Contacts of the helix formed by residues 291 - 305 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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281D LEU 2.5 26.0 + - - -
282D PHE* 3.0 9.5 + - - -
283D SER 3.0 22.4 - - - -
284D GLY* 3.3 7.8 - - - +
286D LYS* 4.3 2.2 - - - +
290D LEU* 1.3 74.4 - - - +
292D GLU* 1.3 64.6 + - - +
293D GLN* 3.1 16.1 - - - +
294D ALA* 3.2 10.4 + - - +
295D LEU* 3.0 20.6 + - - +
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Residues in contact with GLU 292 (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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286D LYS* 4.2 32.1 + - - +
291D SER* 1.3 73.1 - - - +
293D GLN* 1.3 67.3 + - - +
295D LEU* 2.9 24.1 + - - +
296D TYR* 3.3 41.2 + - + -
385D LYS* 4.2 11.6 + - - -
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Residues in contact with GLN 293 (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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120D ILE* 3.6 18.5 - - + +
274D LEU* 5.4 1.3 - - + +
281D LEU* 3.5 39.2 - - + +
282D PHE* 4.6 7.4 - - + -
291D SER* 3.1 13.0 - - - +
292D GLU* 1.3 78.8 + - - +
294D ALA* 1.3 63.7 + - - +
296D TYR* 3.0 23.2 + - - +
297D TYR* 3.1 10.6 + - - +
382D ILE* 3.7 34.1 - - + +
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Residues in contact with ALA 294 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282D PHE* 3.6 38.9 - - + +
290D LEU* 3.7 25.4 - - + -
291D SER* 3.2 14.6 + - - +
292D GLU 3.3 0.2 - - - -
293D GLN* 1.3 78.4 - - - +
295D LEU* 1.3 57.7 + - - +
297D TYR* 3.0 7.1 + - - +
298D ILE* 2.8 32.3 + - - +
356D ILE* 4.8 2.5 - - + -
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Residues in contact with LEU 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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286D LYS* 4.0 25.8 - - + -
287D TYR* 4.9 7.2 - - + +
290D LEU* 4.1 19.7 - - + -
291D SER 3.0 25.8 - - - +
292D GLU* 2.9 9.5 + - - +
294D ALA* 1.3 76.7 - - - +
296D TYR* 1.3 59.1 + - + +
298D ILE* 3.5 6.7 + - + -
299D GLY 2.9 21.0 + - - -
334D TYR* 3.5 40.6 - - + +
387D HIS* 5.5 7.6 - - + +
388D PRO* 3.0 28.5 - - + +
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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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292D GLU* 3.3 47.0 + - + +
293D GLN* 3.0 13.3 + - - +
295D LEU* 1.3 76.2 - - + +
297D TYR* 1.3 66.6 - - - +
299D GLY* 3.1 1.9 + - - -
300D GLY 2.9 19.2 + - - -
381D GLY* 3.3 24.8 - - - +
382D ILE* 3.6 15.9 - - + -
385D LYS* 3.3 61.5 - - + +
386D ILE 3.3 19.2 - - - +
387D HIS* 4.3 19.6 - + - -
388D PRO* 4.8 0.2 - - + -
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Residues in contact with TYR 297 (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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124D VAL* 4.3 7.0 - - + +
126D PHE* 4.6 0.2 - - - -
272D MET* 3.7 32.1 - - + +
273D SER 6.4 0.2 - - - -
274D LEU* 3.7 26.5 - - + -
282D PHE* 3.7 22.2 - + + -
293D GLN 3.1 10.8 + - - +
294D ALA 3.0 11.6 + - - +
296D TYR* 1.3 74.3 - - - +
298D ILE* 1.3 57.0 + - - +
300D GLY* 2.9 5.9 + - - -
301D VAL* 2.9 46.6 + - + +
356D ILE* 3.7 21.3 - - + -
374D LEU 4.0 2.7 - - - -
375D LEU* 3.2 35.9 + - + +
378D GLY* 3.4 35.5 - - - -
379D LEU 4.4 0.2 - - - -
382D ILE* 4.0 4.8 - - + +
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Residues in contact with ILE 298 (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 LEU* 4.5 8.5 - - + -
294D ALA 2.8 20.5 + - - +
295D LEU* 3.5 11.2 - - - +
297D TYR* 1.3 76.7 - - - +
299D GLY* 1.3 57.2 + - - +
301D VAL* 3.4 7.8 + - - +
302D ILE* 2.9 56.2 + - + +
334D TYR* 3.9 26.9 - - + -
343D ILE* 4.2 9.9 - - + -
345D ILE* 3.7 29.6 - - + -
356D ILE* 3.8 22.4 - - + -
388D PRO* 3.9 10.5 - - + -
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Residues in contact with GLY 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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295D LEU 2.9 12.0 + - - -
296D TYR 3.1 4.4 + - - -
298D ILE* 1.3 76.8 - - - +
300D GLY* 1.3 56.9 + - - +
302D ILE* 3.7 4.9 - - - +
303D LYS* 2.8 29.3 + - - +
386D ILE* 3.7 27.9 - - - +
387D HIS 4.8 0.2 - - - -
388D PRO* 4.0 15.0 - - - -
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Residues in contact with GLY 300 (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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296D TYR 2.9 10.7 + - - -
297D TYR 2.9 1.8 + - - -
299D GLY* 1.3 74.1 - - - +
301D VAL* 1.3 65.0 + - - +
303D LYS* 2.8 16.0 + - - +
304D HIS* 2.8 22.1 + - - -
377D ALA 3.1 24.2 - - - -
381D GLY* 3.7 14.0 - - - -
386D ILE* 4.8 2.2 - - - -
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Residues in contact with VAL 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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272D MET* 5.4 0.2 - - + -
297D TYR* 2.9 44.6 + - + +
298D ILE* 3.6 8.7 - - - +
300D GLY* 1.3 72.3 - - - +
302D ILE* 1.3 58.8 + - + +
304D HIS 3.4 0.7 + - - -
305D ALA* 2.8 30.9 + - + +
308D ILE* 3.7 19.9 - - + +
332D LEU* 6.4 0.2 - - + -
343D ILE* 5.1 9.0 - - + -
356D ILE* 5.1 1.1 - - + -
358D VAL* 4.3 32.8 - - + -
360D PHE* 4.5 8.1 - - + -
374D LEU* 4.3 16.4 - - + +
377D ALA* 3.7 2.3 + - + -
378D GLY* 4.5 1.3 - - - -
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Residues in contact with ILE 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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298D ILE* 2.9 45.7 + - + +
299D GLY* 3.7 5.2 - - - +
301D VAL* 1.3 77.0 - - - +
303D LYS* 1.3 63.8 + - - +
305D ALA* 3.6 11.4 - - - +
332D LEU* 3.6 48.3 - - + +
333D ALA* 4.3 7.4 - - - -
334D TYR* 4.7 1.6 - - + -
343D ILE* 4.0 17.0 - - + -
388D PRO* 4.6 16.8 - - + +
408D PRO* 4.4 13.3 - - + +
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Residues in contact with LYS 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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299D GLY 2.8 13.5 + - - +
300D GLY* 2.8 11.9 + - - +
302D ILE* 1.3 79.2 - - - +
304D HIS* 1.3 79.8 + - + +
305D ALA* 3.6 0.7 + - - +
306D LYS 5.1 0.9 + - - -
380D ASP* 5.2 1.8 + - - -
384D ASN* 5.8 1.8 + - - -
386D ILE* 3.6 33.4 - - + +
424D ASP* 4.2 4.0 - - - +
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Residues in contact with HIS 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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300D GLY* 2.8 22.8 + - - +
301D VAL 3.6 0.9 - - - -
303D LYS* 1.3 98.0 - - + +
305D ALA* 1.3 65.8 + - - +
306D LYS 3.4 2.0 - - - -
307D ALA* 2.9 7.5 + - - +
308D ILE* 2.8 21.5 + - + +
377D ALA* 3.4 32.1 - - + -
380D ASP* 3.0 30.4 + - - -
424D ASP* 2.8 36.8 + - - +
427D PHE* 3.5 32.8 - + + -
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Residues in contact with ALA 305 (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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301D VAL 2.8 17.8 + - - +
302D ILE 3.6 5.2 - - - +
303D LYS 3.3 2.4 + - - -
304D HIS* 1.3 74.4 - - - +
306D LYS* 1.3 55.2 + - + +
308D ILE* 2.8 10.8 + - - +
309D ASN* 2.7 37.9 + - - -
332D LEU* 3.4 42.0 - - + -
360D PHE* 4.8 8.3 - - + -
410D VAL* 4.9 3.1 - - + -
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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