Contacts of the helix formed by residues 291 - 305 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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281F LEU 2.5 25.8 + - - -
282F PHE* 3.0 9.7 + - - -
283F SER 3.0 21.5 - - - -
284F GLY* 3.3 7.6 - - - +
286F LYS* 4.3 2.0 - - - +
290F LEU* 1.3 74.0 - - - +
292F GLU* 1.3 64.8 + - - +
293F GLN* 3.1 16.3 + - - +
294F ALA* 3.2 10.6 + - - +
295F LEU* 3.0 21.2 + - - +
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Residues in contact with GLU 292 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286F LYS* 4.2 33.1 + - - +
291F SER* 1.3 71.0 - - - +
293F GLN* 1.3 66.7 + - - +
295F LEU* 2.9 24.4 + - - +
296F TYR* 3.3 43.2 + - + -
385F LYS* 4.2 11.6 + - - -
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Residues in contact with GLN 293 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120F ILE* 3.6 18.9 - - + +
274F LEU* 5.4 1.3 - - + +
281F LEU* 3.5 38.6 - - + +
282F PHE* 4.6 8.1 - - + -
291F SER* 3.1 13.0 - - - +
292F GLU* 1.3 78.6 + - - +
294F ALA* 1.3 63.6 - - - +
296F TYR* 3.0 22.9 + - - +
297F TYR* 3.1 10.2 + - - +
382F ILE* 3.7 33.7 - - + +
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Residues in contact with ALA 294 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282F PHE* 3.6 39.8 - - + +
290F LEU* 3.7 25.4 - - + -
291F SER* 3.2 15.0 + - - +
292F GLU 3.3 0.2 - - - -
293F GLN* 1.3 78.4 - - - +
295F LEU* 1.3 57.7 + - - +
297F TYR* 2.9 7.0 + - - +
298F ILE* 2.8 32.2 + - - +
356F ILE* 4.8 2.7 - - + -
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Residues in contact with LEU 295 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286F LYS* 4.0 26.0 - - + -
287F TYR* 4.9 7.2 - - + +
290F LEU* 4.1 18.8 - - + -
291F SER 3.0 26.0 - - - +
292F GLU* 2.9 10.0 + - - +
294F ALA* 1.3 76.5 - - - +
296F TYR* 1.3 58.5 + - + +
298F ILE* 3.5 6.0 + - + -
299F GLY 2.9 21.5 + - - -
334F TYR* 3.5 41.5 - - + +
387F HIS* 5.5 7.6 - - + +
388F PRO* 3.0 28.7 - - + +
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Residues in contact with TYR 296 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292F GLU* 3.3 47.4 + - + +
293F GLN* 3.0 13.9 + - - +
295F LEU* 1.3 74.1 - - + +
297F TYR* 1.3 67.7 + - - +
299F GLY* 3.1 1.7 + - - -
300F GLY 2.9 19.1 + - - -
381F GLY* 3.3 25.0 - - - +
382F ILE* 3.6 15.7 - - + -
385F LYS* 3.3 61.1 + - + +
386F ILE 3.3 18.5 - - - +
387F HIS* 4.3 19.2 - + + -
388F PRO* 4.8 0.7 - - + -
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Residues in contact with TYR 297 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124F VAL* 4.3 6.8 - - + +
126F PHE* 4.6 0.2 - - - -
272F MET* 3.7 31.3 - - + +
273F SER 6.4 0.2 - - - -
274F LEU* 3.7 26.7 - - + -
282F PHE* 3.7 22.2 - + + -
293F GLN 3.1 10.4 + - - +
294F ALA 2.9 11.9 + - - +
296F TYR* 1.3 74.9 - - - +
298F ILE* 1.3 57.5 + - + +
300F GLY* 2.9 6.1 + - - -
301F VAL* 2.9 46.7 + - + +
356F ILE* 3.7 22.2 - - + -
374F LEU 4.0 2.9 - - - -
375F LEU* 3.2 35.1 + - + +
378F GLY* 3.4 37.5 - - - -
379F LEU 4.4 0.2 - - - -
382F ILE* 4.0 4.2 - - + +
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Residues in contact with ILE 298 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290F LEU* 4.5 8.5 - - + -
294F ALA 2.8 20.1 + - - +
295F LEU* 3.5 11.4 - - - +
297F TYR* 1.3 76.5 - - - +
299F GLY* 1.3 57.1 + - - +
301F VAL* 3.4 7.8 + - - +
302F ILE* 2.9 55.2 + - + +
334F TYR* 3.9 26.7 - - + -
343F ILE* 4.2 11.2 - - + -
345F ILE* 3.7 28.9 - - + -
356F ILE* 3.8 22.9 - - + -
388F PRO* 3.9 10.3 - - + -
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Residues in contact with GLY 299 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295F LEU 2.9 11.8 + - - -
296F TYR 3.1 4.2 + - - -
298F ILE* 1.3 76.1 - - - +
300F GLY* 1.3 57.2 + - - +
302F ILE* 3.4 5.7 + - - +
303F LYS* 2.8 28.8 + - - +
386F ILE* 3.7 27.8 - - - +
388F PRO* 3.9 15.7 - - - +
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Residues in contact with GLY 300 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296F TYR 2.9 10.5 + - - -
297F TYR 2.9 1.8 + - - -
299F GLY* 1.3 73.2 - - - +
301F VAL* 1.3 66.2 + - - +
303F LYS* 2.8 15.6 + - - +
304F HIS* 2.8 22.3 + - - -
377F ALA 3.1 24.2 - - - -
381F GLY* 3.7 14.0 - - - -
386F ILE* 4.8 2.2 - - - -
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Residues in contact with VAL 301 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272F MET* 5.4 0.2 - - + -
297F TYR* 2.9 45.0 + - + +
298F ILE* 3.6 8.5 - - - +
300F GLY* 1.3 74.0 - - - +
302F ILE* 1.3 59.1 + - + +
304F HIS 3.6 0.9 - - - -
305F ALA* 2.8 30.0 + - - +
308F ILE* 3.7 19.5 - - + +
332F LEU* 6.4 0.2 - - + -
343F ILE* 5.1 8.3 - - + -
356F ILE* 5.1 0.9 - - + -
358F VAL* 4.3 33.4 - - + -
360F PHE* 4.5 7.6 - - + -
374F LEU* 4.3 16.6 - - + +
377F ALA* 3.7 2.3 + - + -
378F GLY* 4.5 1.1 - - - -
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Residues in contact with ILE 302 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298F ILE* 2.9 45.7 + - + +
299F GLY* 3.6 5.4 - - - +
301F VAL* 1.3 76.8 - - - +
303F LYS* 1.3 63.9 + - - +
305F ALA* 3.6 11.8 - - - +
332F LEU* 3.6 48.5 - - + +
333F ALA* 4.3 7.0 - - - -
334F TYR* 4.7 1.6 - - + -
343F ILE* 4.0 17.7 - - + -
388F PRO* 4.6 17.3 - - + +
408F PRO* 4.4 13.7 - - + +
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Residues in contact with LYS 303 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299F GLY 2.8 14.2 + - - +
300F GLY* 2.8 11.7 + - - +
302F ILE* 1.3 80.2 - - - +
304F HIS* 1.3 80.7 + - + +
305F ALA* 3.3 0.7 + - - +
306F LYS 5.1 1.2 + - - -
380F ASP* 5.2 1.8 + - - -
384F ASN* 5.8 1.6 + - - -
386F ILE* 3.6 33.6 - - + +
424F ASP* 4.2 4.6 - - - +
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Residues in contact with HIS 304 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300F GLY* 2.8 22.4 + - - +
301F VAL 3.6 0.7 - - - -
303F LYS* 1.3 98.1 - - + +
305F ALA* 1.3 65.9 + - - +
306F LYS 3.4 2.0 - - - -
307F ALA* 2.9 7.0 + - - +
308F ILE* 2.8 21.2 + - + -
377F ALA* 3.4 33.0 - - + -
380F ASP* 3.0 30.9 + - - -
424F ASP* 2.8 37.8 + - - +
427F PHE* 3.5 31.0 - + + -
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Residues in contact with ALA 305 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301F VAL 2.8 17.4 + - - +
302F ILE 3.6 5.6 - - - +
303F LYS 3.3 2.2 - - - -
304F HIS* 1.3 73.1 - - - +
306F LYS* 1.3 54.2 + - + +
308F ILE* 2.8 11.5 + - - +
309F ASN* 2.7 38.3 + - - -
332F LEU* 3.4 42.8 - - + -
360F PHE* 4.8 7.4 - - + -
410F 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