Contacts of the helix formed by residues 287 - 304 (chain D) in PDB entry 1LFD
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 THR 287 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286D ASN* 1.3 72.4 + - - +
288D LYS* 1.3 63.9 + - - +
290D PHE* 3.1 9.4 + - + +
291D GLU* 3.1 38.1 + - + +
324D THR* 3.4 29.7 + - - +
325D VAL* 3.7 12.6 - - + -
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Residues in contact with LYS 288 (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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56A ASP* 4.3 24.4 + - - -
231B LYS* 5.5 17.9 - - + +
286D ASN* 3.2 9.0 + - - +
287D THR* 1.3 78.2 - - - +
289D SER* 1.3 58.6 + - - +
291D GLU* 3.2 18.0 + - - +
292D ASP* 2.9 61.6 + - - +
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Residues in contact with SER 289 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211D ALA* 4.0 10.0 + - - +
214D VAL* 3.5 22.2 - - - -
281D VAL 4.8 1.2 - - - +
282D PHE* 3.6 9.1 - - - +
283D ALA 3.0 20.8 + - - -
286D ASN* 2.7 44.8 + - - +
288D LYS* 1.3 76.7 - - - +
290D PHE* 1.3 56.6 + - - +
292D ASP* 3.4 9.0 + - - +
293D ILE* 3.0 23.2 + - - +
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Residues in contact with PHE 290 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282D PHE* 3.7 35.4 - + + -
286D ASN 3.4 0.2 + - - -
287D THR* 3.1 14.0 + - + +
289D SER* 1.3 79.1 + - - +
291D GLU* 1.3 64.1 + - + +
293D ILE* 3.0 13.3 - - + +
294D HIS* 2.8 35.4 + + - -
313D LEU* 4.8 0.4 - - + -
325D VAL* 3.9 27.4 - - + -
329D GLN* 3.9 27.4 - - + -
330D ALA* 3.6 38.8 - - + -
333D LEU* 3.7 27.8 - - + -
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Residues in contact with GLU 291 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287D THR* 3.1 30.1 + - + +
288D LYS* 3.2 20.0 + - - +
290D PHE* 1.3 80.2 - - + +
292D ASP* 1.3 62.8 + - - +
294D HIS* 3.1 29.8 + - + +
295D GLN* 4.1 2.1 + - - +
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Residues in contact with ASP 292 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211D ALA* 3.6 24.6 - - + +
288D LYS* 2.9 56.4 + - - +
289D SER* 3.6 7.6 - - - +
291D GLU* 1.3 76.0 - - - +
293D ILE* 1.3 63.8 + - - +
294D HIS 3.1 2.5 - - - -
295D GLN* 3.0 20.3 + - + +
296D TYR* 3.2 23.7 + - + -
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Residues in contact with ILE 293 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209D VAL 4.4 0.4 - - - +
210D GLY* 4.3 10.1 - - - -
211D ALA 5.4 0.2 - - - +
280D CYS* 3.5 36.7 - - + +
281D VAL 3.4 25.1 - - - +
282D PHE* 4.5 3.4 - - + -
289D SER 3.0 13.4 + - - +
290D PHE* 3.0 25.8 - - + +
292D ASP* 1.3 76.2 - - - +
294D HIS* 1.3 66.3 + - - +
296D TYR* 3.5 14.9 + - + +
297D ARG* 3.1 22.5 + - - +
313D LEU* 3.9 25.4 - - + -
333D LEU* 4.1 11.7 - - + -
337D TYR* 5.1 2.1 - - + -
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Residues in contact with HIS 294 (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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290D PHE* 2.8 47.0 + + - -
291D GLU* 3.1 17.7 + - + +
292D ASP 3.1 0.4 - - - -
293D ILE* 1.3 75.6 - - - +
295D GLN* 1.3 55.0 + - - +
297D ARG* 3.1 3.8 + - - +
298D GLU* 2.8 50.1 + - - +
333D LEU* 3.4 32.7 - - + +
337D TYR* 3.4 25.2 + - - +
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Residues in contact with GLN 295 (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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268D ARG* 6.0 2.7 - - - +
291D GLU 4.1 1.3 + - - +
292D ASP* 3.0 16.0 + - - +
294D HIS* 1.3 79.6 - - - +
296D TYR* 1.3 53.6 + - + +
298D GLU* 3.2 24.4 + - - +
299D GLN* 2.7 41.3 + - - +
302D ARG* 4.3 19.4 - - - +
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Residues in contact with TYR 296 (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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209D VAL* 3.8 28.7 - - + -
210D GLY* 3.2 43.0 + - - -
211D ALA* 3.8 6.5 + - - -
258D THR* 5.7 0.4 - - - -
259D ALA 4.2 4.4 + - - -
260D GLY 3.9 6.6 + - - -
262D GLU* 4.7 2.3 + - - -
268D ARG* 3.0 43.5 + - - -
271D TYR* 4.2 6.3 - - - -
272D MET* 4.3 13.2 - - + -
280D CYS* 5.0 0.4 - - - -
292D ASP* 3.2 33.4 + - + -
293D ILE* 3.7 17.9 - - + +
294D HIS 3.3 0.4 - - - -
295D GLN* 1.3 78.3 - - + +
297D ARG* 1.3 58.2 + - - +
299D GLN* 3.1 8.5 + - - +
300D ILE* 2.8 38.5 + - + +
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Residues in contact with ARG 297 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280D CYS* 5.0 3.1 - - - -
293D ILE 3.1 14.3 + - - +
294D HIS 3.4 8.1 - - - +
296D TYR* 1.3 77.0 - - - +
298D GLU* 1.3 68.3 + - - +
300D ILE* 3.5 10.5 + - - +
301D LYS* 3.2 59.2 + - - +
307D ASP 5.8 2.0 + - - -
311D MET* 3.6 29.5 - - + +
336D SER 4.9 1.6 + - - -
337D TYR* 3.5 74.7 + - + +
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Residues in contact with GLU 298 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294D HIS* 2.8 34.5 + - + +
295D GLN* 3.5 23.8 + - - +
297D ARG* 1.3 86.0 - - - +
299D GLN* 1.3 56.9 + - - +
301D LYS* 3.7 11.8 - - - +
302D ARG* 3.0 38.5 + - - +
337D TYR* 5.6 1.6 - - + +
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Residues in contact with GLN 299 (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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265D SER 4.8 2.8 + - - -
268D ARG* 3.6 42.6 + - - +
269D ASP* 4.8 8.9 + - - +
272D MET* 3.7 21.3 - - + +
295D GLN* 2.7 27.2 + - - +
296D TYR* 3.6 8.5 - - - +
298D GLU* 1.3 72.1 - - - +
300D ILE* 1.3 59.0 + - - +
302D ARG* 3.4 29.0 + - - +
303D VAL* 2.9 40.1 + - + +
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Residues in contact with ILE 300 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209D VAL* 4.4 8.3 - - + -
272D MET* 3.9 27.8 - - + -
278D PHE* 3.7 51.8 - - + -
280D CYS* 4.0 13.9 - - - -
296D TYR 2.8 27.5 + - - +
297D ARG 3.8 3.1 - - - +
299D GLN* 1.3 71.8 - - - +
301D LYS* 1.3 59.0 + - - +
302D ARG 3.3 0.2 + - - -
303D VAL* 3.8 0.9 - - - +
304D LYS* 2.9 33.7 + - + +
309D VAL* 4.2 9.6 - - + -
311D MET* 3.8 26.0 - - + -
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Residues in contact with LYS 301 (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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297D ARG* 3.2 52.0 + - - +
298D GLU* 3.7 12.2 - - - +
300D ILE* 1.3 78.9 - - - +
302D ARG* 1.3 56.8 + - - +
304D LYS* 4.7 1.3 - - - -
305D ASP* 2.9 24.1 + - - -
306D SER 3.2 33.8 + - - +
307D ASP* 3.5 29.5 + - - +
309D VAL* 4.8 8.3 - - + +
311D MET* 6.0 0.4 - - + -
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Residues in contact with ARG 302 (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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295D GLN* 4.3 15.0 - - - +
298D GLU* 3.0 32.9 + - - +
299D GLN* 3.5 38.0 + - - +
301D LYS* 1.3 74.5 - - - +
303D VAL* 1.3 69.7 + - + +
305D ASP* 3.2 15.0 + - - +
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Residues in contact with VAL 303 (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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269D ASP* 3.5 51.8 - - - +
272D MET* 4.1 17.9 - - + -
273D ARG* 4.1 25.8 - - + +
299D GLN* 2.9 30.8 + - + +
300D ILE 3.8 2.5 - - - +
302D ARG* 1.3 81.0 - - + +
304D LYS* 1.3 62.8 + - - +
305D ASP* 3.3 3.1 + - - +
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Residues in contact with LYS 304 (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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272D MET 3.0 25.1 - - - +
273D ARG* 2.9 28.5 + - + +
274D THR 4.4 0.8 - - - -
275D GLY 2.8 24.8 + - - -
276D GLU* 4.8 3.7 - - - +
278D PHE* 4.1 6.3 - - - -
300D ILE* 2.9 27.9 + - + +
301D LYS* 4.1 4.0 - - - +
303D VAL* 1.3 75.0 - - - +
305D ASP* 1.3 72.5 + - - +
306D SER* 3.5 17.0 + - - +
309D VAL* 4.4 15.0 - - + -
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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
------------------------------------------------------------
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