Contacts of the helix formed by residues 365 - 380 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346A GLU* 3.4 33.4 - - + +
347A LEU* 3.8 29.6 - - + -
350A VAL* 3.8 20.4 - - + -
351A ILE* 4.2 12.8 - - + -
361A ASP 3.4 18.4 - - - +
362A ARG 3.3 10.2 + - - +
363A SER 3.4 0.6 - - - -
364A HIS* 1.3 82.4 - - - +
366A PRO* 1.3 66.6 - - - +
367A TYR 3.3 2.9 - - - -
368A MET* 3.2 18.6 + - + +
369A GLU* 3.2 11.5 + - - +
468A PHE* 3.8 24.0 - - + -
472A ALA* 5.2 0.9 - - + -
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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
----------------------------------------------------------
346A GLU* 3.0 14.6 - - - +
363A SER 4.9 3.8 - - - +
364A HIS* 3.4 11.0 - - - +
365A LEU* 1.3 89.3 - - - +
367A TYR* 1.3 55.5 + - - +
369A GLU* 3.3 2.9 + - + +
370A ALA* 2.8 24.3 + - - +
433A LEU* 4.2 4.5 - - + -
437A GLY 3.2 20.0 - - - +
438A ALA* 4.3 1.3 - - - -
439A ILE* 3.3 34.2 - - + +
363D SER* 3.2 27.6 - - - +
364D HIS* 4.5 3.4 - - + +
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Residues in contact with TYR 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A ARG* 4.0 0.2 + - - -
339A VAL* 3.8 27.7 - - + +
342A LYS* 3.8 37.6 - - + +
343A ILE* 3.5 35.0 - - + -
346A GLU* 3.0 24.2 + - + +
366A PRO* 1.3 75.5 - - + +
368A MET* 1.3 65.3 + - - +
370A ALA* 3.4 5.2 + - + +
371A PHE* 3.0 19.6 + - + +
429A PRO* 4.3 12.0 - - + +
430A GLU* 2.8 38.4 + - - -
433A LEU* 3.6 25.7 - - + +
364D HIS* 5.5 2.2 - - + +
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Residues in contact with MET 368 (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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343A ILE* 3.9 33.1 - - + +
346A GLU* 3.2 7.6 + - - +
347A LEU* 5.5 4.5 - - + -
365A LEU* 3.2 22.4 + - + +
367A TYR* 1.3 77.2 - - - +
369A GLU* 1.3 61.7 + - - +
371A PHE* 3.2 26.6 + - + -
372A ILE* 3.1 32.1 + - + +
468A PHE* 3.7 30.7 - - + +
471A LEU* 4.3 27.8 - - + -
472A ALA* 4.5 14.8 - - - -
475A LEU* 4.8 1.6 - - + -
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Residues in contact with GLU 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A ARG* 3.4 43.2 + - + +
365A LEU 3.2 9.2 + - - +
366A PRO* 3.6 8.1 - - + +
368A MET* 1.3 78.2 - - - +
370A ALA* 1.3 59.0 + - - +
372A ILE* 4.4 17.8 - - - +
373A LEU* 2.9 62.6 + - + +
439A ILE* 4.0 17.3 - - + -
464A ARG* 4.4 6.8 + - - -
468A PHE* 5.9 0.3 - - - -
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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
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366A PRO 2.8 17.6 + - - +
367A TYR* 3.7 10.1 - - + +
368A MET 3.3 0.2 - - - -
369A GLU* 1.3 77.5 - - - +
371A PHE* 1.3 56.6 + - - +
373A LEU* 3.6 5.8 + - - +
374A GLU* 3.0 29.8 + - - +
429A PRO* 3.4 30.3 - - + +
432A PHE* 4.0 6.2 - - + -
433A LEU* 4.1 15.9 - - + -
439A ILE* 3.8 8.7 - - + +
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Residues in contact with PHE 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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329A SER* 3.4 42.6 - - - -
332A TYR* 4.1 6.7 - - + -
333A LEU* 3.5 26.0 - - + -
339A VAL* 3.7 15.7 - - + -
343A ILE* 3.7 13.9 - - + -
367A TYR* 3.0 13.9 + - + +
368A MET* 3.6 24.2 - - + +
369A GLU 3.2 0.4 - - - -
370A ALA* 1.3 75.2 - - - +
372A ILE* 1.3 63.1 + - + +
374A GLU* 3.3 1.6 + - - +
375A THR* 2.9 42.8 + - - -
427A PHE* 3.6 28.7 - + - -
429A PRO* 4.0 10.9 - - + +
471A LEU* 3.9 11.9 - - + -
475A LEU* 5.7 0.2 - - + -
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Residues in contact with ILE 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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329A SER* 5.5 1.1 - - - +
368A MET* 3.1 29.3 + - + +
369A GLU* 3.9 20.2 - - - +
371A PHE* 1.3 78.4 - - + +
373A LEU* 1.3 64.8 + - + +
375A THR* 3.2 6.6 + - - -
376A PHE* 3.0 52.5 + - + -
464A ARG* 5.1 7.0 - - + +
467A VAL* 4.3 10.8 - - + -
468A PHE* 3.9 36.6 - - + +
471A LEU* 4.2 19.1 - - + -
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Residues in contact with LEU 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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369A GLU* 2.9 46.5 + - + +
370A ALA 3.9 3.1 - - - +
372A ILE* 1.3 77.2 - - + +
374A GLU* 1.3 57.1 + - - +
376A PHE* 3.4 9.9 + - + +
377A ARG* 2.9 27.9 + - - +
432A PHE* 3.9 26.7 - - + -
439A ILE* 4.3 9.0 - - + -
444A SER* 3.5 41.3 - - - +
447A VAL* 4.0 11.7 - - + +
464A ARG* 3.8 25.1 - - - +
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Residues in contact with GLU 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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370A ALA 3.0 18.1 + - - +
371A PHE 3.9 2.0 - - - +
372A ILE 3.3 0.2 - - - -
373A LEU* 1.3 74.2 - - - +
375A THR* 1.3 60.7 + - - +
377A ARG* 2.8 34.2 + - - -
378A HIS* 2.9 29.2 + - - +
426A GLU 3.3 1.4 - - - +
427A PHE* 3.4 26.3 - - + -
428A LEU 3.0 18.3 + - - +
429A PRO* 4.0 13.0 - - + -
431A ARG* 2.7 33.0 + - - -
432A PHE* 3.2 14.5 - - + -
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Residues in contact with THR 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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325A ALA* 4.2 4.5 - - - +
328A TRP* 4.1 8.7 - - + -
329A SER* 3.6 30.6 + - - +
332A TYR* 3.9 18.2 - - + -
371A PHE* 2.9 42.4 + - - -
372A ILE* 3.2 7.4 + - - -
374A GLU* 1.3 77.0 - - - +
376A PHE* 1.3 69.4 + - + +
379A SER* 2.8 32.5 + - - +
381A PHE* 5.7 0.7 - - + -
427A PHE* 4.1 5.2 - - - -
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Residues in contact with PHE 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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325A ALA* 4.0 16.2 - - + -
329A SER* 6.1 0.2 - - - -
372A ILE* 3.0 41.7 + - + -
373A LEU* 3.6 11.0 - - + +
375A THR* 1.3 82.7 - - + +
377A ARG* 1.3 57.1 + - - +
379A SER* 4.4 1.3 - - - -
380A SER* 2.9 29.5 + - - -
381A PHE* 3.6 27.4 - + - -
415A ASN* 4.1 1.7 + - - -
447A VAL* 4.2 8.1 - - + -
449A ILE* 3.8 32.3 - - + +
450A PHE* 4.1 18.2 - + - -
463A ALA 5.6 1.1 - - - -
464A ARG* 4.7 20.6 - - + -
467A VAL* 4.8 11.4 - - + -
601A HEM 4.0 16.4 - - + -
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Residues in contact with ARG 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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373A LEU 2.9 16.6 + - - +
374A GLU* 2.8 42.9 + - - +
375A THR 3.3 0.2 - - - -
376A PHE* 1.3 75.0 - - - +
378A HIS* 1.3 74.1 + - - +
380A SER* 2.8 19.8 + - - -
415A ASN* 2.7 53.2 + - + +
416A HIS* 3.3 16.0 + - - -
421A TRP* 3.8 37.2 - - + -
424A PRO* 2.9 37.8 + - - +
426A GLU 3.2 6.1 + - - -
431A ARG* 3.2 16.8 - - - +
432A PHE* 4.1 1.3 - - - -
447A VAL* 4.1 12.6 - - + -
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Residues in contact with HIS 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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332A TYR* 2.7 36.0 + + - +
374A GLU 2.9 21.4 + - - +
377A ARG* 1.3 88.0 - - - +
379A SER* 1.3 61.6 + - - +
412A TRP* 4.8 0.9 + - - -
416A HIS* 3.2 21.8 + - - -
424A PRO 3.9 4.7 - - - -
425A SER* 3.0 24.6 + - - -
426A GLU 3.7 26.0 - - - -
427A PHE* 4.0 16.1 + + + -
492A PRO* 6.1 0.2 - - - +
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Residues in contact with SER 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A TRP* 4.1 28.5 - - - +
332A TYR* 3.3 17.6 + - - -
375A THR 2.8 19.7 + - - -
378A HIS* 1.3 80.7 - - - +
380A SER* 1.3 73.3 + - - +
381A PHE* 3.1 23.8 + - - -
412A TRP* 4.2 3.5 + - - -
492A PRO* 4.7 8.7 - - - +
498A MET* 3.4 16.5 - - - +
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Residues in contact with SER 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A PHE 2.9 15.4 + - - -
377A ARG 2.8 20.2 + - - -
379A SER* 1.3 81.8 + - - +
381A PHE* 1.3 54.0 + - - +
382A VAL 2.7 20.0 + - - -
383A PRO* 3.1 14.4 - - - +
412A TRP* 3.4 26.9 - - - -
415A ASN* 2.8 28.4 + - - +
416A HIS* 3.7 2.1 - - - -
449A ILE* 4.4 5.2 - - - -
498A MET* 3.4 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
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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