Contacts of the helix formed by residues 366 - 384 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A THR* 4.4 0.6 - - - +
23A ASP 3.2 15.6 + - - -
24A THR 2.7 26.3 + - - +
25A LYS 3.7 14.6 + - - +
26A GLY* 3.4 10.6 - - - -
104A PRO* 3.8 7.7 - - - +
311A LEU 3.7 5.4 + - - +
314A PRO* 4.4 2.0 - - - +
364A ALA 3.6 1.8 + - - -
365A ALA* 1.3 70.0 - - - +
367A PRO* 1.3 71.7 - - - +
368A TYR* 3.2 25.0 + - - +
369A LEU* 3.1 29.1 + - + +
370A CYS* 2.7 23.8 + - - +
442A TYR* 5.3 4.5 - - + +
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Residues in contact with PRO 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A GLY* 4.8 3.6 - - - +
232A ALA* 3.4 32.1 - - + +
235A ILE* 3.3 31.9 - - + -
236A GLN* 3.8 20.0 - - - +
239A LYS* 5.0 2.9 - - - +
268A MET* 5.4 3.6 - - + -
365A ALA* 3.1 10.9 - - + +
366A ASN* 1.3 86.8 - - - +
368A TYR* 1.3 55.9 + - + +
370A CYS* 4.4 1.8 - - + -
371A PHE* 2.7 52.1 + - + -
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Residues in contact with TYR 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A THR* 3.4 28.9 + - + -
88A ARG* 3.7 14.4 + - - -
104A PRO* 3.4 33.0 - - + +
105A ARG* 3.9 22.5 + - + +
108A ALA* 3.9 24.5 - - + +
229A THR* 4.0 6.3 - - + -
232A ALA* 3.2 30.6 + - + -
233A ASP* 2.6 36.9 + - - -
236A GLN* 4.2 9.3 - - + +
366A ASN* 3.2 13.4 + - - +
367A PRO* 1.3 77.4 - - + +
369A LEU* 1.3 65.2 + - - +
371A PHE* 3.8 2.9 - - - +
372A ALA* 3.0 25.2 + - - +
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Residues in contact with LEU 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A THR* 4.0 12.1 - - + +
104A PRO* 3.6 31.4 - - + +
107A ILE* 4.1 18.4 - - + -
311A LEU* 3.0 29.1 - - + +
366A ASN* 3.1 21.6 + - + +
368A TYR* 1.3 78.1 - - - +
370A CYS* 1.3 64.2 + - - +
372A ALA* 3.5 2.0 - - - +
373A ALA 3.0 19.8 + - - -
434A PHE* 4.3 15.7 - - + -
442A TYR* 3.5 38.1 - - + -
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Residues in contact with CYS 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268A MET* 6.0 1.3 - - - -
270A CYS* 5.1 0.7 - - - -
308A ILE* 4.7 0.5 - - - +
311A LEU* 3.8 15.4 + - - +
312A ALA* 3.1 33.0 - - - +
361A PRO* 4.3 7.6 - - - -
365A ALA* 3.8 18.6 - - + -
366A ASN 2.7 21.9 + - - +
367A PRO* 3.5 2.9 - - + +
369A LEU* 1.3 73.5 - - - +
371A PHE* 1.3 74.3 + - + +
373A ALA* 3.3 2.9 + - - +
374A LEU* 3.1 34.2 + - - +
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Residues in contact with PHE 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A PHE* 3.3 35.2 - + + -
128A PRO* 3.6 23.6 - - + -
228A MET* 3.5 37.5 - - + -
231A LYS* 4.1 10.3 - - + -
232A ALA* 3.6 30.1 - - + -
235A ILE* 4.2 11.7 - - + -
268A MET* 4.9 7.0 - - + -
270A CYS* 4.1 19.5 - - - -
367A PRO* 2.7 32.2 + - + +
368A TYR* 3.8 2.9 - - - +
370A CYS* 1.3 81.5 - - + +
372A ALA* 1.3 63.0 + - - +
374A LEU* 3.1 2.3 + - - -
375A LEU* 2.9 19.8 + - - +
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Residues in contact with ALA 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A ILE* 4.7 5.8 - - + -
108A ALA* 4.7 2.2 - - - -
111A ALA* 4.2 13.5 - - + -
228A MET* 3.7 19.9 - - + +
368A TYR 3.0 18.4 + - - +
369A LEU 3.5 3.6 - - - +
371A PHE* 1.3 74.8 - - - +
373A ALA* 1.3 55.5 + - - +
375A LEU* 2.9 5.0 + - - +
376A MET* 2.7 38.8 + - + +
434A PHE* 3.9 21.5 - - + -
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Residues in contact with ALA 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308A ILE* 3.9 25.0 - - + +
311A LEU* 3.6 21.1 - - + -
369A LEU 3.0 15.9 + - - +
370A CYS 3.6 5.2 - - - +
372A ALA* 1.3 75.7 - - - +
374A LEU* 1.3 62.5 + - - +
377A ALA* 3.1 26.2 + - - +
427A PHE* 3.7 3.1 - - - -
428A LEU* 3.9 23.1 - - + +
434A PHE* 4.7 0.4 - - - -
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Residues in contact with LEU 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A PHE* 4.0 15.7 - - + -
270A CYS* 4.3 18.6 - - + -
272A MET* 3.8 24.5 - - + -
297A TYR* 3.7 9.4 + - - -
301A VAL* 4.3 13.9 - - + +
308A ILE* 3.3 37.5 - - + -
358A VAL* 4.8 4.3 - - + -
360A PHE* 4.6 8.3 - - + -
361A PRO* 4.4 7.4 - - + -
370A CYS* 3.1 32.0 + - - +
371A PHE* 3.3 7.6 - - - +
373A ALA* 1.3 77.7 - - - +
375A LEU* 1.3 62.1 + - - +
377A ALA* 3.4 2.9 + - - +
378A GLY* 3.0 18.2 + - - -
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Residues in contact with LEU 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A ALA* 3.7 27.4 - - + +
115A LEU* 4.4 2.0 - - + -
124A VAL* 3.8 33.7 - - + -
126A PHE* 4.4 2.2 - - + -
228A MET* 4.0 12.6 - - - -
274A LEU* 4.4 3.6 - - + -
297A TYR* 3.2 22.2 + - + +
371A PHE 2.9 11.4 + - - +
372A ALA* 2.9 8.5 + - - +
374A LEU* 1.3 76.5 - - - +
376A MET* 1.3 65.6 + - - +
378A GLY* 3.0 2.8 + - - -
379A LEU* 2.9 60.6 + - + +
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Residues in contact with MET 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A ALA* 4.0 17.3 - - + -
114A TYR* 4.3 20.0 - - + -
372A ALA* 2.7 27.3 + - + +
375A LEU* 1.3 78.3 - - - +
377A ALA* 1.3 60.6 + - - +
379A LEU* 3.5 5.0 + - - +
380A ASP* 3.1 27.0 + - - +
427A PHE* 3.6 23.2 - - - +
428A LEU* 3.7 25.1 - - + +
430A ALA* 3.4 21.1 - - + +
433A VAL* 3.4 40.8 - - + -
434A PHE* 5.1 0.2 - - + -
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Residues in contact with ALA 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300A GLY* 3.1 30.9 - - - +
301A VAL* 4.1 1.1 - - - -
304A HIS* 3.4 17.1 - - + -
308A ILE* 3.6 20.4 - - + -
373A ALA 3.1 18.9 + - - +
374A LEU 3.8 2.2 - - - +
376A MET* 1.3 77.1 - - - +
378A GLY* 1.3 63.5 + - - +
380A ASP 3.6 0.2 + - - -
381A GLY 3.2 7.8 + - - -
427A PHE* 3.4 21.3 - - + -
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Residues in contact with GLY 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297A TYR* 3.4 52.5 - - - -
301A VAL* 4.5 0.6 - - - +
374A LEU 3.0 8.6 + - - -
375A LEU 3.0 6.0 + - - -
377A ALA* 1.3 76.8 - - - +
379A LEU* 1.3 63.2 + - - +
381A GLY 3.2 8.5 + - - -
382A ILE* 3.2 12.8 + - - +
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Residues in contact with LEU 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A TYR* 3.6 38.6 - - + -
115A LEU* 3.3 35.0 - - + -
118A THR* 4.9 1.8 - - - +
120A ILE* 4.0 19.3 - - + -
274A LEU* 4.3 13.0 - - + -
375A LEU* 2.9 44.4 + - + +
376A MET* 3.9 7.4 - - - +
377A ALA 3.4 0.2 - - - -
378A GLY* 1.3 77.1 - - - +
380A ASP* 1.3 58.5 + - - +
382A ILE* 3.0 8.1 + - + +
383A LYS* 2.9 34.9 + - - +
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Residues in contact with ASP 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303A LYS* 4.8 2.1 + - - +
304A HIS* 3.0 32.8 + - - +
376A MET 3.1 18.6 + - - +
377A ALA 3.9 0.7 - - - +
379A LEU* 1.3 76.9 - - - +
381A GLY* 1.3 61.7 + - - +
383A LYS* 3.8 23.3 + - - +
384A ASN* 3.2 33.1 + - - +
386A ILE* 3.8 12.1 - - - +
427A PHE* 4.0 16.7 - - + +
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Residues in contact with GLY 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296A TYR* 3.3 28.0 - - - +
300A GLY* 3.7 9.9 - - - -
377A ALA 3.2 9.1 + - - -
378A GLY 3.2 2.0 + - - -
379A LEU 3.1 0.8 - - - -
380A ASP* 1.3 77.7 + - - +
382A ILE* 1.3 57.9 + - - +
385A LYS 3.2 3.6 + - - -
386A ILE* 2.8 42.3 + - - -
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Residues in contact with ILE 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A ILE* 3.7 36.3 - - + -
274A LEU* 4.4 6.7 - - + -
293A GLN* 3.7 42.0 - - + +
296A TYR* 3.6 23.6 - - + -
297A TYR* 4.0 14.8 - - + +
378A GLY 3.2 13.6 + - - +
379A LEU* 3.0 9.6 + - + +
381A GLY* 1.3 75.4 - - - +
383A LYS* 1.3 71.4 + - - +
385A LYS* 3.0 23.6 + - - +
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Residues in contact with LYS 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A TYR* 3.1 30.0 + - - +
118A THR* 4.8 12.3 - - + -
120A ILE* 4.2 14.6 - - + -
379A LEU* 2.9 23.7 + - - +
380A ASP* 3.8 27.5 + - - +
382A ILE* 1.3 75.7 - - - +
384A ASN* 1.3 70.7 + - - +
385A LYS* 3.3 11.4 + - - +
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Residues in contact with ASN 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303A LYS* 5.8 2.0 + - - +
380A ASP* 3.2 27.2 + - - +
381A GLY 3.8 0.2 - - - -
383A LYS* 1.3 95.7 + - - +
385A LYS* 1.3 68.9 + - - +
386A ILE* 3.0 19.4 + - + +
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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