Contacts of the helix formed by residues 366 - 384 (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 ASN 366 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22F THR* 4.4 1.0 - - - +
23F ASP 3.2 16.0 + - - -
24F THR 2.7 26.8 + - - +
25F LYS 3.7 14.2 + - - +
26F GLY* 3.4 9.9 - - - -
104F PRO* 3.8 7.5 - - - +
311F LEU 3.7 5.0 + - - +
314F PRO* 4.4 2.2 - - - +
364F ALA 3.6 2.2 + - - -
365F ALA* 1.3 69.8 - - - +
367F PRO* 1.3 72.3 - - - +
368F TYR* 3.2 24.8 + - - +
369F LEU* 3.1 28.6 + - + +
370F CYS* 2.7 23.6 + - - +
442F TYR* 5.3 4.0 - - + +
446F ARG* 5.4 0.2 - - - +
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Residues in contact with PRO 367 (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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26F GLY* 4.8 4.5 - - - +
232F ALA* 3.4 31.4 - - + +
235F ILE* 3.3 31.9 - - + -
236F GLN* 3.8 19.5 - - - +
239F LYS* 5.0 2.7 - - - +
268F MET* 5.4 3.6 - - + -
365F ALA* 3.1 11.7 - - + +
366F ASN* 1.3 86.8 - - - +
368F TYR* 1.3 57.0 + - + +
370F CYS* 4.4 1.8 - - + -
371F PHE* 2.7 51.2 + - + -
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Residues in contact with TYR 368 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22F THR* 3.4 30.6 + - + -
88F ARG* 3.7 14.6 + - - -
104F PRO* 3.4 32.8 - - + +
105F ARG* 3.9 23.3 + - + -
108F ALA* 3.9 24.0 - - + +
229F THR* 4.0 6.1 - - + -
232F ALA* 3.2 29.5 + - + -
233F ASP* 2.6 36.7 + - - -
236F GLN* 4.2 9.0 - - + +
366F ASN* 3.2 12.7 + - - +
367F PRO* 1.3 74.8 - - + +
369F LEU* 1.3 65.8 + - - +
371F PHE* 3.4 3.1 + - - +
372F ALA* 3.0 25.6 + - - +
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Residues in contact with LEU 369 (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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24F THR* 4.0 11.7 - - + +
104F PRO* 3.6 32.3 - - + +
107F ILE* 4.1 18.4 - - + -
311F LEU* 3.0 29.7 - - + +
366F ASN* 3.1 21.1 + - + +
368F TYR* 1.3 76.5 - - - +
370F CYS* 1.3 64.5 + - - +
372F ALA* 3.5 1.8 - - - +
373F ALA 3.0 19.9 + - - -
434F PHE* 4.3 14.8 - - + -
442F TYR* 3.5 37.5 - - + -
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Residues in contact with CYS 370 (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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268F MET* 6.0 1.3 - - - -
270F CYS* 5.1 1.1 - - - -
308F ILE* 4.7 0.5 - - - +
311F LEU* 3.8 14.9 - - - +
312F ALA* 3.1 32.1 - - - -
361F PRO* 4.3 7.9 - - - -
365F ALA* 3.8 18.8 - - + -
366F ASN 2.7 21.5 + - - +
367F PRO* 3.5 2.9 - - + +
369F LEU* 1.3 74.1 - - - +
371F PHE* 1.3 74.4 + - + +
373F ALA* 3.3 2.9 + - - +
374F LEU* 3.1 34.0 + - - +
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Residues in contact with PHE 371 (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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126F PHE* 3.3 34.5 - + + -
128F PRO* 3.6 23.6 - - + -
228F MET* 3.5 37.2 - - + -
231F LYS* 4.1 10.8 - - + -
232F ALA* 3.6 30.3 - - + -
235F ILE* 4.2 11.7 - - + -
268F MET* 4.9 7.0 - - + -
270F CYS* 4.1 20.6 - - - -
367F PRO* 2.7 31.7 + - + +
368F TYR* 3.8 3.1 - - - +
370F CYS* 1.3 81.0 - - + +
372F ALA* 1.3 63.0 + - - +
374F LEU* 3.1 2.3 + - - -
375F LEU* 2.9 19.4 + - - +
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Residues in contact with ALA 372 (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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107F ILE* 4.7 5.8 - - + -
108F ALA* 4.7 2.0 - - - -
111F ALA* 4.2 13.5 - - + -
228F MET* 3.7 20.5 - - + +
368F TYR 3.0 18.6 + - - +
369F LEU* 3.5 3.8 - - - +
371F PHE* 1.3 74.4 - - - +
373F ALA* 1.3 55.7 + - - +
375F LEU* 2.9 4.4 + - - +
376F MET* 2.7 39.0 + - + +
434F PHE* 3.9 21.3 - - + -
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Residues in contact with ALA 373 (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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308F ILE* 3.9 24.3 - - + +
311F LEU* 3.6 21.3 - - + -
369F LEU 3.0 17.4 + - - +
370F CYS 3.6 4.5 - - - +
372F ALA* 1.3 75.0 - - - +
374F LEU* 1.3 64.0 + - - +
377F ALA* 3.1 26.2 + - - +
427F PHE* 3.7 3.7 - - + -
428F LEU* 3.9 22.8 - - + +
434F PHE* 4.7 0.6 - - - -
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Residues in contact with LEU 374 (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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126F PHE* 4.0 15.3 - - + -
270F CYS* 4.3 19.3 - - + -
272F MET* 3.8 24.5 - - + -
297F TYR* 3.7 10.1 + - - -
301F VAL* 4.3 15.2 - - + +
308F ILE* 3.3 35.9 - - + -
358F VAL* 4.7 3.6 - - + -
360F PHE* 4.6 8.7 - - + -
361F PRO* 4.4 6.7 - - + -
370F CYS* 3.1 32.7 + - - +
371F PHE 3.1 7.6 + - - +
373F ALA* 1.3 78.1 - - - +
375F LEU* 1.3 61.7 + - - +
377F ALA* 3.8 2.3 - - - +
378F GLY* 3.0 18.0 + - - -
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Residues in contact with LEU 375 (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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111F ALA* 3.7 27.1 - - + +
115F LEU* 4.4 1.8 - - + -
124F VAL* 3.8 33.2 - - + -
126F PHE* 4.4 2.2 - - + -
228F MET* 4.0 11.7 - - - -
274F LEU* 4.4 3.8 - - + -
297F TYR* 3.2 22.4 + - + +
371F PHE 2.9 11.8 + - - +
372F ALA 2.9 8.1 + - - +
374F LEU* 1.3 76.3 - - - +
376F MET* 1.3 65.2 + - - +
378F GLY* 3.0 2.6 + - - -
379F LEU* 2.9 60.1 + - + +
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Residues in contact with MET 376 (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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111F ALA* 4.0 16.8 - - + -
114F TYR* 4.3 19.5 - - + -
372F ALA* 2.7 27.1 + - + +
375F LEU* 1.3 76.9 - - - +
377F ALA* 1.3 59.9 + - - +
379F LEU* 3.9 4.9 - - - +
380F ASP* 3.1 27.0 + - - +
427F PHE* 3.6 23.8 - - - +
428F LEU* 3.7 25.6 - - + +
430F ALA* 3.4 20.9 - - + +
433F VAL* 3.4 41.7 - - + -
434F PHE* 5.1 0.2 - - + -
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Residues in contact with ALA 377 (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* 3.1 31.2 - - - +
301F VAL* 4.1 1.3 - - - -
304F HIS* 3.4 16.2 - - + -
308F ILE* 3.6 20.4 - - + -
373F ALA 3.1 19.5 + - - +
374F LEU 3.8 2.2 - - - +
376F MET* 1.3 76.1 - - - +
378F GLY* 1.3 62.7 + - - +
380F ASP 3.6 0.2 + - - -
381F GLY 3.2 7.6 + - - -
427F PHE* 3.4 21.9 - - + -
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Residues in contact with GLY 378 (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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297F TYR* 3.4 52.9 - - - -
301F VAL* 4.5 0.4 - - - +
374F LEU 3.0 8.6 + - - -
375F LEU 3.0 6.0 + - - -
377F ALA* 1.3 76.4 - - - +
379F LEU* 1.3 63.0 + - - +
381F GLY 3.2 8.7 + - - -
382F ILE* 3.2 12.8 + - - +
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Residues in contact with LEU 379 (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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114F TYR* 3.6 39.0 - - + -
115F LEU* 3.3 35.0 - - + -
118F THR* 4.9 1.6 - - - +
120F ILE* 4.0 19.3 - - + -
274F LEU* 4.3 12.8 - - + -
375F LEU* 2.9 44.6 + - + +
376F MET* 3.9 8.1 - - - +
378F GLY* 1.3 77.4 - - - +
380F ASP* 1.3 57.0 + - - +
382F ILE* 3.0 8.6 + - + +
383F LYS* 2.9 35.4 + - - +
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Residues in contact with ASP 380 (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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303F LYS* 4.8 2.4 + - - +
304F HIS* 3.0 33.1 + - - +
376F MET 3.1 18.2 + - - +
377F ALA 3.9 0.9 - - - +
378F GLY 3.3 0.2 - - - -
379F LEU* 1.3 77.5 - - - +
381F GLY* 1.3 61.0 + - - +
383F LYS* 3.8 23.8 + - - +
384F ASN* 3.2 32.6 + - - +
386F ILE* 3.8 12.5 - - - +
427F PHE* 4.0 16.5 - - + +
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Residues in contact with GLY 381 (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* 3.3 26.5 - - - +
300F GLY* 3.7 10.3 - - - -
377F ALA 3.2 9.5 + - - -
378F GLY 3.2 1.7 + - - -
379F LEU 3.1 0.8 - - - -
380F ASP* 1.3 76.3 + - - +
382F ILE* 1.3 57.7 + - - +
385F LYS 3.2 3.5 + - - -
386F ILE* 2.8 41.9 + - - -
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Residues in contact with ILE 382 (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* 3.7 37.2 - - + -
274F LEU* 4.4 6.3 - - + -
293F GLN* 3.7 43.1 - - + +
296F TYR* 3.6 23.7 - - + -
297F TYR* 4.0 15.3 - - + +
378F GLY 3.2 13.4 + - - +
379F LEU* 3.0 9.6 + - + +
381F GLY* 1.3 76.0 - - - +
383F LYS* 1.3 71.0 + - - +
385F LYS* 3.0 24.1 + - - +
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Residues in contact with LYS 383 (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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114F TYR* 3.1 28.9 + - - +
118F THR* 4.8 11.7 - - + -
120F ILE* 4.2 14.6 - - + -
379F LEU* 2.9 24.2 + - - +
380F ASP* 3.8 26.6 + - - +
382F ILE* 1.3 76.8 - - - +
384F ASN* 1.3 71.2 + - - +
385F LYS* 3.3 11.3 + - - +
430F ALA* 5.7 3.6 - - - +
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Residues in contact with ASN 384 (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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303F LYS* 5.8 1.6 + - - -
380F ASP* 3.2 27.7 + - - +
381F GLY 3.8 0.4 - - - -
383F LYS* 1.3 96.3 + - - +
385F LYS* 1.3 69.0 + - - +
386F ILE* 3.0 18.6 + - + +
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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