Contacts of the helix formed by residues 291 - 305 (chain L) in PDB entry 1FPY
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 SER 291 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281L LEU 2.5 26.2 + - - -
282L PHE* 3.0 10.6 + - - -
283L SER 3.0 20.9 - - - -
284L GLY* 3.3 8.0 - - - +
286L LYS* 4.3 2.5 - - - +
290L LEU* 1.3 74.3 - - - +
292L GLU* 1.3 64.1 + - - +
293L GLN* 3.1 15.6 - - - +
294L ALA* 3.2 11.3 + - - +
295L LEU* 3.0 20.1 + - - +
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Residues in contact with GLU 292 (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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286L LYS* 4.2 32.0 + - - +
291L SER* 1.3 72.7 - - - +
293L GLN* 1.3 67.7 + - - +
295L LEU* 2.9 23.8 + - + +
296L TYR* 3.3 44.2 + - + +
385L LYS* 4.2 11.8 + - - -
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Residues in contact with GLN 293 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120L ILE* 3.6 18.0 - - - +
274L LEU* 5.4 1.1 - - + -
281L LEU* 3.5 39.6 - - + +
282L PHE* 4.6 7.4 - - + -
291L SER* 3.1 12.8 - - - +
292L GLU* 1.3 79.2 + - - +
294L ALA* 1.3 64.2 + - - +
296L TYR* 3.0 22.8 + - - +
297L TYR* 3.1 10.0 + - - +
382L ILE* 3.7 34.6 - - + +
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Residues in contact with ALA 294 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282L PHE* 3.6 39.0 - - + +
290L LEU* 3.7 25.8 - - + -
291L SER* 3.2 14.3 + - - +
292L GLU 3.2 0.2 + - - -
293L GLN* 1.3 79.1 - - - +
295L LEU* 1.3 58.3 + - - +
297L TYR* 2.9 6.8 + - - +
298L ILE* 2.8 32.2 + - - +
356L ILE* 4.8 2.5 - - + -
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Residues in contact with LEU 295 (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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286L LYS* 4.0 26.5 - - + -
287L TYR* 4.9 7.0 - - + +
290L LEU* 4.1 20.0 - - + -
291L SER 3.0 26.2 - - - +
292L GLU* 2.9 9.3 + - - +
294L ALA* 1.3 76.5 - - - +
296L TYR* 1.3 57.7 + - + +
298L ILE* 4.0 4.9 - - + -
299L GLY 2.9 21.7 + - - -
334L TYR* 3.5 41.7 - - + +
387L HIS* 5.5 7.9 - - + +
388L PRO* 3.0 29.7 - - + +
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Residues in contact with TYR 296 (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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292L GLU* 3.3 46.1 + - + +
293L GLN* 3.0 13.8 + - - +
295L LEU* 1.3 76.2 - - + +
297L TYR* 1.3 66.4 + - - +
299L GLY* 3.1 2.3 + - - -
300L GLY 2.9 19.2 + - - -
381L GLY* 3.3 23.8 - - - +
382L ILE* 3.6 15.9 - - + -
385L LYS* 3.3 61.5 + - + +
386L ILE 3.2 18.6 - - - -
387L HIS* 4.3 19.3 - + - -
388L PRO* 4.8 0.4 - - + -
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Residues in contact with TYR 297 (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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124L VAL* 4.3 6.7 - - + +
272L MET* 3.7 31.1 - - + +
274L LEU* 3.7 26.2 - - + -
282L PHE* 3.7 22.4 - + + -
293L GLN 3.1 10.6 + - - +
294L ALA 2.9 11.0 + - - +
296L TYR* 1.3 74.4 - - - +
298L ILE* 1.3 56.1 + - + +
300L GLY* 2.9 5.9 + - - -
301L VAL* 2.9 46.4 + - + +
356L ILE* 3.7 21.1 - - + -
374L LEU 4.0 2.9 - - - -
375L LEU* 3.2 34.8 + - + +
378L GLY* 3.4 37.8 - - - -
379L LEU 4.4 0.2 - - - -
382L ILE* 4.0 5.5 - - + +
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Residues in contact with ILE 298 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290L LEU* 4.5 8.3 - - + -
294L ALA 2.8 21.0 + - - +
295L LEU* 3.5 11.4 - - - +
297L TYR* 1.3 76.9 - - - +
299L GLY* 1.3 57.0 + - - +
301L VAL* 3.4 7.9 + - - +
302L ILE* 2.9 56.6 + - + +
334L TYR* 3.9 26.7 - - + -
343L ILE* 4.2 9.9 - - + -
345L ILE* 3.7 29.6 - - + -
356L ILE* 3.8 22.2 - - + -
388L PRO* 3.9 10.3 - - + -
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Residues in contact with GLY 299 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295L LEU 2.9 12.4 + - - -
296L TYR 3.1 4.0 + - - -
298L ILE* 1.3 76.1 - - - +
300L GLY* 1.3 57.8 + - - +
302L ILE* 3.4 5.0 + - - +
303L LYS* 2.8 28.9 + - - +
386L ILE* 3.7 27.1 - - - +
387L HIS 4.6 0.4 - - - -
388L PRO* 4.0 15.3 - - - -
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Residues in contact with GLY 300 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296L TYR 2.9 10.7 + - - -
297L TYR 2.9 0.9 + - - -
299L GLY* 1.3 72.8 - - - +
301L VAL* 1.3 65.6 + - - +
303L LYS* 2.8 15.9 + - - +
304L HIS* 2.8 21.9 + - - -
377L ALA 3.1 25.4 - - - -
381L GLY* 3.7 13.6 - - - -
386L ILE* 4.8 2.2 - - - -
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Residues in contact with VAL 301 (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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272L MET* 5.4 0.4 - - + -
297L TYR* 2.9 44.8 + - + +
298L ILE* 3.6 8.7 - - - +
300L GLY* 1.3 73.7 - - - +
302L ILE* 1.3 58.7 + - + +
304L HIS 3.6 1.0 - - - -
305L ALA* 2.8 30.9 + - - +
308L ILE* 3.7 19.1 - - + +
332L LEU* 6.4 0.2 - - + -
343L ILE* 5.1 8.7 - - + -
356L ILE* 5.1 0.9 - - + -
358L VAL* 4.3 33.9 - - + -
360L PHE* 4.5 7.6 - - + -
374L LEU* 4.3 15.7 - - + +
377L ALA* 3.7 2.3 + - + -
378L GLY* 4.5 1.1 - - - -
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Residues in contact with ILE 302 (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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298L ILE* 2.9 45.2 + - + +
299L GLY* 3.7 4.9 - - - +
301L VAL* 1.3 76.4 - - - +
303L LYS* 1.3 64.1 + - - +
305L ALA* 3.6 11.7 - - - +
332L LEU* 3.6 48.8 - - + +
333L ALA* 4.3 6.5 - - - -
334L TYR* 4.7 1.8 - - + -
343L ILE* 4.0 17.7 - - + -
388L PRO* 4.6 16.4 - - + +
408L PRO* 4.4 12.4 - - + +
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Residues in contact with LYS 303 (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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299L GLY 2.8 13.8 + - - +
300L GLY* 2.8 12.1 + - - +
302L ILE* 1.3 80.5 - - - +
304L HIS* 1.3 80.1 + - + +
305L ALA 3.6 0.5 + - - -
306L LYS 5.1 0.9 + - - -
380L ASP* 4.8 1.4 + - - +
384L ASN* 5.8 1.8 + - - -
386L ILE* 3.6 33.8 - - + +
424L ASP* 4.2 5.0 - - - +
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Residues in contact with HIS 304 (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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300L GLY* 2.8 23.8 + - - +
301L VAL 3.6 1.1 - - - -
303L LYS* 1.3 96.8 - - + +
305L ALA* 1.3 65.6 + - - +
306L LYS 3.4 2.2 - - - -
307L ALA* 2.9 7.2 + - - +
308L ILE* 2.8 21.9 + - + -
377L ALA* 3.4 31.2 - - + -
380L ASP* 3.0 30.9 + - - -
424L ASP* 2.8 38.0 + - - +
427L PHE* 3.5 34.1 - + + -
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Residues in contact with ALA 305 (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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301L VAL 2.8 16.5 + - - +
302L ILE 3.6 6.5 - - - +
303L LYS 3.3 2.2 + - - +
304L HIS* 1.3 73.8 - - - +
306L LYS* 1.3 54.6 + - + +
308L ILE* 2.8 11.3 + - - +
309L ASN* 2.7 39.2 + - - -
332L LEU* 3.4 42.2 - - + -
360L PHE* 4.8 7.6 - - + -
410L VAL* 4.9 2.9 - - + -
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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