Contacts of the helix formed by residues 366 - 384 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B THR* 4.4 0.6 - - - +
23B ASP 3.2 16.2 + - - -
24B THR 2.7 26.0 + - - +
25B LYS 3.7 15.1 + - - +
26B GLY* 3.4 10.1 - - - -
104B PRO* 3.8 7.7 - - - +
311B LEU 3.7 6.1 + - - +
314B PRO* 4.4 2.0 - - - +
364B ALA 3.6 1.8 + - - -
365B ALA* 1.3 69.4 - - - +
367B PRO* 1.3 70.3 - - - +
368B TYR* 3.2 24.3 + - - +
369B LEU* 3.1 28.5 + - + +
370B CYS* 2.7 24.0 + - - +
442B TYR* 5.3 4.0 - - + +
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Residues in contact with PRO 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B GLY* 4.8 4.3 - - - +
232B ALA* 3.4 31.6 - - + +
235B ILE* 3.3 31.9 - - + -
236B GLN* 3.8 20.6 - - - +
239B LYS* 5.0 2.5 - - - +
268B MET* 5.4 3.8 - - + -
365B ALA* 3.1 12.0 - - + +
366B ASN* 1.3 87.3 - - - +
368B TYR* 1.3 57.6 + - + +
370B CYS* 4.4 1.8 - - + -
371B PHE* 2.7 50.9 + - + -
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Residues in contact with TYR 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B THR* 3.4 29.7 + - + -
88B ARG* 3.7 14.2 + - - -
104B PRO* 3.4 32.8 - - + +
105B ARG* 3.9 23.1 + - + +
108B ALA* 3.9 23.5 - - + +
229B THR* 4.0 6.3 - - + -
232B ALA* 3.2 30.1 + - + -
233B ASP* 2.6 36.0 + - - -
236B GLN* 4.2 9.5 - - + +
366B ASN* 3.2 14.1 + - - +
367B PRO* 1.3 74.6 - - + +
369B LEU* 1.3 64.6 + - - +
371B PHE* 3.4 2.6 + - - +
372B ALA* 3.0 25.7 + - - +
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Residues in contact with LEU 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B THR* 4.0 11.7 - - + +
104B PRO* 3.6 31.9 - - + +
107B ILE* 4.1 18.4 - - + -
311B LEU* 3.0 29.6 - - + +
366B ASN* 3.1 21.6 + - + +
368B TYR* 1.3 76.1 - - - +
370B CYS* 1.3 65.3 + - - +
372B ALA* 3.3 2.2 + - - +
373B ALA 3.0 19.4 + - - -
434B PHE* 4.3 15.5 - - + -
442B TYR* 3.5 37.2 - - + -
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Residues in contact with CYS 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268B MET* 6.0 2.2 - - - -
270B CYS* 5.1 0.9 - - - -
308B ILE* 4.7 0.3 - - - +
311B LEU* 3.8 13.9 - - - +
312B ALA* 3.1 32.3 - - - -
361B PRO* 4.3 7.4 - - - -
365B ALA* 3.8 17.9 - - + -
366B ASN 2.7 21.6 + - - +
367B PRO* 3.5 3.4 - - + +
369B LEU* 1.3 73.7 - - - +
371B PHE* 1.3 74.9 + - + +
373B ALA* 3.3 2.9 + - - +
374B LEU* 3.1 35.1 + - - +
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Residues in contact with PHE 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B PHE* 3.3 36.1 - + + -
128B PRO* 3.6 22.9 - - + -
228B MET* 3.5 37.0 - - + -
231B LYS* 4.1 10.5 - - + -
232B ALA* 3.6 30.1 - - + -
235B ILE* 4.2 11.4 - - + -
268B MET* 4.9 7.2 - - + -
270B CYS* 4.1 19.1 - - - -
367B PRO* 2.7 31.5 + - + +
368B TYR* 3.8 2.9 - - - +
370B CYS* 1.3 81.0 - - + +
372B ALA* 1.3 64.0 + - - +
374B LEU* 3.1 2.5 + - + -
375B LEU* 2.9 19.1 + - - +
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Residues in contact with ALA 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B ILE* 4.7 5.8 - - + -
108B ALA* 4.7 2.0 - - - -
111B ALA* 4.2 13.9 - - + -
228B MET* 3.7 19.3 - - + +
368B TYR 3.0 18.6 + - - +
369B LEU* 3.5 3.8 - - - +
371B PHE* 1.3 75.4 - - - +
373B ALA* 1.3 55.4 + - - +
375B LEU* 2.9 4.8 + - - +
376B MET* 2.7 38.9 + - + +
434B PHE* 3.9 21.8 - - + -
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Residues in contact with ALA 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B ILE* 3.9 23.9 - - + +
311B LEU* 3.6 21.8 - - + -
369B LEU 3.0 17.2 + - - +
370B CYS 3.6 4.7 - - - +
372B ALA* 1.3 75.5 - - - +
374B LEU* 1.3 63.4 + - - +
377B ALA* 3.1 26.2 + - - +
427B PHE* 3.7 3.9 - - + -
428B LEU* 3.9 21.7 - - + +
434B PHE* 4.7 0.4 - - - -
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Residues in contact with LEU 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B PHE* 4.0 15.9 - - + -
270B CYS* 4.3 19.1 - - + -
272B MET* 3.8 23.8 - - + -
297B TYR* 3.7 9.5 + - - -
301B VAL* 4.3 15.2 - - + +
308B ILE* 3.3 36.8 - - + -
358B VAL* 4.8 4.0 - - + -
360B PHE* 4.6 8.3 - - + -
361B PRO* 4.4 5.8 - - + -
370B CYS* 3.1 32.5 + - - +
371B PHE 3.3 7.6 - - - +
373B ALA* 1.3 78.5 - - - +
375B LEU* 1.3 61.3 + - - +
377B ALA* 3.4 2.6 + - - +
378B GLY* 3.0 18.2 + - - -
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Residues in contact with LEU 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B ALA* 3.7 27.1 - - + +
115B LEU* 4.4 2.0 - - + -
124B VAL* 3.8 33.9 - - + -
126B PHE* 4.4 2.4 - - + -
228B MET* 4.0 12.3 - - - -
274B LEU* 4.4 3.6 - - + -
297B TYR* 3.2 22.4 + - + +
371B PHE 2.9 11.6 + - - +
372B ALA 2.9 7.4 + - - +
374B LEU* 1.3 76.7 - - - +
376B MET* 1.3 66.6 + - - +
378B GLY* 3.0 2.6 + - - -
379B LEU* 2.9 60.3 + - + +
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Residues in contact with MET 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B ALA* 4.0 17.3 - - + -
114B TYR* 4.3 19.5 - - + -
372B ALA* 2.7 26.7 + - + +
375B LEU* 1.3 77.8 - - - +
377B ALA* 1.3 60.8 + - - +
379B LEU* 3.9 4.5 - - - +
380B ASP* 3.1 26.9 + - - +
427B PHE* 3.6 23.0 - - - +
428B LEU* 3.7 26.5 - - + +
430B ALA* 3.4 20.4 - - + +
433B VAL* 3.4 41.3 - - + -
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Residues in contact with ALA 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300B GLY* 3.1 30.1 - - - +
301B VAL* 4.1 1.3 - - - -
304B HIS* 3.4 16.6 - - + -
308B ILE* 3.6 20.6 - - + -
373B ALA 3.1 19.1 + - - +
374B LEU 3.8 2.5 - - - +
376B MET* 1.3 76.3 - - - +
378B GLY* 1.3 62.3 + - - +
381B GLY 3.2 7.8 + - - -
427B PHE* 3.4 21.7 - - + -
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Residues in contact with GLY 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297B TYR* 3.4 53.5 - - - -
301B VAL* 4.5 0.4 - - - +
374B LEU 3.0 8.6 + - - -
375B LEU 3.0 6.3 + - - -
377B ALA* 1.3 76.4 - - - +
379B LEU* 1.3 63.1 + - - +
381B GLY 3.2 8.7 + - - -
382B ILE* 3.2 12.3 + - - +
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Residues in contact with LEU 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B TYR* 3.6 38.4 - - + +
115B LEU* 3.3 34.1 - - + -
118B THR* 4.9 2.0 - - - +
120B ILE* 4.0 20.9 - - + -
274B LEU* 4.3 12.6 - - + -
375B LEU* 2.9 45.9 + - + +
376B MET* 3.9 7.2 - - - +
377B ALA 3.4 0.2 - - - -
378B GLY* 1.3 76.6 - - - +
380B ASP* 1.3 57.7 + - - +
382B ILE* 3.0 7.5 + - + +
383B LYS* 2.9 35.5 + - - +
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Residues in contact with ASP 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303B LYS* 4.8 2.3 + - - +
304B HIS* 3.0 33.6 + - - +
376B MET 3.1 18.6 + - - +
377B ALA 3.9 0.9 - - - +
379B LEU* 1.3 77.9 - - - +
381B GLY* 1.3 61.5 + - - +
383B LYS* 3.8 22.3 + - - +
384B ASN* 3.2 33.8 + - - +
386B ILE* 3.8 12.1 - - - +
427B PHE* 4.0 16.6 - - + +
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Residues in contact with GLY 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296B TYR* 3.3 28.7 - - - +
300B GLY* 3.7 10.1 - - - -
377B ALA 3.2 9.3 + - - -
378B GLY 3.2 1.5 + - - -
379B LEU 3.1 0.8 - - - -
380B ASP* 1.3 79.2 + - - +
382B ILE* 1.3 56.9 + - - +
385B LYS 3.2 3.6 + - - -
386B ILE* 2.8 41.3 + - - -
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Residues in contact with ILE 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B ILE* 3.7 37.0 - - + -
274B LEU* 4.4 5.8 - - + -
282B PHE* 5.5 0.2 - - + -
293B GLN* 3.7 42.0 - - + +
296B TYR* 3.6 22.1 - - + -
297B TYR* 4.0 15.3 - - + +
378B GLY 3.2 14.0 + - - +
379B LEU* 3.0 9.8 + - - +
381B GLY* 1.3 76.0 - - - +
383B LYS* 1.3 71.0 + - - +
385B LYS* 3.0 24.2 + - - +
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Residues in contact with LYS 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B TYR* 3.1 30.5 + - - +
118B THR* 4.8 11.4 - - + -
120B ILE* 4.2 14.4 - - + -
379B LEU* 2.9 23.5 + - - +
380B ASP* 3.8 27.0 + - - +
382B ILE* 1.3 76.6 - - - +
384B ASN* 1.3 71.4 + - - +
385B LYS* 3.3 11.6 + - - +
430B ALA* 5.7 3.4 - - - +
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Residues in contact with ASN 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303B LYS* 5.8 1.7 + - - -
380B ASP* 3.2 26.4 + - - +
381B GLY 3.8 0.2 - - - -
383B LYS* 1.3 95.8 - - - +
385B LYS* 1.3 68.4 + - - +
386B ILE* 3.0 18.8 + - + +
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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
------------------------------------------------------------
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