Contacts of the helix formed by residues 366 - 384 (chain B) in PDB entry 6CM9
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 ASP 366 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332B ILE* 3.2 43.2 - - - +
335B LYS* 4.4 17.4 + - - +
364B GLU* 3.7 5.1 + - + +
365B VAL* 1.3 77.4 - - + +
367B VAL* 1.3 53.2 + - - +
368B ASP* 4.0 7.3 + - - +
369B PHE* 2.9 21.4 + - + +
370B VAL* 2.8 35.2 + - - +
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Residues in contact with VAL 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B VAL 2.9 14.1 + - - +
366B ASP* 1.3 69.7 + - - +
368B ASP* 1.3 63.3 + - - +
370B VAL* 3.9 6.9 - - - +
371B ARG* 3.0 51.8 + - - +
405B TYR* 3.9 38.4 - - + +
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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
----------------------------------------------------------
332B ILE* 4.0 16.5 - - + +
336B LEU* 4.4 10.3 - - + +
366B ASP* 3.3 3.7 - - - +
367B VAL* 1.3 78.6 - - - +
369B PHE* 1.3 58.3 + - - +
371B ARG* 3.9 7.1 - - - +
372B LYS* 3.0 29.4 + - - +
375B ARG* 5.5 0.2 + - - -
43M GLU 3.6 8.0 - - - +
44M GLY* 3.3 32.7 - - - +
45M MET* 5.8 5.6 - - - -
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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
----------------------------------------------------------
326B VAL* 4.1 15.7 - - + -
332B ILE* 5.3 0.7 - - + -
335B LYS* 3.2 58.8 - - + -
336B LEU* 4.5 9.1 - - + +
339B LEU* 3.5 15.7 - - + -
361B TYR* 3.6 55.2 - + + -
364B GLU* 4.2 17.5 - - + -
366B ASP* 2.9 27.0 + - + +
368B ASP* 1.3 77.2 - - - +
370B VAL* 1.3 59.6 + - - +
372B LYS* 3.4 3.9 + - - +
373B ALA* 2.9 25.8 + - - +
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Residues in contact with VAL 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B TYR 4.0 7.4 - - - +
362B ALA* 4.2 14.6 - - + +
364B GLU* 3.9 37.0 - - + +
366B ASP 2.8 25.9 + - - +
367B VAL 3.9 3.8 - - - +
369B PHE* 1.3 68.9 - - - +
371B ARG* 1.3 67.0 + - - +
373B ALA* 3.1 6.9 + - - +
374B VAL* 3.0 26.9 + - + +
405B TYR* 3.6 28.3 - - + +
406B VAL* 3.7 18.8 - - + -
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Residues in contact with ARG 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B VAL* 3.0 38.5 + - + +
368B ASP* 3.9 6.5 - - - +
370B VAL* 1.3 75.0 - - - +
372B LYS* 1.3 56.4 + - - +
374B VAL* 3.4 2.8 + - - +
375B ARG* 3.0 54.1 + - - +
405B TYR* 3.6 33.2 + - + +
408B GLN* 4.4 2.0 + - - -
409B GLU* 3.1 43.5 + - + +
441B GLU* 3.5 21.0 + - - -
443B GLU* 3.3 15.2 + - - -
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Residues in contact with LYS 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B LEU* 4.1 35.4 - - + +
339B LEU* 3.7 23.3 - - + -
340B ASP* 4.6 18.1 + - - +
343B ILE* 4.8 12.3 - - - +
368B ASP 3.0 19.5 + - - +
369B PHE 3.6 4.9 - - - +
371B ARG* 1.3 77.9 - - - +
373B ALA* 1.3 56.0 + - - +
375B ARG* 3.5 16.8 + - + +
376B ALA* 2.9 27.1 + - - +
379B ARG* 5.3 6.9 - - - +
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Residues in contact with ALA 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B LEU* 3.8 11.8 - - + +
358B LEU* 3.8 15.7 - - + +
361B TYR* 3.9 31.4 - - + -
362B ALA* 4.5 3.1 - - + +
369B PHE 2.9 17.4 + - - +
370B VAL* 3.1 7.8 + - - +
372B LYS* 1.3 75.9 - - - +
374B VAL* 1.3 57.9 + - - +
376B ALA* 3.2 3.8 + - - +
377B ILE* 2.9 30.6 + - - +
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Residues in contact with VAL 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362B ALA* 4.3 9.6 - - + -
370B VAL* 3.0 20.8 + - + +
371B ARG 4.0 2.9 - - - +
372B LYS 3.3 0.2 - - - -
373B ALA* 1.3 73.7 - - - +
375B ARG* 1.3 64.7 + - - +
377B ILE* 3.1 10.5 + - + +
378B GLY 3.0 16.6 + - - -
395B LEU* 3.9 24.2 - - + -
398B LEU* 4.1 21.3 - - + -
406B VAL* 4.8 7.9 - - + +
409B GLU* 4.0 11.7 - - + -
410B ALA* 3.9 24.0 - - + +
413B VAL* 3.6 12.7 - - + +
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Residues in contact with ARG 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B ILE* 5.3 0.2 - - - -
368B ASP 5.5 0.2 + - - -
371B ARG* 3.0 48.0 + - - +
372B LYS* 3.9 17.4 - - + +
374B VAL* 1.3 77.4 - - - +
376B ALA* 1.3 57.4 + - - +
378B GLY* 3.2 2.4 + - - +
379B ARG* 2.9 37.3 + - + +
409B GLU* 2.8 38.4 + - - +
412B VAL* 6.4 0.2 - - - +
413B VAL* 4.3 9.4 - - + -
443B GLU* 4.4 9.1 + - - -
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Residues in contact with ALA 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B LEU* 4.7 10.5 - - + +
343B ILE* 3.7 32.6 - - + +
358B LEU* 3.9 19.8 - - + +
372B LYS* 2.9 19.3 + - - +
373B ALA* 3.2 8.3 + - - +
375B ARG* 1.3 74.2 - - - +
377B ILE* 1.3 58.8 + - - +
379B ARG* 4.2 0.3 - - - +
380B CYS* 2.9 32.7 + - - +
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Residues in contact with ILE 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B LEU* 4.5 9.6 - - + -
358B LEU* 3.7 34.3 - - + +
362B ALA* 5.8 0.2 - - + -
373B ALA 2.9 19.5 + - - +
374B VAL* 3.1 13.0 + - + +
376B ALA* 1.3 74.1 - - - +
378B GLY* 1.3 58.4 + - - +
380B CYS* 3.5 3.0 + - - +
381B ALA* 2.9 28.8 + - - +
391B CYS* 4.3 17.3 - - + +
394B THR* 4.1 21.1 - - + -
395B LEU* 3.8 31.9 - - + -
398B LEU* 4.2 20.9 - - + -
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Residues in contact with GLY 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B VAL 3.0 10.7 + - - -
375B ARG 3.2 4.4 + - - -
377B ILE* 1.3 78.8 - - - +
379B ARG* 1.3 56.5 + - - +
381B ALA* 3.2 6.2 + - - +
382B ILE* 3.0 37.3 + - - +
413B VAL* 3.6 24.2 - - - +
416B ASP* 6.4 1.6 - - - -
417B ILE* 5.0 2.4 - - - +
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Residues in contact with ARG 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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340B ASP* 5.9 1.0 + - - -
343B ILE* 3.9 42.1 - - + +
344B ARG* 5.1 4.9 - - - +
372B LYS* 5.3 7.4 - - - +
375B ARG* 2.9 20.3 + - + +
376B ALA 3.4 0.2 + - - -
378B GLY* 1.3 76.2 - - - +
380B CYS* 1.3 57.6 + - - +
382B ILE* 3.4 11.7 + - + +
383B LYS* 3.0 28.8 + - - +
551B GLU* 4.3 11.9 + - - +
553B ASP* 2.4 41.9 + - - +
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Residues in contact with CYS 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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343B ILE* 4.8 9.1 - - + +
346B ALA* 3.9 21.3 - - + -
351B ILE* 5.4 4.7 - - - -
354B VAL* 3.8 31.0 - - + -
355B LEU* 4.9 12.3 - - + -
358B LEU* 4.9 0.7 - - + -
376B ALA 2.9 19.1 + - - +
377B ILE* 3.9 5.2 - - - +
379B ARG* 1.3 77.2 - - - +
381B ALA* 1.3 62.3 + - - +
383B LYS* 3.4 5.6 + - - +
384B VAL* 3.3 37.5 + - - +
387B SER* 5.4 1.1 - - - -
391B CYS* 5.1 3.1 - - - -
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Residues in contact with ALA 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 ILE 2.9 19.0 + - - +
378B GLY 3.2 4.7 + - - +
380B CYS* 1.3 75.9 - - - +
382B ILE* 1.3 60.1 + - - +
384B VAL 2.9 22.3 - - - +
388B ALA* 4.4 6.4 - - + +
391B CYS* 3.6 30.0 - - + -
417B ILE* 3.7 22.9 - - + -
421B TYR* 3.6 16.1 - - + -
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Residues in contact with ILE 382 (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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378B GLY 3.0 24.4 + - - +
379B ARG* 3.9 9.9 - - + +
380B CYS 3.3 0.4 - - - -
381B ALA* 1.3 77.5 - - + +
383B LYS* 1.3 63.1 + - - +
385B GLU* 5.6 0.2 - - - +
416B ASP* 4.1 29.8 - - + +
417B ILE* 5.2 4.5 - - + -
420B LYS* 3.5 35.4 + - + +
421B TYR* 3.5 16.9 + - + -
550B GLU* 4.6 15.9 - - + -
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Residues in contact with LYS 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B ILE* 3.4 16.5 + - + +
344B ARG* 2.7 38.6 + - - +
345B LEU* 3.9 1.4 - - - +
346B ALA* 3.4 28.8 + - + +
347B SER* 5.7 1.1 - - - +
379B ARG 3.0 17.9 + - - +
380B CYS* 3.9 6.5 - - - +
381B ALA 3.3 0.8 - - - -
382B ILE* 1.3 79.2 - - - +
384B VAL* 1.3 62.1 + - + +
385B GLU* 4.2 6.4 - - - +
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Residues in contact with VAL 384 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B ALA 3.9 7.6 - - - +
347B SER* 3.7 26.5 - - - +
348B GLN* 3.4 24.9 - - + +
351B ILE* 3.7 15.0 - - + -
380B CYS* 3.3 21.1 + - - +
381B ALA* 2.9 18.3 - - - +
383B LYS* 1.3 83.1 - - + +
385B GLU* 1.3 64.3 + - - +
386B GLN* 3.3 4.2 + - + +
387B SER* 3.3 25.8 + - - +
388B ALA 4.3 2.6 + - - -
421B TYR* 4.0 0.9 - - - -
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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