Contacts of the helix formed by residues 247 - 259 (chain D) in PDB entry 1LBI
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246D ASN* 1.3 73.1 - - - +
248D GLN* 1.3 59.4 + - + +
250D ALA* 3.2 6.8 - - - +
251D LEU 3.1 13.2 + - - -
273D TYR 3.1 7.6 + - - -
274D ASP* 3.6 7.2 + - - -
275D ASP* 3.1 9.4 + - - -
276D THR* 3.0 34.1 + - - +
279D SER* 2.3 33.1 + - - +
282D TYR* 3.0 26.4 - - + +
286D LEU* 3.7 4.5 - - + -
288D THR* 2.8 28.8 - - - +
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Residues in contact with GLN 248 (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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277C GLU* 5.6 4.4 - - - +
278C ASP* 3.1 22.6 + - - +
73D LEU* 3.5 25.2 - - - +
74D HIS* 3.1 46.1 + - + +
75D ALA 5.2 0.5 + - - -
220D TRP 3.2 18.4 + - - +
221D SER* 4.4 2.4 - - - +
222D ALA* 2.9 36.1 - - + +
246D ASN* 3.4 8.0 + - - +
247D ASP* 1.3 73.9 - - + +
249D MET* 1.3 66.2 + - - +
250D ALA 3.0 0.9 - - - -
251D LEU* 3.1 10.0 + - - +
252D GLY 3.2 0.9 + - - -
276D THR* 5.4 0.9 - - + +
282D TYR* 4.2 7.4 - - - +
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Residues in contact with MET 249 (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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185D LEU* 3.9 11.0 - - + +
186D ALA 3.6 20.0 - - - +
187D GLY* 3.9 4.9 - - - +
218D GLY* 3.7 29.8 - - - -
220D TRP* 3.7 31.4 - - + -
221D SER 3.4 20.0 - - - +
224D SER* 3.9 2.2 - - - +
225D GLY* 3.5 14.6 - - - -
244D VAL* 3.7 9.6 - - + -
245D ALA* 4.1 16.8 - - + +
246D ASN* 2.9 31.3 + - - +
248D GLN* 1.3 73.2 - - - +
250D ALA* 1.3 50.9 + - - +
252D GLY 3.3 1.0 + - - -
253D ALA* 2.7 35.2 + - - +
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Residues in contact with ALA 250 (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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244D VAL* 3.4 18.5 - - + +
246D ASN 3.3 14.6 + - - +
247D ASP 3.2 11.9 - - - +
248D GLN 3.0 0.4 - - - -
249D MET* 1.3 80.0 - - - +
251D LEU* 1.3 56.6 + - - +
253D ALA* 3.6 5.9 - - - +
254D MET* 2.9 35.4 + - - +
270D VAL* 4.4 2.1 - - + +
272D GLY* 4.3 2.0 - - - -
286D LEU* 3.6 29.8 - - + -
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Residues in contact with LEU 251 (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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251C LEU* 6.0 1.6 - - + -
278C ASP* 3.2 29.6 - - + +
281C CYS 3.4 29.2 - - - +
282C TYR* 3.8 26.0 - - + -
283C ILE* 4.3 13.0 - - + +
222D ALA* 4.1 5.4 - - + -
247D ASP 3.1 12.3 + - - +
248D GLN 3.1 8.9 + - - +
250D ALA* 1.3 74.5 - - - +
252D GLY* 1.3 53.5 + - - +
254D MET* 3.2 6.8 + - + +
255D ARG* 2.7 34.7 + - - +
282D TYR* 3.5 39.9 - - + +
283D ILE 5.3 0.9 - - - +
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Residues in contact with GLY 252 (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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281C CYS* 4.3 4.5 - - - -
222D ALA* 3.2 26.5 + - - +
226D PHE* 3.3 22.3 - - - +
248D GLN 3.2 7.1 + - - -
249D MET 3.6 0.2 - - - -
251D LEU* 1.3 76.8 - - - +
253D ALA* 1.3 58.1 + - - +
255D ARG* 3.1 6.1 + - - +
256D ALA 2.8 24.6 + - - -
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Residues in contact with ALA 253 (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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185D LEU* 4.6 1.6 - - + -
225D GLY 3.6 2.3 + - - +
229D THR* 3.0 26.4 - - - +
242D MET* 4.4 11.4 - - + -
244D VAL* 4.4 14.8 - - + -
249D MET 2.7 21.8 + - - +
250D ALA* 3.6 10.1 - - - +
252D GLY* 1.3 71.3 - - - +
254D MET* 1.3 57.6 + - - +
256D ALA* 3.3 1.7 + - - +
257D ILE* 2.8 35.9 + - - +
270D VAL* 4.8 4.0 - - + -
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Residues in contact with MET 254 (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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283C ILE* 4.2 9.0 - - + -
250D ALA 2.9 24.8 + - - +
251D LEU* 3.3 8.7 - - + +
253D ALA* 1.3 75.7 - - - +
255D ARG* 1.3 56.6 + - - +
257D ILE* 3.8 2.5 - - - +
258D THR* 2.7 38.3 + - - -
264D VAL* 3.7 24.4 - - + +
270D VAL* 4.1 9.2 - - + -
282D TYR* 4.0 18.4 - - + -
283D ILE 4.2 2.9 - - - +
284D PRO* 3.2 53.6 - - + +
286D LEU* 4.2 15.0 - - - -
328D THR* 4.2 8.7 - - - -
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Residues in contact with ARG 255 (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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234B ASN* 4.4 19.0 + - - +
235B GLU* 6.2 0.2 - - - +
280C SER* 2.8 30.0 + - - -
281C CYS* 3.8 15.7 - - - +
282C TYR 3.6 22.4 - - - +
283C ILE* 3.8 15.0 - - + +
285C PRO* 3.9 9.1 - - - +
223D MET* 4.1 20.6 - - - +
226D PHE* 3.7 25.7 - - - -
251D LEU 2.7 19.8 + - - +
252D GLY* 3.1 7.8 + - - +
254D MET* 1.3 73.5 - - - +
256D ALA* 1.3 60.0 + - - +
258D THR* 4.0 2.4 - - - -
259D GLU* 2.9 60.5 + - + +
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Residues in contact with ALA 256 (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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226D PHE* 3.6 26.0 - - + +
229D THR* 3.4 24.0 - - + -
230D MET* 3.7 13.8 - - - +
233D LEU* 4.7 0.4 - - - -
252D GLY 2.8 13.1 + - - +
253D ALA 3.3 8.7 - - - +
255D ARG* 1.3 74.5 - - - +
257D ILE* 1.3 67.4 + - - +
258D THR 3.2 0.3 + - - -
259D GLU* 3.2 8.7 + - - -
260D SER* 3.0 18.5 + - - -
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Residues in contact with ILE 257 (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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229D THR* 3.9 12.8 - - + +
233D LEU* 4.4 6.1 - - + -
242D MET* 4.3 6.1 - - - -
253D ALA* 2.8 27.6 + - + +
254D MET* 3.8 6.1 - - - +
256D ALA* 1.3 71.1 - - - +
258D THR* 1.3 63.9 + - - +
260D SER* 3.2 13.0 + - - -
262D LEU* 3.2 43.0 + - + +
263D ARG 4.4 0.2 - - - -
264D VAL* 4.4 13.5 - - + +
268D ILE* 3.5 44.9 - - + +
270D VAL* 3.8 22.4 - - + -
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Residues in contact with THR 258 (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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283C ILE* 4.2 26.2 - - + +
344C ASP* 4.2 11.1 - - - +
254D MET 2.7 23.1 + - - -
255D ARG 4.1 3.6 - - - -
256D ALA 3.2 0.2 - - - -
257D ILE* 1.3 76.4 - - - +
259D GLU* 1.3 60.8 + - + +
260D SER 3.0 5.8 + - - -
261D GLY* 3.0 15.6 + - - -
262D LEU 3.7 11.3 + - - +
264D VAL* 3.5 17.2 + - - +
284D PRO* 5.5 1.0 - - - +
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Residues in contact with GLU 259 (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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351A ARG* 4.1 9.0 + - - -
234B ASN* 4.1 10.4 + - - -
283C ILE 4.3 1.0 - - - +
285C PRO* 3.7 4.9 - - - +
340C ARG* 2.8 38.4 + - - +
344C ASP* 4.4 13.4 - - - +
347C MET* 3.9 18.9 - - - +
226D PHE* 4.0 5.9 - - - -
230D MET* 4.4 9.5 - - + +
255D ARG* 2.9 59.2 + - + +
256D ALA 3.2 3.7 + - - +
258D THR* 1.3 76.5 - - + +
260D SER* 1.3 56.1 + - - +
261D GLY 3.3 2.5 - - - -
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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