Contacts of the helix formed by residues 364 - 381 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303B HIS* 3.4 55.7 - + + +
306B ARG* 3.3 46.2 - - - -
307B ILE 3.8 20.2 - - - -
308B VAL* 4.0 10.1 - - + -
336B VAL* 4.0 19.1 - - + -
363B THR* 1.3 95.5 + - + +
365B SER* 1.3 63.2 + - - +
366B PRO* 3.5 2.9 - - - -
367B ASP 3.7 4.7 + - - -
368B TRP* 3.2 21.2 - - + +
434B CYS* 4.8 1.3 - - - -
438B SER* 6.2 0.2 - - - -
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Residues in contact with SER 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B GLU* 3.5 8.5 - - - -
362B TYR* 4.3 11.2 - - - +
363B THR* 4.4 3.8 + - - -
364B PHE* 1.3 74.3 + - - +
366B PRO* 1.3 75.1 - - - +
367B ASP 2.9 1.9 + - - -
368B TRP* 3.0 14.7 + - - +
369B TRP 3.1 9.0 + - - -
428B PRO* 3.9 13.5 - - - +
431B ARG* 3.4 20.9 + - - -
434B CYS* 3.5 26.6 - - - +
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Residues in contact with PRO 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B VAL* 4.7 4.5 - - + -
310B ARG* 5.2 10.5 - - + -
351B TYR 4.8 1.0 - - - +
352B MET* 6.4 0.4 - - - -
353B ALA* 4.3 9.1 + - + +
355B GLU* 4.8 2.2 - - - +
356B VAL* 3.7 23.3 - - + -
362B TYR* 3.4 41.5 - - + -
363B THR 4.1 2.0 - - - +
364B PHE 3.5 3.8 - - - -
365B SER* 1.3 96.2 - - - +
367B ASP* 1.3 60.9 + - - +
369B TRP* 3.4 10.9 - - + +
370B ALA* 2.9 28.6 + - - +
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Residues in contact with ASP 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B LEU* 3.7 16.0 - - + +
303B HIS* 2.7 36.4 + - + +
308B VAL* 3.3 11.6 - - - +
309B TYR* 3.0 29.9 + - + +
310B ARG* 2.8 30.0 + - - -
311B ASP 4.6 0.7 + - - -
312B LEU* 4.1 6.5 + - + +
364B PHE 3.7 0.4 + - - +
365B SER 2.9 1.2 + - - -
366B PRO* 1.3 73.6 - - - +
368B TRP* 1.3 62.7 + - - +
370B ALA* 3.1 8.8 + - - +
371B LEU* 2.8 27.4 + - - +
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Residues in contact with TRP 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B CYS* 3.8 24.9 - - + -
299B LEU* 4.7 10.3 - - + -
300B GLU* 4.9 2.2 - - - -
303B HIS* 3.4 29.2 + + - -
364B PHE* 3.2 27.6 + - + +
365B SER 3.0 6.0 + - - +
367B ASP* 1.3 73.0 - - - +
369B TRP* 1.3 66.8 + - - +
371B LEU* 3.3 24.8 + - + +
372B GLY 3.2 13.9 + - - -
423B LEU* 3.6 17.8 - - + +
431B ARG* 4.8 1.6 - - - -
432B LEU 3.9 16.8 - - - +
433B GLY* 4.3 14.5 + - - -
434B CYS* 4.3 14.1 - - - -
438B SER* 5.4 1.2 - - - +
439B ALA* 3.5 43.7 - - + +
442B VAL* 3.6 33.9 - - + -
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Residues in contact with TRP 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B GLY 5.4 0.2 + - - -
351B TYR 3.2 21.5 - - - -
352B MET 3.1 14.1 + - - -
353B ALA* 3.2 20.2 - - + -
354B PRO* 3.7 15.0 - - + -
365B SER 3.1 4.8 + - - -
366B PRO 3.4 8.1 - - - +
368B TRP* 1.3 75.8 - - - +
370B ALA* 1.3 57.1 + - - +
372B GLY* 2.9 19.1 + - - -
373B CYS* 3.1 24.4 + - - -
385B PHE* 4.3 9.8 - + - -
401B VAL* 3.4 27.8 - - + -
423B LEU 3.9 17.0 - - - -
424B LEU* 3.4 46.0 - - + +
425B CYS 3.5 11.4 - - - -
426B LYS* 4.0 15.3 - - + -
431B ARG* 3.4 39.0 - - - +
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Residues in contact with ALA 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B ASP 5.9 0.7 - - - +
312B LEU* 3.6 37.8 - - + +
351B TYR* 4.0 12.7 - - + +
366B PRO 2.9 18.1 + - - +
367B ASP* 3.4 8.3 - - - +
369B TRP* 1.3 76.8 - - - +
371B LEU* 1.3 56.1 + - - +
373B CYS* 3.4 14.1 + - - +
374B LEU* 2.9 27.7 + - - +
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Residues in contact with LEU 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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292B ALA* 4.2 17.0 - - + +
295B ILE* 3.5 40.4 - - + -
296B CYS* 4.6 9.9 - - + -
299B LEU* 4.6 7.0 - - + -
312B LEU* 3.5 7.8 - - + +
367B ASP 2.8 13.1 + - - +
368B TRP* 3.4 40.8 - - + +
369B TRP 3.1 0.4 - - - -
370B ALA* 1.3 72.9 - - - +
372B GLY* 1.3 61.9 + - - +
374B LEU* 3.3 3.0 + - + +
375B LEU* 2.8 30.9 + - + +
423B LEU* 4.4 14.4 - - + -
442B VAL* 4.6 7.4 - - + -
448B PHE* 6.4 1.3 - - + -
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Residues in contact with GLY 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B TRP 3.2 4.9 + - - -
369B TRP 2.9 8.1 + - - -
371B LEU* 1.3 74.8 - - - +
373B CYS* 1.3 56.1 + - - +
374B LEU 3.0 0.3 + - - -
375B LEU* 3.0 3.3 + - - +
376B TYR* 2.7 36.0 + - - +
420B CYS* 4.7 4.2 - - - +
423B LEU* 4.0 25.2 - - - +
424B LEU* 4.1 15.1 - - - +
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Residues in contact with CYS 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B GLY 4.1 6.7 - - - +
351B TYR* 3.6 35.4 - - + -
369B TRP* 3.1 46.2 + - - -
370B ALA* 3.4 8.3 - - - +
372B GLY* 1.3 73.9 - - - +
374B LEU* 1.3 57.0 + - - +
376B TYR* 3.6 6.6 - - - +
377B GLU* 3.1 27.9 + - - +
384B PRO* 4.1 13.4 - - + +
385B PHE* 4.7 7.6 - - - -
424B LEU* 3.8 11.4 - - - +
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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
----------------------------------------------------------
271B LEU* 4.5 8.5 - - + -
275B ILE* 6.2 0.9 - - + -
295B ILE* 3.4 33.4 - - + -
312B LEU* 4.5 10.8 - - + +
313B LYS* 3.5 13.0 - - - +
314B PRO* 3.4 45.1 - - + -
317B ILE* 4.2 15.9 - - + -
351B TYR* 4.6 4.0 - - + -
370B ALA 2.9 15.1 + - - +
371B LEU* 3.6 6.7 - - + +
372B GLY 3.0 0.2 - - - -
373B CYS* 1.3 73.8 - - - +
375B LEU* 1.3 61.2 + - - +
376B TYR 3.1 1.8 - - - -
377B GLU* 2.9 6.0 + - + +
378B MET* 2.8 42.4 + - + +
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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
----------------------------------------------------------
288B ALA 3.9 24.5 - - - +
289B VAL* 4.7 5.4 - - + +
292B ALA* 4.2 16.6 - - + -
371B LEU* 2.8 22.8 + - + +
372B GLY* 3.8 4.9 - - - +
374B LEU* 1.3 72.1 - - - +
376B TYR* 1.3 65.3 + - - +
378B MET* 3.6 13.5 + - + +
379B ILE* 3.4 35.0 + - + +
419B LEU* 3.8 30.7 - - + -
420B CYS* 4.0 19.1 - - - -
423B LEU* 4.9 5.6 - - + -
447B LEU* 4.1 10.5 - - + -
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Residues in contact with TYR 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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372B GLY 2.7 22.1 + - - +
373B CYS* 3.6 7.0 - - - +
375B LEU* 1.3 71.3 - - - +
377B GLU* 1.3 54.2 + - - +
379B ILE* 2.8 26.0 + - - +
380B ALA* 2.8 28.2 + - + +
382B GLN* 3.3 33.1 + - + -
383B SER 4.0 1.1 + - - -
384B PRO* 3.3 42.1 - - + +
406B GLU* 4.6 9.4 - - + -
407B GLU* 2.6 38.9 + - - -
408B TYR* 4.9 9.0 - + - -
409B SER 5.6 0.2 + - - -
412B PHE* 4.1 26.9 - + - -
420B CYS* 4.6 5.2 - - + -
424B LEU* 4.7 14.4 - - + -
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Residues in contact with GLU 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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275B ILE* 4.1 15.8 - - + +
276B TYR* 2.5 34.6 + - + +
314B PRO* 3.6 13.7 - - + +
351B TYR* 2.4 40.4 + - - -
373B CYS 3.1 11.3 + - - +
374B LEU* 2.9 9.6 + - + +
376B TYR* 1.3 76.8 - - - +
378B MET* 1.3 56.4 + - - +
381B GLY* 3.1 24.0 + - - -
382B GLN 3.4 24.0 - - - +
383B SER* 4.0 15.4 + - - -
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Residues in contact with MET 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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271B LEU* 4.7 10.8 - - + -
275B ILE* 4.2 15.0 - - + -
282B GLY* 3.5 6.9 - - - -
283B PHE* 3.3 44.7 + - + +
288B ALA* 3.3 42.0 - - + +
291B TYR* 4.0 23.8 - - - -
292B ALA* 4.2 12.1 - - + +
295B ILE* 4.5 9.9 - - + -
371B LEU* 6.0 0.4 - - + -
374B LEU* 2.8 18.2 + - + +
375B LEU* 3.6 28.7 - - + +
376B TYR 2.8 1.8 + - - -
377B GLU* 1.3 78.0 - - - +
379B ILE* 1.3 59.8 + - - +
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Residues in contact with ILE 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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283B PHE 4.5 10.1 - - - +
284B PRO 5.1 3.8 - - - +
285B GLU* 4.8 17.3 - - + +
288B ALA* 4.1 16.2 - - + -
289B VAL* 5.7 3.8 - - + -
375B LEU* 3.5 28.7 - - + +
376B TYR 2.8 11.3 + - - +
378B MET* 1.3 74.3 - - - +
380B ALA* 1.3 63.3 + - - +
381B GLY 3.3 0.2 - - - -
411B ARG* 3.0 42.2 + - + +
412B PHE* 3.9 35.7 - - + +
416B ALA* 4.5 15.0 - - + -
420B CYS* 5.0 1.3 - - - -
447B LEU* 6.1 0.9 - - + -
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Residues in contact with ALA 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B TYR* 2.8 47.5 + - + +
379B ILE* 1.3 74.6 - - - +
381B GLY* 1.3 57.6 + - - +
382B GLN* 3.3 11.5 + - + +
409B SER* 5.1 4.3 - - - +
411B ARG* 2.8 26.9 + - - +
412B PHE* 4.1 16.7 - - + -
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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
----------------------------------------------------------
275B ILE* 4.5 5.1 - - - +
276B TYR* 4.3 16.5 - - - -
281B ALA* 4.2 15.4 - - - +
282B GLY* 4.3 17.5 - - - -
377B GLU* 3.1 19.9 + - - -
378B MET 4.2 0.2 + - - -
379B ILE 3.3 2.4 - - - -
380B ALA* 1.3 76.6 - - - +
382B GLN* 1.3 59.2 + - - +
411B ARG* 4.1 7.0 - - - -
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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
------------------------------------------------------------
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