Contacts of the helix formed by residues 360 - 378 (chain A) in PDB entry 1Y8B
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 GLY 360 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340A VAL* 3.1 25.9 - - - +
342A HIS 5.6 0.2 - - - -
343A LEU* 4.6 4.7 - - - -
345A THR* 5.2 6.7 + - - -
346A ILE 5.7 0.8 + - - -
347A PRO* 5.1 1.8 - - - +
348A VAL* 5.7 1.3 - - - +
358A PRO 3.1 4.3 + - - -
359A GLU* 1.3 80.7 - - - +
361A ILE* 1.3 52.9 + - - +
362A LEU* 2.5 19.2 + - - +
363A ASP* 2.7 21.1 + - - +
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Residues in contact with ILE 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A VAL* 3.7 25.6 - - + +
46A LEU* 4.4 11.9 - - + -
47A ALA* 3.7 26.5 - - - +
50A ASN* 3.4 28.9 - - - +
340A VAL* 3.6 9.5 - - + +
343A LEU* 4.8 2.2 - - + -
359A GLU* 2.8 39.3 + - - +
360A GLY* 1.3 70.8 - - - +
362A LEU* 1.3 59.4 + - - +
363A ASP 3.0 0.2 - - - -
364A GLY* 2.7 22.3 + - - +
365A VAL* 2.9 22.1 + - + +
392A LYS* 4.3 15.5 - - - +
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Residues in contact with LEU 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A PHE* 4.0 17.9 - - + -
43A VAL* 5.6 1.6 - - + -
283A LYS* 6.0 0.2 - - - -
348A VAL* 4.2 15.9 - - + +
349A ILE* 3.4 61.9 - - + +
359A GLU* 3.6 33.7 - - + +
360A GLY* 2.5 9.6 + - - +
361A ILE* 1.3 79.1 - - + +
363A ASP* 1.3 62.9 + - - +
365A VAL* 4.5 3.4 - - - +
366A MET* 2.9 57.9 + - + +
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Residues in contact with ASP 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A VAL* 5.4 5.9 - - - +
283A LYS* 2.9 36.1 + - - +
286A LEU* 5.3 0.7 - - - +
338A ARG* 3.1 29.0 + - - +
339A ASN 4.3 4.4 - - - +
340A VAL* 4.3 15.0 - - - -
341A GLY 4.9 6.3 + - - -
348A VAL* 4.2 5.7 - - - +
360A GLY* 2.7 18.8 + - - +
362A LEU* 1.3 80.2 - - - +
364A GLY* 1.3 58.1 + - - +
366A MET* 4.9 0.2 - - - -
367A THR* 2.7 30.7 + - - +
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Residues in contact with GLY 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A ARG 4.8 3.1 - - - -
340A VAL* 4.9 4.9 - - - +
360A GLY 4.1 0.6 + - - -
361A ILE* 2.7 11.6 + - - +
363A ASP* 1.3 79.8 - - - +
365A VAL* 1.3 60.9 + - - +
367A THR* 3.1 15.9 - - - +
368A GLY* 3.8 4.2 + - - -
388A ILE* 5.7 0.2 - - - +
390A LYS* 3.2 37.7 + - - -
392A LYS* 5.8 0.4 - - - -
409A ILE* 5.7 2.1 - - - +
413A LEU* 5.6 0.5 - - - +
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Residues in contact with VAL 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A PHE* 3.8 27.6 - - + -
39A PHE* 4.3 10.8 - - + -
42A ILE* 4.8 19.5 - - + -
43A VAL* 4.9 12.8 - - + -
46A LEU* 6.1 4.0 - - + -
361A ILE* 2.9 29.2 + - + +
362A LEU* 4.5 1.6 - - - -
364A GLY* 1.3 76.3 - - - +
366A MET* 1.3 80.7 + - - +
368A GLY* 2.8 16.1 + - - -
369A ALA 3.5 3.5 + - - -
409A ILE* 5.3 7.4 - - + -
412A MET* 5.5 0.2 - - + -
413A LEU* 4.3 13.1 - - + +
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Residues in contact with MET 366 (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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17A LYS* 6.2 2.0 - - - +
20A VAL* 5.9 7.0 - - + -
35A PHE* 3.9 17.0 - - + -
39A PHE* 3.4 31.2 - - + -
283A LYS* 5.9 0.4 - - - +
287A TYR* 3.4 36.7 + - + +
338A ARG* 5.0 0.9 - - - +
349A ILE* 4.5 9.4 - - + -
362A LEU* 2.9 41.7 + - + +
363A ASP* 4.8 2.2 - - - +
365A VAL* 1.3 76.1 - - - +
367A THR* 1.3 54.5 + - - +
368A GLY 2.5 16.6 + - - -
369A ALA* 2.7 25.4 + - - +
370A ILE* 3.5 4.9 - - - +
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Residues in contact with THR 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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287A TYR* 5.8 0.4 - - - -
290A LEU* 3.3 19.9 - - - +
337A ILE* 2.7 43.1 - - + +
338A ARG* 3.8 19.4 - - - +
363A ASP 2.7 26.2 + - - +
364A GLY* 3.1 20.6 - - - +
366A MET* 1.3 77.3 - - - +
368A GLY* 1.3 59.2 + - - +
370A ILE* 3.8 14.9 + - - +
371A ALA* 3.7 12.5 + - - +
388A ILE* 5.2 1.8 - - + -
390A LYS* 4.5 3.6 - - - +
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Residues in contact with GLY 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A GLY 4.4 2.7 - - - -
365A VAL 2.8 10.1 + - - -
366A MET 2.5 11.1 + - - -
367A THR* 1.3 78.4 - - - +
369A ALA* 1.3 54.4 + - - -
370A ILE 2.9 4.9 - - - -
371A ALA* 2.7 36.4 + - - +
372A LEU* 3.5 1.9 - - - +
388A ILE* 6.1 3.1 - - - -
413A LEU* 3.5 22.8 - - - +
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Residues in contact with ALA 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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20A VAL* 5.7 3.6 - - + -
24A VAL* 3.6 21.3 - - + -
25A LEU* 6.4 0.7 - - + -
28A THR* 3.1 23.0 + - - +
30A LEU* 4.1 16.8 - - + -
35A PHE* 5.0 8.7 - - + -
287A TYR* 5.1 2.2 - - - +
365A VAL 3.5 4.0 + - - +
366A MET* 2.7 22.3 + - + +
368A GLY* 1.3 71.4 - - - +
370A ILE* 1.3 59.4 + - + +
372A LEU* 3.5 10.0 - - - +
413A LEU* 3.8 11.9 - - - +
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Residues in contact with ILE 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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24A VAL* 4.2 15.0 - - + -
28A THR* 4.3 8.1 - - + +
287A TYR* 4.0 23.8 - - + +
290A LEU* 5.0 8.1 - - + +
291A LEU* 4.2 28.7 - - + +
294A MET* 3.6 37.2 - - + +
295A GLN* 5.6 3.4 - - - +
366A MET 3.5 17.7 - - - +
367A THR* 4.0 13.2 - - - +
368A GLY 2.9 0.8 - - - -
369A ALA* 1.3 78.2 - - - +
371A ALA* 1.3 66.5 + - - +
372A LEU* 2.8 5.0 + - - +
373A TYR* 2.9 18.8 + - + +
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Residues in contact with ALA 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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294A MET* 5.9 3.1 - - - -
337A ILE* 5.6 4.9 - - + +
367A THR 3.7 4.6 + - - +
368A GLY* 2.7 29.4 + - - +
370A ILE* 1.3 74.6 - - - +
372A LEU* 1.3 51.8 + - + +
373A TYR* 2.4 14.7 + - - -
374A ASP* 2.7 24.6 + - - +
375A LEU* 3.9 4.1 + - + +
386A VAL* 3.5 36.9 - - + +
413A LEU* 5.7 1.6 - - + +
420A LEU* 5.7 3.6 - - + -
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Residues in contact with LEU 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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28A THR* 3.4 43.1 - - - +
30A LEU* 3.8 23.1 - - + -
368A GLY 3.5 10.5 - - - +
369A ALA* 3.5 17.5 - - - +
370A ILE 2.8 0.6 + - - +
371A ALA* 1.3 75.8 - - + +
373A TYR* 1.3 55.9 + - - +
374A ASP 2.9 0.7 - - - -
375A LEU* 2.6 47.9 + - + -
376A LYS* 2.7 16.9 + - + +
412A MET 6.0 0.4 - - - +
413A LEU* 3.7 22.4 - - + +
415A MET* 4.0 20.9 - - + -
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Residues in contact with TYR 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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28A THR* 5.6 1.0 - - - +
294A MET* 4.2 29.6 - - + -
295A GLN* 3.3 36.5 + - - -
370A ILE* 2.9 17.5 + - + +
371A ALA 2.4 7.9 + - - -
372A LEU* 1.3 74.1 - - - +
374A ASP* 1.3 64.7 + - - +
376A LYS* 5.0 4.3 - - - -
377A VAL* 3.1 39.5 + - + +
381A SER* 4.6 3.5 - - - -
382A ARG* 3.5 44.1 + - + -
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Residues in contact with ASP 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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294A MET* 5.0 7.8 - - - +
371A ALA* 2.7 11.7 + - - +
373A TYR* 1.3 79.5 - - - +
375A LEU* 1.3 60.4 + - + +
377A VAL* 2.7 29.2 - - - +
378A GLN* 3.6 5.0 + - - -
381A SER* 3.0 18.6 + - - +
383A THR* 2.4 31.1 + - - +
384A GLY 5.4 0.2 - - - +
385A SER* 2.6 14.9 - - - +
386A VAL* 3.5 27.8 - - + +
419A THR* 4.4 11.9 + - - +
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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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371A ALA* 4.4 5.4 - - + +
372A LEU* 2.6 37.1 + - + +
374A ASP* 1.3 75.7 - - + +
376A LYS* 1.3 68.9 + - - +
378A GLN* 2.9 23.4 + - - +
386A VAL* 5.4 1.3 - - + -
413A LEU 2.8 25.4 - - - +
414A GLY* 2.8 31.0 - - - +
415A MET* 4.1 14.7 - - + +
416A ALA* 4.0 10.7 - - + +
418A ASN 3.8 6.5 - - - +
419A THR* 3.1 31.9 - - - +
420A LEU* 5.0 5.4 - - + -
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Residues in contact with LYS 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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27A GLY 4.6 15.7 - - - +
28A THR* 5.1 13.6 + - - +
29A GLY* 5.6 4.0 - - - -
372A LEU 2.7 19.3 + - - +
373A TYR* 4.6 4.7 - - - +
375A LEU* 1.3 74.6 - - - +
377A VAL* 1.3 70.5 + - + +
378A GLN* 3.3 5.5 - - - +
415A MET* 4.3 13.5 - - + +
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Residues in contact with VAL 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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373A TYR* 3.1 26.9 - - + +
374A ASP* 2.7 32.1 - - - +
376A LYS* 1.3 77.0 - - + +
378A GLN* 1.3 70.3 + - - +
379A LYS* 2.5 29.8 + - + +
380A ASN 4.4 8.5 - - - +
381A SER* 4.0 22.2 - - - +
382A ARG* 6.2 1.1 - - - -
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Residues in contact with GLN 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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374A ASP 4.1 4.0 - - - -
375A LEU* 2.9 19.3 + - - +
376A LYS 3.3 4.5 - - - +
377A VAL* 1.3 87.2 - - - +
379A LYS* 1.3 57.9 + - - +
415A MET 5.2 1.1 - - - +
416A ALA* 3.8 15.3 - - + +
417A PRO* 3.2 36.9 - - - +
419A THR* 4.7 11.5 - - - +
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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