Contacts of the helix formed by residues 365 - 380 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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346B GLU* 3.5 42.8 - - + +
347B LEU* 3.7 27.8 - - + -
350B VAL* 3.8 13.5 - - + -
351B ILE* 4.1 13.5 - - + -
357B PRO* 5.5 0.2 - - + -
361B ASP* 3.4 17.8 + - + +
362B ARG 3.5 7.9 + - - +
363B SER 3.5 2.0 - - - -
364B HIS* 1.3 83.4 - - - +
366B PRO* 1.3 66.7 - - - +
367B TYR 3.2 2.9 - - - -
368B MET* 3.1 18.8 + - + +
369B GLU* 3.2 11.6 + - - +
468B PHE* 3.9 24.2 - - + -
472B ALA* 5.1 1.1 - - + -
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Residues in contact with PRO 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B GLU* 3.0 14.4 - - - +
350B VAL* 5.9 0.2 - - + -
363B SER 4.9 4.7 - - - +
364B HIS* 3.4 10.5 - - - +
365B LEU* 1.3 88.9 - - - +
367B TYR* 1.3 54.7 + - - +
369B GLU* 3.5 2.4 + - + +
370B ALA* 2.9 23.4 + - - +
433B LEU* 4.0 3.5 - - + +
437B GLY 3.3 27.8 - - - +
438B ALA* 4.3 2.2 - - - -
439B ILE* 3.2 35.8 - - + +
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Residues in contact with TYR 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B VAL* 3.4 44.7 - - + +
342B LYS* 3.5 38.0 - - + +
343B ILE* 3.6 23.6 - - + -
346B GLU* 2.9 25.6 + - + +
366B PRO* 1.3 75.2 - - - +
368B MET* 1.3 59.1 + - - +
370B ALA* 3.7 4.7 - - + +
371B PHE* 2.9 24.7 + - + +
429B PRO* 4.2 11.4 - - + +
430B GLU* 3.0 34.4 + - - -
433B LEU* 3.7 24.4 - - + +
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Residues in contact with MET 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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343B ILE* 4.1 31.6 - - + +
346B GLU* 3.1 8.2 + - - +
347B LEU* 5.5 3.4 - - + -
365B LEU* 3.1 23.4 + - + +
367B TYR* 1.3 76.3 - - - +
369B GLU* 1.3 61.8 + - - +
371B PHE* 3.2 26.5 + - + -
372B ILE* 3.0 29.0 + - + +
468B PHE* 3.6 31.2 - - + +
471B LEU* 4.1 31.4 - - + -
472B ALA* 4.4 15.3 - - - -
475B LEU* 4.7 1.1 - - + -
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Residues in contact with GLU 369 (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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362B ARG* 3.4 46.1 + - + +
365B LEU 3.2 9.0 + - - +
366B PRO* 3.8 7.9 - - + +
368B MET* 1.3 78.6 - - - +
370B ALA* 1.3 57.4 + - - +
372B ILE* 3.2 19.8 + - - +
373B LEU* 2.8 59.7 + - + +
439B ILE* 4.2 14.6 - - + -
464B ARG* 4.6 7.6 + - - +
468B PHE* 5.6 2.0 - - - +
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Residues in contact with ALA 370 (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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366B PRO 2.9 18.9 + - - +
367B TYR* 3.7 7.2 - - + +
369B GLU* 1.3 76.4 - - - +
371B PHE* 1.3 57.6 + - - +
373B LEU* 3.5 6.7 + - - +
374B GLU* 3.0 29.5 + - - +
429B PRO* 3.4 26.9 - - + +
432B PHE* 3.9 6.4 - - + -
433B LEU* 4.2 13.9 - - + -
439B ILE* 3.7 15.0 - - + +
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Residues in contact with PHE 371 (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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329B SER* 3.5 28.9 - - - -
332B TYR* 4.2 5.2 - - + -
333B LEU* 3.5 36.8 - - + -
339B VAL* 3.7 18.2 - - + -
343B ILE* 3.7 15.0 - - + -
367B TYR* 2.9 17.8 + - + +
368B MET* 3.6 20.9 - - + +
370B ALA* 1.3 74.1 - - - +
372B ILE* 1.3 63.2 + - + +
374B GLU* 3.2 1.9 + - - +
375B THR* 2.9 43.7 + - - -
427B PHE* 3.4 33.7 - + - -
429B PRO* 3.9 11.8 - - + +
471B LEU* 3.9 10.5 - - + -
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Residues in contact with ILE 372 (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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329B SER* 5.5 1.1 - - - +
368B MET* 3.0 29.0 + - + +
369B GLU* 3.8 21.1 - - - +
371B PHE* 1.3 79.0 - - + +
373B LEU* 1.3 64.5 + - + +
375B THR* 3.2 7.3 + - - -
376B PHE* 3.1 52.2 + - + -
464B ARG* 5.0 5.8 - - + +
467B VAL* 4.1 12.1 - - + -
468B PHE* 3.8 37.9 - - + +
471B LEU* 4.2 17.7 - - + -
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Residues in contact with LEU 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B GLU* 2.8 49.4 + - + +
370B ALA 3.7 4.0 - - - +
372B ILE* 1.3 74.1 - - + +
374B GLU* 1.3 57.1 + - - +
376B PHE* 3.3 10.5 + - + +
377B ARG* 2.9 27.5 + - - +
432B PHE* 3.8 25.4 - - + -
439B ILE* 4.2 11.4 - - + -
444B SER* 3.4 42.6 - - - +
447B VAL* 4.0 12.3 - - + +
464B ARG* 4.3 19.1 - - - +
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Residues in contact with GLU 374 (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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370B ALA 3.0 18.5 + - - +
371B PHE 3.8 3.4 - - - +
373B LEU* 1.3 74.5 - - - +
375B THR* 1.3 60.6 + - - +
377B ARG* 2.9 31.2 + - - +
378B HIS* 2.9 28.2 + - - +
426B GLU 3.2 1.0 - - - +
427B PHE* 3.5 24.0 - - + -
428B LEU 3.0 19.1 + - - +
429B PRO* 3.8 13.7 - - + -
431B ARG* 2.8 43.0 + - - -
432B PHE* 3.2 6.5 - - + -
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Residues in contact with THR 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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325B ALA* 4.3 4.5 - - - +
328B TRP* 4.2 7.9 - - + -
329B SER* 3.6 31.4 + - - +
332B TYR* 4.1 14.4 - - + -
371B PHE* 2.9 38.8 + - - -
372B ILE* 3.2 10.1 + - - -
374B GLU* 1.3 75.0 - - - +
376B PHE* 1.3 71.6 + - + +
379B SER* 2.8 32.0 + - - +
381B PHE* 5.9 0.9 - - + -
427B PHE* 3.9 9.1 - - - -
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Residues in contact with PHE 376 (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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325B ALA* 4.1 22.9 - - + -
372B ILE* 3.1 42.3 + - + -
373B LEU* 3.6 11.0 - - + +
375B THR* 1.3 83.2 - - + +
377B ARG* 1.3 58.8 + - - +
379B SER* 4.4 1.6 - - - -
380B SER* 3.0 29.6 + - - -
381B PHE* 4.0 16.6 - + - -
415B ASN* 4.2 1.6 + - - -
447B VAL* 4.1 13.7 - - + -
449B ILE* 3.8 26.0 - - + +
450B PHE* 4.1 20.4 - + - -
463B ALA 5.7 0.4 - - - -
464B ARG* 4.6 22.9 - - + -
467B VAL* 4.9 12.6 - - + -
601B HEM 4.3 14.6 - - + -
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Residues in contact with ARG 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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373B LEU 2.9 16.8 + - - +
374B GLU* 2.9 42.4 + - - +
375B THR 3.3 0.2 - - - -
376B PHE* 1.3 77.1 - - - +
378B HIS* 1.3 74.1 + - - +
380B SER* 2.8 20.8 + - - -
415B ASN* 2.7 55.8 + - + +
416B HIS* 3.3 14.8 - - - -
421B TRP* 3.7 39.8 - - + -
424B PRO* 2.9 37.7 + - - +
426B GLU 3.3 9.3 + - - -
431B ARG* 3.4 10.4 - - - +
432B PHE* 4.1 1.3 - - + -
447B VAL* 4.0 13.9 - - + -
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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
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332B TYR* 2.9 33.4 + + + +
374B GLU* 2.9 19.7 + - - +
377B ARG* 1.3 102.1 - - - +
379B SER* 1.3 61.7 + - - +
412B TRP* 4.9 0.5 + - - -
416B HIS* 3.1 23.6 + - - -
424B PRO 3.6 10.5 - - - -
425B SER* 2.9 26.6 + - - -
426B GLU 3.7 11.2 - - - -
427B PHE* 4.0 17.9 + + + -
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Residues in contact with SER 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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328B TRP* 4.1 22.5 - - - -
332B TYR* 3.4 25.1 + - - -
375B THR* 2.8 23.2 + - - +
378B HIS* 1.3 80.7 - - - +
380B SER* 1.3 71.0 + - - +
381B PHE* 3.1 23.7 + - - -
412B TRP* 4.3 3.5 + - - -
492B PRO* 4.7 10.0 - - - +
498B MET* 3.5 14.7 - - - +
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Residues in contact with SER 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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376B PHE 3.0 15.1 + - - -
377B ARG 2.8 20.5 + - - -
379B SER* 1.3 80.9 + - - +
381B PHE* 1.3 58.4 + - - +
382B VAL 2.8 15.2 + - - -
383B PRO* 3.1 13.4 - - - +
412B TRP* 3.4 26.8 - - - -
415B ASN* 2.9 28.1 + - - +
416B HIS* 3.7 2.8 + - - -
449B ILE* 4.4 4.9 - - - -
498B MET* 3.3 7.4 - - - +
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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