.4 - - + -
265C PRO* 4.3 20.6 - - + -
327C PHE* 4.1 22.0 - - + -
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Residues in contact with THR 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216C ALA* 4.7 11.2 - - + +
219C PHE* 3.6 21.2 + - + +
220C ASP 2.9 22.9 + - - -
221C PRO* 3.4 7.9 - - - +
222C ALA 3.3 0.2 - - - -
223C VAL* 1.3 77.9 - - - +
225C GLU* 1.3 61.8 + - - +
227C ILE* 3.6 7.5 + - + +
228C GLN* 3.4 23.0 + - - +
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Residues in contact with GLU 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221C PRO 2.9 18.7 + - - +
222C ALA 3.7 3.4 - - - +
224C THR* 1.3 73.0 - - - +
226C TYR* 1.3 66.6 + - - +
228C GLN* 3.3 10.2 + - + +
229C ARG* 3.0 33.6 + - + +
330C VAL* 3.9 20.1 - - + +
333C LYS* 3.0 30.9 + - - -
334C HIS* 3.2 27.4 + - + +
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Residues in contact with TYR 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209C TYR* 5.4 1.1 - - + -
222C ALA 2.9 18.3 + - - +
223C VAL* 3.1 5.1 + - - +
225C GLU* 1.3 76.3 - - - +
227C ILE* 1.3 64.7 + - + +
229C ARG* 3.2 21.3 - - - +
230C LYS* 3.3 43.3 + - + +
261C ILE* 4.0 34.3 - - + +
263C LEU* 4.3 13.9 - - + -
323C ASP* 3.6 23.4 + - - +
326C GLU* 3.2 32.1 + - - -
327C PHE* 3.8 37.5 - + + -
330C VAL* 3.8 11.9 - - + +
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Residues in contact with ILE 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209C TYR* 4.0 15.9 - - + -
211C LEU* 3.7 38.1 - - + -
213C GLU* 3.9 10.5 - - + +
219C PHE* 4.1 12.3 - - + -
223C VAL* 2.9 31.4 + - + +
224C THR* 4.1 6.3 - - + +
226C TYR* 1.3 82.4 - - + +
228C GLN* 1.3 60.9 + - - +
230C LYS* 2.8 25.6 + - - +
231C LYS* 3.1 40.6 + - - +
263C LEU* 5.5 1.6 - - + -
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Residues in contact with GLN 228 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224C THR 3.4 11.1 + - - +
225C GLU* 3.3 12.7 + - - +
227C ILE* 1.3 78.8 - - - +
229C ARG* 1.3 57.0 + - - +
231C LYS* 4.5 5.6 - - - +
232C PHE* 2.9 55.8 + - + +
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Residues in contact with ARG 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225C GLU* 3.0 27.9 + - + +
226C TYR* 3.2 15.0 - - - +
228C GLN* 1.3 77.0 - - - +
230C LYS* 1.3 62.5 + - - +
232C PHE 4.0 7.2 - - - -
233C PRO* 3.5 19.6 - - - +
234C PRO* 3.6 36.5 + - + +
326C GLU* 3.1 36.5 + - - +
330C VAL* 4.2 22.0 - - - +
333C LYS* 5.1 4.6 - - - +
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Residues in contact with LYS 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205C LYS* 5.4 0.6 - - - +
209C TYR* 4.1 21.5 - - + -
226C TYR* 3.3 49.3 + - + +
227C ILE* 2.8 11.1 + - - +
229C ARG* 1.3 83.4 + - - +
231C LYS* 1.3 61.8 + - - +
232C PHE 3.5 0.2 - - - -
233C PRO* 4.2 3.3 - - - +
239C PRO* 3.2 6.1 - - - +
240C TYR* 2.9 82.5 + - + +
326C GLU* 3.1 29.5 + - - +
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Residues in contact with LYS 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209C TYR* 3.2 30.1 - - + +
213C GLU* 2.9 24.3 + - - -
227C ILE* 3.1 24.1 + - + +
228C GLN* 3.3 2.7 + - - -
230C LYS* 1.3 81.2 - - - +
232C PHE* 1.3 77.6 + - + +
233C PRO* 3.7 2.9 - - - -
239C PRO* 3.2 25.5 - - - +
213D GLU* 3.6 23.7 + - - +
214D ALA* 4.5 2.0 - - - +
216D ALA* 3.7 20.5 - - + +
217D LYS* 3.6 11.4 + - - +
231D LYS* 4.1 9.3 - - - +
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Residues in contact with PHE 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228C GLN* 2.9 41.0 + - + +
229C ARG* 4.0 0.2 - - - -
231C LYS* 1.3 96.5 - - + +
233C PRO* 1.3 68.0 - - - +
234C PRO* 3.3 10.4 - - - +
216D ALA* 4.0 21.5 - - + -
217D LYS* 3.5 38.6 - - + -
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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