Contacts of the helix formed by residues 365 - 380 (chain C) in PDB entry 6DWM
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 LEU 365 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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346C GLU* 3.7 28.7 - - + +
347C LEU* 3.8 32.8 - - + -
350C VAL* 4.1 16.4 - - + -
351C ILE* 4.2 13.2 - - + -
361C ASP* 3.5 13.0 - - + +
362C ARG 3.3 11.4 + - - +
363C SER 3.4 0.6 - - - -
364C HIS* 1.3 82.7 - - - +
366C PRO* 1.3 67.6 - - - +
367C TYR 3.3 3.3 + - - -
368C MET* 3.4 9.8 + - + +
369C GLU* 3.2 19.6 + - - +
468C PHE* 3.4 35.2 - - + -
472C ALA* 4.9 0.2 - - + -
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Residues in contact with PRO 366 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346C GLU* 3.1 16.2 - - - +
350C VAL* 5.8 0.4 - - + -
363C SER 4.9 4.0 - - - +
364C HIS* 3.3 11.0 - - - +
365C LEU* 1.3 89.6 - - - +
367C TYR* 1.3 55.0 + - - +
369C GLU* 3.3 2.4 + - + -
370C ALA* 2.9 22.5 + - - +
433C LEU* 4.3 2.2 - - + -
437C GLY 3.2 26.7 - - - +
438C ALA* 4.2 8.3 - - - -
439C ILE* 3.3 31.0 - - + +
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Residues in contact with TYR 367 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339C VAL* 3.8 31.9 - - + +
342C LYS* 3.4 50.4 - - + +
343C ILE* 3.7 23.3 - - + -
346C GLU* 2.8 30.4 + - + +
366C PRO* 1.3 71.7 - - - +
368C MET* 1.3 64.6 + - - +
370C ALA* 3.7 4.2 - - + +
371C PHE* 3.0 24.0 + - + +
429C PRO* 4.2 10.5 - - + +
430C GLU* 2.8 25.9 + - - -
433C LEU* 3.5 28.0 - - + +
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Residues in contact with MET 368 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343C ILE* 3.7 33.4 - - + +
346C GLU* 3.1 9.0 + - - +
347C LEU* 5.5 3.1 - - + -
365C LEU* 3.6 22.4 - - + +
367C TYR* 1.3 76.8 - - - +
369C GLU* 1.3 57.9 + - - +
371C PHE* 3.3 33.8 + - + +
372C ILE* 3.0 37.7 + - + +
468C PHE* 3.6 28.3 - - + -
471C LEU* 4.1 30.7 - - + -
472C ALA* 4.3 15.5 - - - -
475C LEU* 4.6 0.7 - - + -
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Residues in contact with GLU 369 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362C ARG* 3.8 39.0 + - + +
365C LEU 3.2 10.6 + - - +
366C PRO* 3.6 8.3 - - + +
367C TYR 3.2 0.2 - - - -
368C MET* 1.3 75.5 - - - +
370C ALA* 1.3 61.7 + - - +
372C ILE* 3.4 15.5 + - - +
373C LEU* 2.9 61.6 + - + +
439C ILE* 4.2 15.0 - - + -
464C ARG* 4.7 6.1 + - - -
468C PHE* 5.9 1.2 - - - -
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Residues in contact with ALA 370 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366C PRO 2.9 16.9 + - - +
367C TYR* 3.7 6.5 - - + +
368C MET 3.3 0.2 - - - -
369C GLU* 1.3 76.7 - - - +
371C PHE* 1.3 61.0 + - - +
373C LEU* 4.5 1.1 - - - -
374C GLU* 3.1 24.6 + - - +
429C PRO* 3.4 28.1 - - + +
432C PHE* 3.8 11.7 - - + -
433C LEU* 3.9 15.0 - - + -
439C ILE* 3.6 16.3 - - + +
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Residues in contact with PHE 371 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329C SER* 3.7 15.9 - - - -
332C TYR* 4.3 3.8 - - + -
333C LEU* 3.3 38.1 - - + -
339C VAL* 4.0 11.9 - - + -
343C ILE* 3.6 17.5 - - + -
367C TYR* 3.0 18.2 + - + +
368C MET* 3.5 21.1 - - + +
369C GLU 3.2 0.2 - - - -
370C ALA* 1.3 73.9 - - - +
372C ILE* 1.3 64.9 + - + +
374C GLU* 3.2 3.3 + - - +
375C THR* 2.9 42.8 + - - -
427C PHE* 3.5 31.2 - + - -
429C PRO* 3.9 13.6 - - + +
471C LEU* 3.9 20.9 - - + -
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Residues in contact with ILE 372 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329C SER* 5.6 0.7 - - - +
368C MET* 3.0 30.2 + - + +
369C GLU* 3.9 16.6 - - - +
371C PHE* 1.3 80.4 - - + +
373C LEU* 1.3 63.5 + - + +
375C THR* 3.3 7.5 + - - -
376C PHE* 3.1 49.6 + - + -
464C ARG* 5.2 4.7 - - + +
467C VAL* 4.2 15.5 - - + -
468C PHE* 3.9 32.5 - - + +
471C LEU* 4.0 21.3 - - + -
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Residues in contact with LEU 373 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369C GLU* 2.9 51.1 + - + +
370C ALA 3.8 4.0 - - - +
372C ILE* 1.3 77.7 - - + +
374C GLU* 1.3 57.7 + - - +
376C PHE* 3.2 10.5 + - + +
377C ARG* 2.8 28.4 + - - +
432C PHE* 3.9 26.2 - - + -
439C ILE* 4.4 7.6 - - + -
444C SER* 3.6 39.0 - - - +
447C VAL* 4.1 10.8 - - + +
464C ARG* 4.0 23.1 - - - +
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Residues in contact with GLU 374 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370C ALA 3.1 19.0 + - - +
371C PHE 3.8 3.4 - - - +
373C LEU* 1.3 74.0 - - - +
375C THR* 1.3 60.6 + - - +
377C ARG* 2.6 35.5 + - - -
378C HIS* 2.9 28.8 + - - +
426C GLU 3.2 1.2 - - - +
427C PHE* 3.5 23.6 - - + -
428C LEU 2.9 20.5 + - - +
429C PRO* 3.9 14.1 - - + -
431C ARG* 2.8 31.6 + - - -
432C PHE* 3.3 12.7 - - + -
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Residues in contact with THR 375 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325C ALA* 4.3 7.0 - - - +
328C TRP* 4.3 6.1 - - + -
329C SER* 3.6 30.2 + - - +
332C TYR* 4.1 13.6 - - + -
371C PHE* 2.9 36.0 + - - -
372C ILE* 3.5 11.7 - - + -
373C LEU 3.2 0.2 - - - -
374C GLU* 1.3 74.7 - - - +
376C PHE* 1.3 67.6 + - + +
379C SER* 2.6 39.0 + - - +
381C PHE* 5.8 0.9 - - + -
427C PHE* 3.8 12.2 - - - -
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Residues in contact with PHE 376 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325C ALA* 4.2 9.2 - - + -
372C ILE* 3.1 41.9 + - + -
373C LEU* 3.2 11.0 + - + +
375C THR* 1.3 81.3 - - + +
377C ARG* 1.3 58.7 + - - +
379C SER* 4.3 0.4 - - - -
380C SER* 3.0 27.5 + - - -
381C PHE* 4.0 19.1 - + - -
415C ASN* 4.1 2.1 + - - -
447C VAL* 4.2 9.0 - - + -
449C ILE* 3.5 33.6 - - + +
450C PHE* 4.2 16.8 - + - -
463C ALA 5.6 1.6 - - - -
464C ARG* 4.4 24.2 - - + -
467C VAL* 4.8 12.3 - - + -
601C HEM 4.1 27.4 - - + -
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Residues in contact with ARG 377 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373C LEU 2.8 17.0 + - - +
374C GLU* 2.6 43.2 + - - +
375C THR 3.3 0.2 - - - -
376C PHE* 1.3 75.2 - - - +
378C HIS* 1.3 73.5 + - - +
380C SER* 2.8 23.0 + - - -
415C ASN* 2.9 48.1 + - + +
416C HIS* 3.4 12.4 + - - -
421C TRP* 3.7 38.8 - - + -
424C PRO* 3.0 37.2 + - - +
426C GLU 3.1 6.3 + - - -
431C ARG* 3.0 18.8 - - - +
432C PHE* 4.2 1.3 - - + -
447C VAL* 4.2 13.0 - - + -
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Residues in contact with HIS 378 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332C TYR* 2.9 34.8 + + - +
374C GLU 2.9 18.2 + - - +
377C ARG* 1.3 85.6 - - - +
379C SER* 1.3 60.6 + - - +
412C TRP* 4.9 0.5 + - - -
416C HIS* 3.1 27.7 + + - -
424C PRO 3.7 20.6 - - - -
425C SER* 3.0 22.9 + - - -
426C GLU 3.7 18.0 - - - -
427C PHE* 4.0 16.1 + + + -
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Residues in contact with SER 379 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328C TRP* 4.2 21.6 - - - -
332C TYR* 3.3 23.5 + - - -
375C THR* 2.6 23.6 + - - +
376C PHE 4.0 0.3 + - - -
378C HIS* 1.3 80.6 - - - +
380C SER* 1.3 70.6 + - - +
381C PHE* 3.1 25.1 + - - -
412C TRP* 4.3 2.9 + - - -
492C PRO* 4.7 9.7 - - - +
498C MET* 3.6 14.9 - - - +
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Residues in contact with SER 380 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376C PHE 3.0 14.5 + - - -
377C ARG 2.8 20.1 + - - -
379C SER* 1.3 81.0 + - - +
381C PHE* 1.3 52.5 + - - +
382C VAL 2.7 19.4 + - - -
383C PRO* 3.1 13.8 - - - +
412C TRP* 3.3 26.5 - - - -
415C ASN* 3.0 26.5 + - - +
416C HIS* 3.8 4.3 - - - -
449C ILE* 4.2 6.1 - - - -
498C MET* 3.5 6.8 - - - +
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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