Contacts of the helix formed by residues 365 - 381 (chain N) in PDB entry 1KYO
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 ILE 365 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357N PHE* 4.7 13.2 - - + -
361N ALA* 2.8 31.4 + - + +
364N LEU* 1.3 83.6 - - + +
366N ILE* 1.3 72.7 + - + +
367N VAL 3.5 0.9 - - - -
368N PRO* 3.1 3.3 - - - +
369N VAL* 3.0 40.4 + - + +
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Residues in contact with ILE 366 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325N PHE* 3.8 41.3 - - + +
328N ILE* 6.0 2.9 - - + -
358N ILE* 5.1 12.1 - - + +
361N ALA* 3.0 14.5 + - + +
362N TYR* 3.8 33.9 - - + +
365N ILE* 1.3 80.3 - - + +
367N VAL* 1.3 56.4 + - - +
369N VAL* 4.7 1.8 - - - -
370N ILE* 2.6 56.4 + - + +
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Residues in contact with VAL 367 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106N TYR* 5.3 1.3 - - - +
305N LEU* 4.4 14.6 - - + -
308N THR 3.8 2.7 - - - +
309N ASP* 3.6 37.0 - - + +
362N TYR* 3.1 50.2 + - + +
363N PHE 4.6 3.4 - - - +
366N ILE* 1.3 78.0 - - - +
368N PRO* 1.4 58.1 - - + +
370N ILE* 4.6 3.1 - - - -
371N SER* 2.6 42.1 + - - +
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Residues in contact with PRO 368 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308N THR* 3.1 30.5 - - + +
310N ARG* 3.9 9.9 - - + -
363N PHE 3.8 12.8 - - - +
364N LEU 3.2 19.5 - - - +
365N ILE 3.1 19.3 - - - +
367N VAL* 1.4 94.1 - - + +
369N VAL* 1.3 58.9 + - + +
371N SER* 3.1 2.9 + - - +
372N THR* 2.7 34.9 + - - -
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Residues in contact with VAL 369 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365N ILE* 3.0 40.3 + - + +
366N ILE* 3.6 2.9 - - - +
368N PRO* 1.3 78.1 - - + +
370N ILE* 1.3 68.9 + - + +
372N THR* 3.4 4.8 + - - -
373N ILE* 3.2 36.2 + - + +
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Residues in contact with ILE 370 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321N LEU* 3.8 39.9 - - + +
322N SER* 4.0 11.2 - - - +
325N PHE* 4.0 23.3 - - + -
366N ILE* 2.6 45.6 + - + +
367N VAL* 4.0 3.4 - - - +
369N VAL* 1.3 75.8 - - + +
371N SER* 1.3 58.0 + - - +
373N ILE* 3.1 19.2 + - + +
374N GLU* 2.9 36.3 + - - +
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Residues in contact with SER 371 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309N ASP* 4.1 4.0 - - - -
310N ARG* 3.3 18.8 + - - +
311N SER* 3.5 28.4 - - - -
319N LYS* 5.2 0.9 - - - -
322N SER* 5.2 2.2 + - - -
367N VAL* 2.6 27.2 + - - -
368N PRO* 3.1 8.5 + - - +
370N ILE* 1.3 70.5 - - - +
372N THR* 1.3 65.2 + - - +
374N GLU* 3.2 14.6 + - - +
375N ASN* 2.9 29.7 + - - +
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Residues in contact with THR 372 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310N ARG* 3.9 14.6 + - - +
368N PRO 2.7 24.5 + - - -
369N VAL* 3.7 5.3 - - - -
371N SER* 1.3 75.1 + - - +
373N ILE* 1.3 64.9 + - + +
375N ASN* 3.0 14.3 + - - +
376N VAL* 3.1 20.1 + - + +
3R GLN* 3.6 29.8 - - - +
11R ILE* 5.1 7.0 - - + -
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Residues in contact with ILE 373 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321N LEU* 5.7 8.7 - - + -
369N VAL* 3.2 28.7 + - + +
370N ILE* 3.1 17.6 + - + +
372N THR* 1.3 80.6 - - + +
374N GLU* 1.3 53.2 + - + +
376N VAL* 3.2 8.3 + - - +
377N LEU* 2.7 55.6 + - + +
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Residues in contact with GLU 374 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311N SER* 5.8 1.3 - - - +
319N LYS* 3.2 27.7 + - + +
321N LEU* 3.2 19.2 + - + -
322N SER* 2.7 41.6 + - - -
370N ILE* 2.9 28.1 + - + +
371N SER* 3.2 11.2 + - - +
373N ILE* 1.3 77.6 - - + +
375N ASN* 1.3 58.1 + - - +
377N LEU* 3.6 8.4 - - + +
378N PHE* 2.8 42.9 + - + -
32R PHE* 3.6 21.4 - - + -
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Residues in contact with ASN 375 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310N ARG 3.0 23.8 + - - -
311N SER* 3.5 10.4 + - - +
312N VAL* 3.1 27.6 + - - +
313N VAL* 5.5 0.2 - - - +
371N SER 2.9 14.1 + - - +
372N THR* 3.3 7.8 - - - +
374N GLU* 1.3 77.6 - - - +
376N VAL* 1.3 63.1 + - - +
378N PHE* 3.4 10.5 + - - +
379N TYR* 3.1 21.3 + - - +
3R GLN* 2.9 25.0 + - - +
8R ILE* 3.4 31.3 - - + +
45R PHE* 6.3 0.4 - - - -
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Residues in contact with VAL 376 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372N THR* 3.1 19.2 + - + +
373N ILE* 3.6 8.5 - - - +
375N ASN* 1.3 75.1 - - + +
377N LEU* 1.3 68.1 + - + +
379N TYR* 2.9 16.0 + - - +
380N ILE* 3.0 27.9 + - + +
3R GLN* 5.0 4.7 - - - +
8R ILE* 4.4 7.6 - - + +
11R ILE* 4.0 33.2 - - + -
12R GLY* 4.5 4.0 - - - -
15R ILE* 4.0 27.4 - - + -
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Residues in contact with LEU 377 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321N LEU* 4.5 10.8 - - + -
373N ILE* 2.7 39.6 + - + +
374N GLU* 3.6 7.4 - - - +
376N VAL* 1.3 75.8 - - + +
378N PHE* 1.3 62.2 + - - +
380N ILE* 3.7 14.1 + - + -
381N GLY* 3.2 18.0 + - - -
25R CYS* 5.2 4.7 - - + +
28R VAL* 4.8 13.7 - - + -
29R ALA* 3.8 24.2 - - + +
32R PHE* 3.7 46.7 - - + -
33R ILE* 4.4 2.1 - - - +
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Residues in contact with PHE 378 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311N SER* 5.7 0.9 - - - -
313N VAL* 4.8 10.1 - - + -
318N PHE* 3.5 30.1 - - + -
319N LYS* 4.7 13.2 - - + -
374N GLU* 2.8 32.6 + - + +
375N ASN* 3.5 10.5 - - - +
377N LEU* 1.3 72.3 - - - +
379N TYR* 1.3 62.9 + - - +
382N ARG* 3.2 27.9 + - - +
32R PHE* 3.6 27.1 - + - -
33R ILE* 4.0 13.8 - - + +
36R ALA* 4.5 3.1 - - + -
38R TYR* 3.9 19.5 - + - -
45R PHE* 3.3 53.4 - + + -
48R LEU* 5.2 1.3 - - + -
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Residues in contact with TYR 379 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375N ASN 3.1 12.7 + - - +
376N VAL 2.9 8.8 + - - +
378N PHE* 1.3 75.6 - - - +
380N ILE* 1.3 68.6 + - + +
381N GLY 3.1 2.7 + - - -
382N ARG* 3.1 19.5 + - - +
383N VAL* 3.2 52.2 + - + +
385N LYS* 4.1 10.0 + - - -
5R PHE* 6.1 1.1 - + - -
8R ILE* 3.6 20.4 - - + -
9R ALA* 3.6 21.8 - - + +
12R GLY* 3.6 29.2 - - - -
13R ASP* 2.7 34.0 + - - -
16R LEU* 4.2 2.0 - - + -
104R LEU* 3.6 24.9 - - + -
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Residues in contact with ILE 380 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376N VAL* 3.0 24.6 + - + +
377N LEU* 3.8 12.1 - - + +
379N TYR* 1.3 75.5 - - + +
381N GLY* 1.3 59.7 + - - +
382N ARG 3.0 5.3 + - - -
383N VAL 3.8 7.9 + - - +
12R GLY* 3.7 37.5 - - - +
15R ILE* 4.4 13.9 - - + -
16R LEU* 3.7 24.1 - - + +
25R CYS* 3.7 32.1 - - + +
26R VAL* 4.1 16.2 - - + +
29R ALA* 3.6 19.7 - - + -
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Residues in contact with GLY 381 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377N LEU 3.2 4.0 + - - -
379N TYR 3.1 2.4 + - - -
380N ILE* 1.3 81.6 - - - +
382N ARG* 1.3 61.2 + - - +
26R VAL* 5.4 0.7 - - - -
29R ALA* 3.5 20.9 - - - -
30R ASN* 3.1 24.0 + - - -
33R ILE* 3.6 23.1 - - - +
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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
------------------------------------------------------------
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