Contacts of the helix formed by residues 367 - 376 (chain M) in PDB entry 2DFS
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 367 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361M CYS* 3.7 0.6 - - - -
366M VAL* 1.4 87.6 - - - +
368M TYR* 1.3 72.0 + - - +
369M GLU* 3.1 13.0 + - - +
370M GLU* 2.8 43.0 + - + +
371M MET* 3.6 12.5 + - - +
584M LYS* 5.0 6.2 - - - +
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Residues in contact with TYR 368 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350M ILE* 4.3 4.7 - - - +
351M PRO 4.3 0.9 + - - -
353M LYS* 4.0 11.2 + - - -
354M HIS* 3.1 31.7 + - - +
357M LEU* 3.6 32.3 - - + +
358M THR* 3.7 33.9 - - + -
361M CYS* 3.8 15.1 - - + +
366M VAL 3.8 1.6 + - - -
367M ASP* 1.3 77.5 + - - +
369M GLU* 1.3 91.4 + - + +
371M MET* 3.4 4.3 + - - +
372M ALA* 2.9 32.1 + - + +
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Residues in contact with GLU 369 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367M ASP* 3.1 10.5 + - - +
368M TYR* 1.3 100.9 - - + +
370M GLU* 1.3 64.5 + - - +
372M ALA* 3.8 13.4 - - - +
373M HIS* 3.0 27.2 + - - +
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Residues in contact with GLU 370 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366M VAL* 5.6 0.3 - - - +
367M ASP* 2.8 33.6 + - + +
368M TYR 3.5 0.2 - - - -
369M GLU* 1.3 72.7 - - - +
371M MET* 1.3 60.3 + - - +
373M HIS* 3.7 4.2 - - - +
374M TRP* 3.2 43.4 + - + +
578M LYS* 2.6 42.3 + - - +
579M VAL* 3.7 23.8 - - + +
582M SER* 4.4 2.3 + - - -
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Residues in contact with MET 371 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357M LEU* 4.4 8.5 - - + -
360M PHE* 4.0 25.1 - - + -
361M CYS* 4.0 16.8 - - - -
366M VAL* 4.7 1.3 - - + -
367M ASP 3.6 17.3 + - - +
368M TYR 3.4 3.5 + - - +
369M GLU 3.3 0.4 - - - -
370M GLU* 1.3 77.7 - - - +
372M ALA* 1.4 59.5 + - - +
374M TRP* 3.1 2.5 + - + -
375M LEU* 3.0 49.7 + - + +
403M LEU* 4.8 5.4 - - + -
576M GLN* 3.9 39.9 - - + +
579M VAL* 4.0 25.0 - - + +
580M LEU* 4.6 9.6 - - - -
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Residues in contact with ALA 372 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350M ILE* 3.3 36.0 - - + +
357M LEU* 4.0 15.0 - - + +
368M TYR* 2.9 22.8 + - + +
369M GLU* 3.4 19.0 + - - +
371M MET* 1.4 75.5 - - - +
373M HIS* 1.3 62.9 + - - +
375M LEU* 3.6 5.7 + - - -
376M CYS* 3.6 8.0 - - - -
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Residues in contact with HIS 373 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369M GLU* 3.0 18.2 + - - +
370M GLU* 3.7 4.9 - - - +
372M ALA* 1.3 75.3 - - - +
374M TRP* 1.3 111.1 + + - +
376M CYS 3.2 3.5 + - - -
377M HIS* 3.1 68.1 + + - +
388M ILE* 4.0 17.4 - - + +
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Residues in contact with TRP 374 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370M GLU* 3.2 40.8 + - + +
371M MET* 3.1 9.7 + - + +
373M HIS* 1.3 107.2 + + - +
375M LEU* 1.3 61.6 + - - +
376M CYS 3.3 0.4 - - - -
377M HIS* 3.5 25.4 - - + +
378M ARG* 4.0 8.3 - - - -
379M LYS* 3.8 28.9 - - + -
388M ILE* 4.5 16.4 - - + -
573M TYR* 4.5 0.9 - - - -
575M GLU* 3.3 45.9 - - + +
576M GLN* 2.9 30.7 + - + +
578M LYS* 6.3 1.0 - - + +
579M VAL* 4.1 8.7 - - + -
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Residues in contact with LEU 375 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335M LEU* 4.8 17.0 - - + -
338M VAL* 4.2 16.6 - - + -
340M PHE* 3.9 21.3 - - + -
350M ILE* 4.2 13.7 - - + -
357M LEU* 3.9 28.0 - - + -
371M MET* 3.0 34.5 + - + +
372M ALA 3.8 6.1 - - - +
373M HIS 3.3 0.4 - - - -
374M TRP* 1.3 77.9 - - - +
376M CYS* 1.4 58.3 + - - +
391M ILE* 3.4 16.9 - - - +
396M ALA* 3.8 13.6 - - - +
400M ARG* 5.1 11.4 - - + -
403M LEU* 5.1 3.6 - - + -
576M GLN* 3.7 20.0 + - - +
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Residues in contact with CYS 376 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340M PHE* 3.9 14.1 - - - -
348M CYS* 3.5 22.7 + - - +
349M ALA* 3.9 20.9 - - - -
350M ILE* 3.5 31.2 - - - -
372M ALA 3.6 4.0 - - - +
373M HIS 3.2 3.4 + - - +
375M LEU* 1.4 78.1 - - - +
377M HIS* 1.3 76.7 + - + +
390M PRO* 3.7 2.9 - - - +
391M ILE* 3.2 34.6 + - - +
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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