Contacts of the helix formed by residues 365 - 380 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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346D GLU* 3.7 29.2 - - + +
347D LEU* 3.9 32.5 - - + -
350D VAL* 3.9 19.1 - - + -
351D ILE* 4.3 6.1 - - + -
357D PRO* 5.6 0.4 - - + -
361D ASP* 3.5 23.6 - - + +
362D ARG 3.3 12.2 + - - +
363D SER 3.4 0.4 - - - -
364D HIS* 1.3 82.5 - - - +
366D PRO* 1.3 64.6 - - - +
367D TYR 3.3 3.1 + - - -
368D MET* 3.5 10.1 + - + +
369D GLU* 3.3 17.8 + - - +
468D PHE* 3.6 30.6 - - + -
472D ALA* 5.1 0.9 - - + -
604D GOL 4.4 0.7 - - - -
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Residues in contact with PRO 366 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346D GLU* 3.1 17.3 - - + +
350D VAL* 5.9 0.2 - - + -
363D SER 4.9 0.9 - - - +
364D HIS* 3.2 10.5 - - - +
365D LEU* 1.3 89.8 - - - +
367D TYR* 1.3 55.0 + - + +
369D GLU* 3.4 1.0 + - + +
370D ALA* 2.9 23.6 + - - +
433D LEU* 4.5 3.8 - - + -
437D GLY 3.4 26.7 - - - +
438D ALA* 4.3 2.0 - - - -
439D ILE* 3.4 35.6 - - + +
604D GOL 4.1 8.3 - - - +
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Residues in contact with TYR 367 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339D VAL* 3.7 35.7 - - + +
342D LYS* 3.5 41.6 - - + +
343D ILE* 3.7 24.7 - - + -
346D GLU* 2.9 26.5 + - + +
366D PRO* 1.3 74.8 - - - +
368D MET* 1.3 59.2 + - - +
370D ALA* 3.2 5.6 + - + +
371D PHE* 2.9 26.4 + - + +
429D PRO* 4.1 12.7 - - + +
430D GLU* 2.8 36.5 + - - -
433D LEU* 3.8 24.2 - - + +
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Residues in contact with MET 368 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343D ILE* 3.7 33.8 - - + +
346D GLU* 3.1 9.2 + - - +
347D LEU* 5.6 4.3 - - + -
365D LEU* 3.7 21.8 - - + +
366D PRO 3.4 0.4 - - - -
367D TYR* 1.3 76.3 - - - +
369D GLU* 1.3 61.2 + - - +
371D PHE* 3.2 34.6 + - + +
372D ILE* 3.0 32.7 + - + +
468D PHE* 3.7 28.0 - - + +
471D LEU* 4.1 31.6 - - + -
472D ALA* 4.4 13.7 - - - -
475D LEU* 4.6 1.1 - - + -
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Residues in contact with GLU 369 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362D ARG* 3.3 37.7 + - + +
365D LEU 3.3 10.3 + - - +
366D PRO 3.8 7.2 - - - +
367D TYR 3.2 0.6 - - - -
368D MET* 1.3 80.0 - - - +
370D ALA* 1.3 58.5 + - - +
372D ILE* 4.5 16.3 - - - +
373D LEU* 2.9 63.4 + - + +
439D ILE* 4.2 6.1 - - + -
464D ARG* 4.2 8.7 + - - +
468D PHE* 5.6 2.3 - - + +
604D GOL 4.0 33.1 + - - +
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Residues in contact with ALA 370 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366D PRO 2.9 17.6 + - - +
367D TYR* 3.2 7.8 + - + +
369D GLU* 1.3 75.9 - - - +
371D PHE* 1.3 57.7 + - - +
373D LEU* 3.8 6.9 - - - +
374D GLU* 3.0 28.9 + - - +
429D PRO* 3.4 28.1 - - + +
432D PHE* 3.9 7.2 - - + -
433D LEU* 4.1 13.9 - - + -
439D ILE* 3.8 13.6 - - + +
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Residues in contact with PHE 371 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329D SER* 3.4 38.4 - - - -
332D TYR* 4.1 6.3 - - + -
333D LEU* 3.5 25.1 - - + -
339D VAL* 3.7 16.4 - - + -
343D ILE* 3.7 13.7 - - + -
367D TYR* 2.9 13.6 + - + +
368D MET* 3.5 24.0 - - + +
369D GLU 3.2 0.2 - - - -
370D ALA* 1.3 74.7 - - - +
372D ILE* 1.3 65.0 + - + +
374D GLU* 2.9 4.3 + - - +
375D THR* 2.8 43.9 + - - -
427D PHE* 3.3 34.1 - + - -
429D PRO* 4.0 11.4 - - + +
471D LEU* 4.0 10.3 - - + -
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Residues in contact with ILE 372 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329D SER* 5.4 1.8 - - - +
368D MET* 3.0 28.6 + - + +
369D GLU* 4.0 16.4 - - - +
371D PHE* 1.3 78.7 - - + +
373D LEU* 1.3 63.5 + - + +
375D THR* 3.3 6.6 + - - -
376D PHE* 3.1 53.0 + - + -
464D ARG* 5.0 4.9 - - + +
467D VAL* 4.0 15.5 - - + -
468D PHE* 3.8 34.8 - - + +
471D LEU* 4.0 20.2 - - + -
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Residues in contact with LEU 373 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369D GLU* 2.9 51.1 + - + +
370D ALA 3.8 4.0 - - - +
372D ILE* 1.3 78.9 - - + +
374D GLU* 1.3 57.2 + - - +
376D PHE* 3.3 8.7 + - + +
377D ARG* 2.9 29.3 + - - +
432D PHE* 3.9 25.1 - - + -
439D ILE* 4.3 7.4 - - + -
444D SER* 3.6 39.0 - - - +
447D VAL* 4.0 11.2 - - + +
464D ARG* 3.8 25.6 - - - +
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Residues in contact with GLU 374 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370D ALA 3.0 17.6 + - - +
371D PHE 2.9 6.2 + - - +
373D LEU* 1.3 74.1 - - - +
375D THR* 1.3 59.6 + - - +
377D ARG* 2.6 48.4 + - - -
378D HIS* 2.8 30.1 + - - +
426D GLU 3.2 0.9 - - - +
427D PHE* 3.5 25.1 - - + -
428D LEU 2.8 33.6 + - - +
429D PRO* 3.8 13.2 - - + -
431D ARG* 2.9 6.7 + - - -
432D PHE* 3.3 12.8 - - + -
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Residues in contact with THR 375 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325D ALA* 4.2 3.6 - - - +
328D TRP* 4.1 9.2 - - + -
329D SER* 3.6 25.8 + - - +
332D TYR* 3.9 23.6 - - + -
371D PHE* 2.8 38.8 + - - -
372D ILE* 3.6 10.1 - - - -
373D LEU 3.3 0.2 - - - -
374D GLU* 1.3 77.2 - - - +
376D PHE* 1.3 64.2 + - + +
379D SER* 2.7 36.9 + - - +
381D PHE* 5.6 0.7 - - + -
427D PHE* 3.9 6.4 - - - -
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Residues in contact with PHE 376 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325D ALA* 3.7 26.9 - - + -
329D SER* 6.0 0.7 - - - -
372D ILE* 3.1 44.5 + - + -
373D LEU* 3.7 11.2 - - + +
375D THR* 1.3 81.5 - - + +
377D ARG* 1.3 57.1 + - - +
379D SER* 4.3 1.1 - - - -
380D SER* 2.8 30.3 + - - -
381D PHE* 3.5 18.6 - + - -
415D ASN* 4.1 1.4 + - - -
447D VAL* 4.2 11.0 - - + -
449D ILE* 3.7 28.1 - - + +
450D PHE* 4.3 15.9 - + - -
463D ALA 5.4 2.2 - - - -
464D ARG* 4.6 19.3 - - + -
467D VAL* 4.7 9.4 - - + -
601D HEM 3.8 18.2 - - + -
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Residues in contact with ARG 377 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373D LEU 2.9 18.5 + - - +
374D GLU* 2.6 43.5 + - - +
376D PHE* 1.3 75.2 - - - +
378D HIS* 1.3 72.0 + - - +
380D SER* 2.8 21.5 + - - -
415D ASN* 2.8 51.1 + - + +
416D HIS* 3.3 11.8 + - - -
421D TRP* 3.9 32.8 - - + -
424D PRO* 3.1 30.7 + - - +
426D GLU 2.9 12.1 + - - -
431D ARG* 2.9 20.0 - - - +
432D PHE* 4.0 3.1 - - - -
447D VAL* 4.0 17.0 - - + +
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Residues in contact with HIS 378 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332D TYR* 3.0 33.9 + + - +
374D GLU* 2.8 22.3 + - - +
377D ARG* 1.3 83.0 - - - +
379D SER* 1.3 59.1 + - - +
412D TRP* 4.8 0.5 + - - -
416D HIS* 2.8 29.7 + + - -
424D PRO 3.6 11.9 - - - -
425D SER* 2.7 27.8 + - - -
426D GLU 3.5 24.9 - - - -
427D PHE* 4.2 14.4 - + + -
492D PRO* 5.9 0.3 - - - +
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Residues in contact with SER 379 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328D TRP* 4.0 23.0 - - - -
332D TYR* 3.2 24.6 + - - -
375D THR* 2.7 22.3 + - - +
376D PHE 4.0 0.2 + - - -
378D HIS* 1.3 79.8 - - - +
380D SER* 1.3 70.7 + - - +
381D PHE* 3.2 23.5 + - - -
412D TRP* 4.3 3.1 + - - -
492D PRO* 4.4 10.2 - - - +
498D MET* 3.4 16.5 - - - +
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Residues in contact with SER 380 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376D PHE 2.8 18.6 + - - -
377D ARG 2.8 20.1 + - - -
379D SER* 1.3 78.3 + - - +
381D PHE* 1.3 52.7 + - - +
382D VAL 2.6 21.1 + - - -
383D PRO* 3.0 13.8 - - - +
412D TRP* 3.5 27.9 - - - -
415D ASN* 3.0 26.4 + - - +
416D HIS* 3.8 3.6 + - - -
449D ILE* 4.3 4.7 - - - -
498D MET* 3.5 6.2 - - - +
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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
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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