Contacts of the helix formed by residues 365 - 385 (chain B) in PDB entry 3D0G
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 THR 365 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294B THR* 3.8 17.5 - - + -
297B MET* 3.1 20.5 - - - +
363B LYS* 2.9 21.0 + - + +
364B VAL* 1.3 78.7 - - - +
366B MET* 1.3 63.0 + - - +
367B ASP* 3.7 7.0 + - - +
368B ASP* 3.2 28.9 + - - +
369B PHE 3.3 10.4 + - - -
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Residues in contact with MET 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B ILE* 3.6 23.6 - - + +
292B ASP* 3.5 9.4 - - - +
293B VAL* 3.3 30.1 - - + -
294B THR* 3.0 24.5 + - - +
297B MET* 3.9 6.3 - - - -
365B THR* 1.3 70.9 - - - +
367B ASP* 1.3 67.4 + - - +
368B ASP 3.1 0.4 - - - -
369B PHE* 3.1 9.2 + - + +
370B LEU* 2.9 32.2 + - + +
413B ALA* 4.4 20.0 - - + +
418B LEU* 4.1 24.5 - - + -
441B LYS* 3.6 26.7 - - - +
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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
----------------------------------------------------------
276B THR* 3.6 29.4 + - - +
277B ASN* 4.3 10.9 + - - -
365B THR* 3.4 7.2 + - - +
366B MET* 1.3 76.7 - - - +
368B ASP* 1.3 62.2 + - - +
370B LEU* 3.4 15.1 + - - +
371B THR* 2.8 34.5 + - - +
441B LYS* 5.1 5.2 + - - +
445B THR* 5.2 2.9 + - - +
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Residues in contact with ASP 368 (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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307B ILE* 4.1 3.4 - - + +
360B MET* 3.2 27.3 - - + +
361B CYS 4.0 2.6 - - - +
362B THR* 3.4 3.3 - - + -
363B LYS* 2.7 51.4 + - - +
365B THR* 3.2 13.6 + - - +
366B MET 3.1 1.2 - - - -
367B ASP* 1.3 80.2 - - - +
369B PHE* 1.3 54.7 + - - +
371B THR* 3.7 6.4 + - - +
372B ALA* 2.7 34.8 + - - +
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Residues in contact with PHE 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B VAL* 5.4 0.9 - - + -
297B MET* 4.1 11.4 - - + +
302B TRP* 4.1 24.9 - + - -
307B ILE* 3.8 18.1 - - + +
310B GLU* 4.6 8.5 - - + -
365B THR 3.3 11.3 + - - +
366B MET* 3.2 20.0 - - + +
368B ASP* 1.3 76.7 - - - +
370B LEU* 1.3 75.1 + - + +
372B ALA* 3.3 9.0 + - - +
373B HIS* 2.9 49.2 + + - -
412B ALA* 3.6 33.7 - - + -
417B HIS* 4.6 1.1 - + - -
418B LEU* 4.1 8.1 - - + -
421B ILE* 3.3 31.9 - - + -
423B LEU* 4.7 3.4 - - + -
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Residues in contact with LEU 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B MET* 2.9 22.9 + - + +
367B ASP* 3.7 16.2 - - - +
369B PHE* 1.3 91.4 - - + +
371B THR* 1.3 67.1 + - - +
373B HIS* 3.1 10.5 + - - +
374B HIS* 3.0 18.2 + - - +
409B SER* 3.5 29.5 + - - +
412B ALA* 4.3 4.3 - - + -
413B ALA* 3.7 37.0 - - + +
441B LYS* 4.6 17.9 - - - +
442B GLN* 5.1 5.2 - - - +
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Residues in contact with THR 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B PRO* 4.2 11.9 - - + -
360B MET* 3.9 18.6 - - + -
367B ASP* 2.8 24.6 + - - +
368B ASP* 3.7 9.4 + - - +
370B LEU* 1.3 70.0 - - - +
372B ALA* 1.3 67.6 + - - +
374B HIS* 2.9 10.3 + - + -
375B GLU* 2.8 44.7 + - - +
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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
----------------------------------------------------------
307B ILE* 3.3 34.1 - - + -
308B PHE* 3.7 33.9 - - + -
311B ALA* 4.6 4.9 - - + -
360B MET* 4.7 1.3 - - - -
368B ASP 2.7 14.1 + - - +
369B PHE 3.5 2.2 - - - +
370B LEU 3.2 0.4 - - - -
371B THR* 1.3 72.0 - - - +
373B HIS* 1.3 67.2 + - - +
375B GLU* 3.4 2.6 + - - +
376B MET* 2.8 27.6 + - - +
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Residues in contact with HIS 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B ILE 4.7 0.9 - - - -
310B GLU* 4.6 2.0 + - - +
311B ALA* 3.5 39.2 + - + +
314B PHE* 4.1 28.9 - + + +
315B PHE* 3.6 7.2 - + + -
369B PHE* 2.9 57.4 + + - -
370B LEU 3.1 7.1 + - - +
372B ALA* 1.3 75.3 - - + +
374B HIS* 1.3 51.8 + - - +
376B MET* 3.2 2.0 + - - +
377B GLY* 2.7 34.5 + - - -
408B MET* 4.0 16.6 - - + +
409B SER* 4.4 6.5 - - - +
412B ALA* 3.7 22.3 - - + +
417B HIS* 4.6 3.6 + - - -
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Residues in contact with HIS 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B LEU 3.0 10.6 + - - +
371B THR* 2.9 15.7 + - + +
373B HIS* 1.3 73.7 - - - +
375B GLU* 1.3 78.1 + - - +
377B GLY* 2.7 14.9 + - - -
378B HIS* 3.0 26.6 + + - -
402B GLU* 2.9 58.6 + - + -
405B GLY* 3.4 25.7 + - - +
406B GLU* 2.7 29.5 + - + +
409B SER* 4.9 2.2 - - - -
518B ARG* 5.0 2.2 - - - -
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Residues in contact with GLU 375 (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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308B PHE* 5.2 0.4 - - + -
346B PRO* 3.4 26.9 - - + +
347B THR* 4.0 24.4 - - - +
348B ALA* 3.8 11.6 + - + +
358B ILE* 3.8 20.9 - - + -
360B MET* 5.2 2.2 - - - -
371B THR* 2.8 39.9 + - + +
372B ALA* 3.7 4.7 - - - +
374B HIS* 1.3 82.6 + - - +
376B MET* 1.3 56.8 + - - +
378B HIS* 2.8 41.9 + - - +
379B ILE* 3.1 9.2 + - - +
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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
----------------------------------------------------------
308B PHE* 3.6 45.1 - - + +
311B ALA* 3.9 2.7 - - + -
312B GLU* 3.4 30.3 - - + +
315B PHE* 3.6 23.6 - - + -
323B MET* 3.6 45.8 - - + +
327B PHE* 4.0 7.2 - - + -
328B TRP* 4.9 0.2 - - + -
358B ILE* 3.6 9.9 - - + +
372B ALA 2.8 21.5 + - - +
373B HIS* 4.6 0.4 - - - -
375B GLU* 1.3 72.0 - - - +
377B GLY* 1.3 51.7 + - - +
379B ILE* 3.1 4.0 + - - +
380B GLN* 2.8 34.1 + - - +
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Residues in contact with GLY 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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315B PHE* 3.5 18.1 - - - -
373B HIS 2.7 17.6 + - - -
374B HIS 2.7 8.8 + - - -
376B MET* 1.3 66.0 - - - +
378B HIS* 1.3 66.8 + - - -
380B GLN* 3.0 5.4 + - - +
381B TYR* 3.0 20.8 + - - +
404B VAL* 4.0 13.8 - - - +
405B GLY* 4.5 3.6 - - - -
408B MET* 4.1 9.2 - - - -
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Residues in contact with HIS 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B ALA* 3.4 17.0 - - + +
374B HIS* 3.0 32.0 + + - -
375B GLU* 2.8 28.3 + - - +
377B GLY* 1.3 69.6 - - - -
379B ILE* 1.3 63.9 + - - +
381B TYR* 2.9 8.4 + - - +
382B ASP* 2.9 26.2 + - - +
401B HIS* 2.7 60.5 + + + +
402B GLU* 2.5 32.1 + - + -
404B VAL* 5.4 0.4 - - - -
405B GLY* 4.7 2.0 - - - -
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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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323B MET* 3.9 13.5 - - + -
327B PHE* 4.9 2.5 - - + -
348B ALA* 3.9 6.3 - - + -
349B TRP 3.2 35.9 - - - +
356B PHE* 4.0 11.0 - - + -
357B ARG 3.4 15.9 - - - +
358B ILE* 3.7 27.8 - - + -
375B GLU 3.1 3.8 + - - +
376B MET* 3.1 11.4 + - - +
378B HIS* 1.3 79.6 - - - +
380B GLN* 1.3 57.2 - - - +
382B ASP* 3.1 11.5 + - - +
383B MET* 2.9 61.2 + - + +
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Residues in contact with GLN 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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315B PHE* 3.4 32.6 - - + +
320B LEU* 3.0 50.4 - - + +
321B PRO* 3.1 27.9 + - - +
323B MET* 3.6 25.0 - - - +
376B MET 2.8 14.0 + - - +
377B GLY* 3.0 6.5 + - - +
379B ILE* 1.3 78.0 - - - +
381B TYR* 1.3 55.0 + - - +
383B MET* 3.3 8.7 + - - +
384B ALA* 3.0 28.8 + - - +
408B MET* 6.1 1.1 - - + -
558B LEU* 4.0 5.6 - - + +
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Residues in contact with TYR 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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377B GLY 3.0 10.9 + - - +
378B HIS 2.9 12.7 + - - +
380B GLN* 1.3 76.7 - - - +
382B ASP* 1.3 58.5 + - - +
384B ALA* 3.3 2.4 + - - +
385B TYR* 3.3 31.4 + + - -
394B ASN 4.5 1.0 + - - -
395B GLY* 3.5 10.7 - - - -
396B ALA* 3.2 24.6 + - - +
400B PHE* 3.8 6.3 - - - +
401B HIS* 3.5 41.7 - + + +
404B VAL* 3.7 30.3 - - + -
557B MET* 3.5 18.5 + - + +
558B LEU* 3.3 47.5 - - + +
561B GLY* 4.8 3.0 + - - -
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Residues in contact with ASP 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B ALA 4.2 7.8 - - - +
350B ASP* 3.6 26.0 - - - +
356B PHE* 3.7 23.1 - - + -
378B HIS* 2.9 21.1 + - - +
379B ILE* 3.1 17.6 + - - +
381B TYR* 1.3 72.9 - - - +
383B MET* 1.3 66.4 + - - +
385B TYR* 2.7 36.8 + - - -
386B ALA* 3.2 19.1 + - - +
401B HIS* 3.0 17.9 + - - -
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Residues in contact with MET 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B PRO* 4.5 18.2 - - + -
322B ASN 4.4 10.1 - - - +
323B MET* 3.5 26.2 - - + -
324B THR* 4.1 20.9 - - + +
327B PHE* 5.5 0.9 - - + -
356B PHE* 3.7 39.0 - - + -
379B ILE* 2.9 41.6 + - + +
380B GLN* 3.6 9.0 - - - +
381B TYR 3.3 0.2 - - - -
382B ASP* 1.3 76.0 - - - +
384B ALA* 1.3 65.9 + - - +
385B TYR 3.1 1.4 + - - -
386B ALA* 3.1 18.6 + - - +
387B ALA 4.5 0.3 + - - -
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Residues in contact with ALA 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B GLN 3.0 13.8 + - - +
381B TYR 3.4 10.3 - - - +
383B MET* 1.3 78.0 - - - +
385B TYR* 1.3 57.2 + - - +
386B ALA 3.8 0.3 + - - -
387B ALA* 4.2 9.5 + - - +
555B PHE* 3.6 29.1 - - + -
558B LEU* 3.5 30.7 - - + -
559B ARG* 3.2 22.1 - - - +
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Residues in contact with TYR 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B ASP* 4.3 9.4 + - - -
381B TYR* 3.3 42.3 + + - -
382B ASP* 2.7 37.4 + - - -
383B MET 3.2 0.8 - - - -
384B ALA* 1.3 77.2 - - - +
386B ALA* 1.3 57.0 + - - +
387B ALA 3.0 5.8 - - - +
388B GLN* 2.9 26.0 + - + +
393B ARG* 3.3 31.9 + - + +
394B ASN* 3.3 37.0 + - - -
395B GLY 3.8 1.1 - - - -
401B HIS* 3.0 12.7 + - - -
558B LEU 3.6 9.2 - - - +
559B ARG 3.7 10.3 - - - +
561B GLY* 3.6 16.2 - - - -
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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