Contacts of the helix formed by residues 247 - 259 (chain C) in PDB entry 1TLF
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 247 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246C ASN* 1.3 72.2 - - - +
248C GLN* 1.3 55.6 + - - +
250C ALA* 3.0 4.7 - - - +
251C LEU 2.8 28.9 + - - -
273C TYR 3.0 9.6 + - - +
274C ASP* 4.2 1.5 + - + +
275C ASP* 2.9 11.4 + - - -
276C THR* 2.8 33.9 + - - +
279C SER* 2.7 30.6 + - - +
282C TYR* 3.6 10.3 - - - +
286C LEU* 3.7 12.4 - - + +
288C THR* 2.5 28.9 + - - -
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Residues in contact with GLN 248 (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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72C ALA 4.8 1.8 + - - -
73C LEU* 3.6 12.6 - - - +
74C HIS* 2.9 60.7 + - + +
220C TRP 3.4 20.8 + - - +
221C SER* 4.1 4.9 - - - +
222C ALA* 3.0 29.3 - - - +
246C ASN* 3.4 6.1 + - - +
247C ASP* 1.3 74.5 - - + +
249C MET* 1.3 65.5 + - - +
250C ALA 3.0 1.1 - - - -
251C LEU* 3.1 9.7 + - - +
252C GLY 3.1 9.4 + - - -
276C THR* 5.4 2.0 - - + +
282C TYR* 4.4 5.4 - - - +
998C IPT 5.5 0.7 + - - -
277D GLU* 5.9 2.2 - - - +
278D ASP* 3.7 24.8 + - - +
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Residues in contact with MET 249 (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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185C LEU* 3.5 28.0 - - + +
186C ALA 3.6 10.5 - - - +
187C GLY* 4.4 6.5 - - - -
218C GLY* 3.5 32.5 - - - +
220C TRP* 3.5 28.5 - - - +
221C SER 3.4 23.3 - - - +
222C ALA* 4.2 0.2 - - - +
224C SER* 4.3 3.4 - - - -
225C GLY* 3.2 14.4 - - - +
244C VAL* 3.8 9.4 - - + +
245C ALA* 4.6 5.4 - - - -
246C ASN* 3.1 23.3 + - - +
248C GLN* 1.3 79.4 - - - +
250C ALA* 1.3 57.3 + - - +
252C GLY 3.0 1.4 + - - -
253C ALA* 2.9 24.9 + - - +
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Residues in contact with ALA 250 (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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244C VAL* 3.5 17.7 - - + +
246C ASN 3.2 16.2 + - - +
247C ASP 3.0 14.1 + - - +
249C MET* 1.3 74.9 - - - +
251C LEU* 1.3 61.1 - - - +
253C ALA* 3.2 2.8 + - - +
254C MET* 3.0 31.5 + - - +
270C VAL* 4.1 15.4 - - + +
272C GLY* 4.2 2.9 - - - -
286C LEU* 3.7 20.4 - - + -
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Residues in contact with LEU 251 (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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222C ALA* 4.5 2.0 - - + -
247C ASP 2.8 6.6 + - - +
248C GLN* 3.1 10.1 + - - +
250C ALA* 1.3 75.9 - - - +
252C GLY* 1.3 63.1 + - - +
254C MET* 3.5 10.6 + - + +
255C ARG* 3.1 22.3 + - - +
282C TYR* 3.5 57.2 - - + +
283C ILE 5.4 2.5 - - - +
251D LEU* 5.9 0.9 - - + -
278D ASP* 4.0 22.9 - - + +
281D CYS* 3.8 20.1 - - + +
282D TYR* 3.9 33.7 - - + -
283D ILE* 5.6 3.1 - - + +
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Residues in contact with GLY 252 (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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222C ALA* 3.2 29.1 - - - +
226C PHE* 3.3 19.2 - - - -
248C GLN 3.1 7.3 + - - -
249C MET 3.0 5.6 + - - -
251C LEU* 1.3 78.4 - - - +
253C ALA* 1.3 55.2 + - - +
255C ARG* 3.1 9.7 - - - +
256C ALA 3.0 21.3 + - - -
281D CYS* 4.6 2.5 - - - -
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Residues in contact with ALA 253 (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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185C LEU* 4.7 6.3 - - + -
225C GLY 3.8 0.8 - - - -
229C THR* 3.3 30.7 - - + +
242C MET* 4.3 14.4 - - - -
244C VAL* 4.7 5.2 - - + -
249C MET 2.9 14.1 + - - +
250C ALA* 3.2 11.2 + - - +
252C GLY* 1.3 67.0 - - - +
254C MET* 1.3 61.7 + - - +
255C ARG 3.0 1.3 - - - -
256C ALA* 3.1 1.9 + - - +
257C ILE* 2.9 37.9 + - + +
270C VAL* 4.8 4.0 - - + -
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Residues in contact with MET 254 (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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250C ALA 3.0 20.0 + - - +
251C LEU* 3.7 13.2 - - + +
253C ALA* 1.3 75.5 - - - +
255C ARG* 1.3 59.8 + - - +
257C ILE* 4.0 2.2 - - - -
258C THR* 3.3 17.7 + - - +
264C VAL* 4.0 25.1 - - + +
270C VAL* 4.2 10.3 - - + -
282C TYR* 4.6 8.7 - - + -
283C ILE 3.2 32.3 - - - +
284C PRO* 3.3 25.1 - - + +
286C LEU* 4.3 14.1 - - - -
328C THR* 3.6 17.5 - - + -
283D ILE* 3.1 20.1 - - + +
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Residues in contact with ARG 255 (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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234B ASN 5.5 1.8 + - - -
226C PHE* 3.6 20.7 - - + -
251C LEU 3.1 13.1 + - - +
252C GLY* 3.1 14.6 - - - +
253C ALA 3.0 0.2 - - - -
254C MET* 1.3 79.1 - - - +
256C ALA* 1.3 54.9 + - - +
258C THR* 3.2 7.8 + - - -
259C GLU* 3.2 59.5 + - - +
280D SER* 4.0 4.0 - - - +
281D CYS* 2.9 54.1 - - + +
282D TYR 3.6 8.2 + - - -
283D ILE* 3.9 10.9 - - - +
285D PRO* 3.5 31.8 - - - +
327D LYS* 5.9 0.8 - - - +
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Residues in contact with ALA 256 (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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226C PHE* 3.8 7.4 - - + +
229C THR* 3.7 28.9 - - + -
230C MET* 3.4 35.5 - - + +
233C LEU* 3.7 2.1 - - - +
252C GLY 3.0 11.3 + - - +
253C ALA 3.1 2.4 + - - +
255C ARG* 1.3 77.4 - - - +
257C ILE* 1.3 54.9 + - - +
259C GLU* 3.8 0.9 - - - -
260C SER* 2.6 34.0 + - - -
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Residues in contact with ILE 257 (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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229C THR* 4.3 10.5 - - + -
233C LEU* 4.3 7.0 - - + -
242C MET* 4.6 5.8 - - - -
253C ALA 2.9 26.9 + - - +
254C MET* 4.1 6.7 - - - +
256C ALA* 1.3 76.2 - - - +
258C THR* 1.3 62.3 + - - +
260C SER* 2.8 19.1 + - - -
261C GLY 3.2 0.2 + - - -
262C LEU* 3.1 48.7 + - + +
263C ARG 3.9 13.9 - - - +
264C VAL* 4.4 4.7 - - + -
268C ILE* 4.0 30.5 - - + +
270C VAL* 3.8 29.6 - - + -
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Residues in contact with THR 258 (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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254C MET 3.3 15.5 + - - +
255C ARG* 3.2 13.3 + - - -
257C ILE* 1.3 75.1 - - - +
259C GLU* 1.3 58.5 + - - +
261C GLY* 2.7 24.6 + - - -
262C LEU 3.3 15.9 - - - +
263C ARG* 5.3 0.4 - - - -
264C VAL* 4.2 14.1 - - + +
283D ILE* 3.6 32.0 - - + +
348D GLN* 3.6 10.6 + - - +
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Residues in contact with GLU 259 (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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234B ASN* 4.5 9.6 + - - +
226C PHE* 3.7 19.7 - - + -
230C MET* 3.9 16.0 - - + +
255C ARG* 3.2 38.6 + - - +
256C ALA* 3.5 10.8 - - - +
258C THR* 1.3 82.2 + - - +
260C SER* 1.3 57.6 + - - +
261C GLY 3.4 2.3 + - - -
344D ASP* 5.4 3.3 - - - +
348D GLN* 3.8 20.8 + - - +
351D ARG* 3.8 15.6 - - - -
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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