Contacts of the helix formed by residues 364 - 381 (chain A) in PDB entry 3NYN
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 PHE 364 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303A HIS* 3.6 50.0 - + + +
306A ARG* 3.6 41.5 - - - -
307A ILE 4.1 16.2 - - - -
308A VAL* 3.9 15.9 - - + -
336A VAL* 3.9 23.8 - - + -
363A THR* 1.3 94.2 + - - +
365A SER* 1.3 64.6 + - - +
366A PRO* 3.1 6.4 - - - -
367A ASP* 3.2 19.2 + - - +
368A TRP* 3.9 11.0 - - + +
434A CYS* 5.0 0.2 - - - -
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Residues in contact with SER 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A GLU* 3.2 18.5 + - - -
362A TYR* 4.1 12.3 - - - +
363A THR* 4.2 4.5 + - - -
364A PHE* 1.3 74.5 + - - +
366A PRO* 1.3 69.4 - - - +
367A ASP 3.0 1.4 + - - -
368A TRP* 3.2 14.2 + - - +
369A TRP 3.3 3.5 + - - -
428A PRO* 4.2 13.5 + - - +
431A ARG* 3.2 17.8 + - - -
434A CYS* 3.6 27.5 - - - +
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Residues in contact with PRO 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A VAL* 4.7 5.8 - - + -
310A ARG* 5.3 10.8 - - + -
351A TYR 4.8 1.9 - - - +
352A MET* 6.3 0.2 - - - -
353A ALA* 4.4 4.8 + - + +
355A GLU* 4.1 7.9 - - - +
356A VAL* 3.7 30.1 - - + -
362A TYR* 3.7 23.6 - - + -
363A THR 3.8 9.2 - - - +
364A PHE 3.1 5.8 - - - +
365A SER* 1.3 98.5 - - - +
367A ASP* 1.3 63.8 + - - +
369A TRP* 3.2 8.7 - - + +
370A ALA* 3.1 19.9 + - - +
431A ARG* 4.2 2.2 - - - +
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Residues in contact with ASP 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A LEU* 3.9 15.9 - - + +
303A HIS* 2.8 36.1 + - + +
308A VAL* 3.5 8.5 - - - +
309A TYR* 2.9 33.6 + - - +
310A ARG* 2.9 28.8 + - - -
311A ASP 4.6 0.9 + - - -
312A LEU* 4.0 5.5 + - - +
364A PHE 3.2 4.6 + - - +
365A SER 3.0 0.2 + - - -
366A PRO* 1.3 73.2 - - - +
368A TRP* 1.3 63.5 + - - +
370A ALA* 2.9 9.4 + - - +
371A LEU* 2.9 26.5 + - - +
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Residues in contact with TRP 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A CYS* 3.8 25.4 - - - -
299A LEU* 4.3 18.8 - - + -
300A GLU* 4.9 1.6 - - - -
303A HIS* 3.6 29.4 + + - -
364A PHE* 3.9 17.7 - - + +
365A SER 3.2 5.1 + - - +
367A ASP* 1.3 73.9 - - - +
369A TRP* 1.3 67.5 + - - +
371A LEU* 3.4 34.3 + - + +
372A GLY 3.2 13.9 + - - -
423A LEU* 3.7 15.9 - - + +
431A ARG* 4.6 1.8 - - - -
432A LEU 3.6 17.0 - - - +
433A GLY* 4.1 16.5 + - - -
434A CYS* 3.9 21.8 - - - -
438A SER* 4.4 1.8 - - - +
439A ALA* 3.8 33.2 - - + -
442A VAL* 3.9 17.3 - - + -
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Residues in contact with TRP 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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350A GLY 4.9 1.4 + - - -
351A TYR* 3.3 25.1 + - - +
352A MET 3.6 5.9 + - - -
353A ALA* 3.1 29.6 - - + +
354A PRO* 3.8 15.7 - - + -
365A SER 3.3 3.8 + - - -
366A PRO 3.2 9.9 - - - +
367A ASP 3.2 0.2 - - - -
368A TRP* 1.3 77.4 - - - +
370A ALA* 1.3 56.7 + - - +
372A GLY* 2.8 21.5 + - - -
373A CYS* 3.0 25.3 + - - -
385A PHE* 4.3 11.6 - + - -
401A VAL* 3.8 21.0 - - + +
423A LEU 3.7 23.8 - - - -
424A LEU* 3.2 49.7 - - + +
425A CYS 3.8 7.4 - - - -
426A LYS* 4.1 17.0 - - + -
431A ARG* 3.6 23.5 - - - +
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Residues in contact with ALA 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A LEU* 3.6 36.6 - - + +
351A TYR* 4.1 16.5 - - + +
366A PRO 3.1 8.3 + - - +
367A ASP* 2.9 10.3 + - - +
369A TRP* 1.3 79.8 - - - +
371A LEU* 1.3 57.4 + - - +
373A CYS* 3.5 12.4 - - - +
374A LEU* 2.8 31.4 + - - +
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Residues in contact with LEU 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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292A ALA* 3.8 34.1 - - + +
295A ILE* 4.2 20.0 - - + -
296A CYS* 4.3 15.7 - - + -
299A LEU* 4.3 3.1 - - + -
312A LEU* 3.4 10.6 - - + +
367A ASP 2.9 12.1 + - - +
368A TRP* 3.6 41.3 - - + +
369A TRP 3.2 0.2 - - - -
370A ALA* 1.3 74.1 - - - +
372A GLY* 1.3 52.1 + - - +
374A LEU* 3.2 3.9 + - + +
375A LEU* 2.7 39.1 + - + +
378A MET* 6.4 0.2 - - + -
423A LEU* 3.9 14.8 - - + -
442A VAL* 4.4 7.6 - - + -
448A PHE* 6.2 1.6 - - + -
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Residues in contact with GLY 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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368A TRP 3.2 4.2 + - - -
369A TRP 2.8 9.9 + - - -
371A LEU* 1.3 75.0 - - - +
373A CYS* 1.3 65.4 + - - -
375A LEU* 3.0 4.3 + - - +
376A TYR* 2.8 23.9 + - - +
420A CYS* 4.7 4.9 - - - -
423A LEU* 3.5 29.0 - - - +
424A LEU* 4.3 11.6 - - - +
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Residues in contact with CYS 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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350A GLY 4.3 13.5 - - - +
351A TYR* 3.9 22.0 - - + -
369A TRP* 3.0 49.2 + - - -
370A ALA* 3.5 8.7 - - - +
372A GLY* 1.3 73.1 - - - +
374A LEU* 1.3 53.5 + - - +
376A TYR* 3.2 7.6 - - - +
377A GLU* 2.7 35.5 + - - +
384A PRO* 4.2 12.9 - - + +
385A PHE* 4.8 5.4 - - - -
424A LEU* 3.7 13.7 - - - +
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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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271A LEU* 4.8 6.5 - - + -
275A ILE* 5.2 2.0 - - + -
295A ILE* 3.7 29.4 - - + -
312A LEU* 4.3 16.4 - - + -
313A LYS* 4.0 4.5 - - - -
314A PRO* 3.5 45.3 - - + -
317A ILE* 4.1 18.4 - - + -
351A TYR* 4.9 2.7 - - + -
370A ALA 2.8 17.0 + - - +
371A LEU* 3.6 5.8 - - + +
373A CYS* 1.3 76.9 - - - +
375A LEU* 1.3 62.3 + - - +
377A GLU* 3.1 8.9 + - + +
378A MET* 2.9 40.9 + - + +
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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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288A ALA* 3.9 21.1 - - + +
289A VAL* 4.5 6.5 - - + +
292A ALA* 3.7 30.1 - - + -
371A LEU* 2.7 22.7 + - + +
372A GLY* 3.6 4.7 - - - +
374A LEU* 1.3 73.7 - - - +
376A TYR* 1.3 64.6 + - - +
378A MET* 3.6 9.2 + - + +
379A ILE* 3.5 25.1 + - + +
419A LEU* 3.5 34.3 - - + -
420A CYS* 3.7 21.3 - - - +
423A LEU* 4.8 5.4 - - + -
447A LEU* 4.4 8.5 - - + -
448A PHE* 5.6 0.2 - - + -
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Residues in contact with TYR 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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372A GLY 2.8 12.1 + - - +
373A CYS* 3.2 13.0 - - - +
375A LEU* 1.3 76.1 - - - +
377A GLU* 1.3 67.1 + - - +
378A MET 2.8 2.1 + - - -
379A ILE* 2.9 4.2 + - - +
380A ALA* 2.9 37.7 + - + +
382A GLN* 3.3 24.5 + - + -
383A SER 4.2 0.4 - - - -
384A PRO* 3.4 36.9 - - + +
406A GLU* 4.5 12.6 - - + -
407A GLU* 2.7 33.1 + - - -
408A TYR* 4.6 13.2 - + - -
409A SER 5.5 0.3 + - - -
412A PHE* 4.1 20.8 - + - -
420A CYS* 4.1 10.8 - - + -
424A LEU* 4.6 13.5 - - + -
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Residues in contact with GLU 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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275A ILE* 4.3 14.0 - - + +
276A TYR* 2.6 31.9 + - - +
314A PRO* 3.6 16.1 - - - +
351A TYR* 2.6 39.9 + - - -
373A CYS 2.7 18.6 + - - +
374A LEU* 3.1 8.3 + - + +
376A TYR* 1.3 72.6 - - - +
378A MET* 1.3 57.0 + - - +
381A GLY* 3.0 24.7 + - - -
382A GLN 3.6 26.0 - - - +
383A SER* 4.1 13.8 + - - -
384A PRO* 4.7 0.2 - - + -
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Residues in contact with MET 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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271A LEU* 4.3 10.1 - - - -
275A ILE* 4.2 15.9 - - + -
282A GLY* 3.3 6.6 - - - -
283A PHE* 3.0 56.4 + - + +
288A ALA* 3.0 38.8 - - + +
291A TYR* 4.1 18.8 - - + -
292A ALA* 4.1 13.0 - - + +
295A ILE* 4.7 5.6 - - + -
371A LEU* 6.4 0.2 - - + -
374A LEU* 2.9 20.6 + - + +
375A LEU* 3.9 23.6 - - + +
376A TYR 2.8 0.4 + - - -
377A GLU* 1.3 76.7 - - - +
379A ILE* 1.3 62.8 + - - +
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Residues in contact with ILE 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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282A GLY* 4.6 1.2 - - - -
283A PHE 4.3 9.9 - - - +
285A GLU* 4.1 29.2 - - + +
288A ALA* 3.8 20.4 - - + -
289A VAL* 5.7 2.5 - - + -
375A LEU* 3.5 21.3 + - + +
376A TYR 2.9 2.9 + - - +
378A MET* 1.3 78.0 - - - +
380A ALA* 1.3 67.4 + - - +
381A GLY 3.2 0.9 + - - -
411A ARG* 3.3 49.4 + - + +
412A PHE* 3.8 33.0 - - + -
416A ALA* 4.2 9.9 - - + +
420A CYS* 5.4 0.2 - - - -
447A LEU* 6.1 0.9 - - + -
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Residues in contact with ALA 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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376A TYR* 2.9 47.0 + - + +
379A ILE* 1.3 77.6 - - - +
381A GLY* 1.3 60.6 + - - +
382A GLN* 3.3 9.7 + - + +
409A SER* 4.9 5.6 + - - +
411A ARG* 3.1 21.3 + - - +
412A PHE* 3.8 17.5 - - + -
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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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275A ILE* 4.8 6.4 - - - +
276A TYR* 4.8 9.3 - - - -
281A ALA* 4.0 16.5 - - - +
282A GLY* 4.2 18.8 - - - -
377A GLU 3.0 14.6 + - - -
379A ILE 3.2 3.2 + - - -
380A ALA* 1.3 76.2 - - - +
382A GLN* 1.3 63.1 + - - +
411A ARG* 4.1 8.1 - - - -
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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
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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