Contacts of the helix formed by residues 384 - 395 (chain M) in PDB entry 3HOU
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 ASN 384 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378M GLU* 4.0 13.7 + - - +
379M VAL 3.2 16.4 + - - -
381M THR* 2.6 41.1 + - - -
383M TYR* 1.3 76.3 - - + +
385M ILE* 1.3 64.0 + - - -
386M ASP* 3.0 3.5 + - - -
387M ARG* 3.3 34.3 + - - +
388M LEU* 2.9 43.5 + - + +
115R THR 5.6 3.2 + - - +
117R PRO* 6.0 4.2 - - - +
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Residues in contact with ILE 385 (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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380M VAL* 3.4 19.1 - - + -
381M THR 2.8 8.8 + - - +
382M PRO* 4.0 8.6 + - + +
383M TYR 3.8 1.2 - - - -
384M ASN* 1.3 78.5 - - - +
386M ASP* 1.3 74.7 + - - +
388M LEU* 3.9 1.8 - - - +
389M THR* 2.4 43.9 + - - +
426M LEU* 3.3 40.2 - - + +
427M GLN* 5.5 0.2 - - - -
428M TYR* 4.2 21.5 - - + +
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Residues in contact with ASP 386 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382M PRO 5.0 5.7 - - - +
383M TYR 5.6 1.8 - - - +
384M ASN 3.1 1.2 - - - -
385M ILE* 1.3 90.6 - - - +
387M ARG* 1.3 68.4 + - - +
389M THR* 3.1 6.8 + - - -
390M GLN* 3.0 23.4 + - - +
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Residues in contact with ARG 387 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378M GLU* 2.9 43.7 + - - -
384M ASN* 3.3 31.4 + - - +
386M ASP* 1.3 80.6 - - - +
388M LEU* 1.3 64.7 + - - +
390M GLN* 3.1 9.3 + - - +
391M LEU* 3.1 31.0 + - + +
434M ARG* 4.0 4.9 - - - +
437M MET* 3.6 30.2 - - + +
115R THR 6.0 0.2 + - - -
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Residues in contact with LEU 388 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378M GLU* 3.5 28.9 - - + +
379M VAL 4.0 5.6 - - - +
380M VAL* 3.9 24.2 - - + -
384M ASN* 2.9 46.4 + - + +
385M ILE 3.9 0.4 - - - +
387M ARG* 1.3 77.2 - - - +
389M THR* 1.3 60.3 + - - +
391M LEU* 3.1 17.9 + - + +
392M VAL* 2.9 31.2 + - - +
426M LEU* 3.7 14.4 - - + -
432M VAL* 3.9 28.4 - - + +
434M ARG* 4.4 2.0 - - - -
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Residues in contact with THR 389 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385M ILE* 2.4 43.1 + - - +
386M ASP* 3.1 6.3 + - - -
388M LEU* 1.3 73.9 - - - +
390M GLN* 1.3 58.2 + - - +
392M VAL* 3.4 5.2 + - + +
393M ARG* 2.8 51.1 + - + +
424M ILE 4.6 16.2 - - - +
425M GLN* 5.2 1.8 - - - -
426M LEU* 4.0 17.9 + - + +
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Residues in contact with GLN 390 (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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386M ASP 3.0 11.1 + - - +
387M ARG* 3.2 14.1 - - - +
389M THR* 1.3 77.9 - - - +
391M LEU* 1.3 53.1 + - + +
393M ARG* 3.4 29.7 + - - +
394M ASN* 2.6 56.9 + - - +
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Residues in contact with LEU 391 (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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387M ARG* 3.1 28.7 + - + +
388M LEU* 3.1 26.1 + - + +
390M GLN* 1.3 75.2 - - + +
392M VAL* 1.3 65.8 + - - +
394M ASN* 2.9 14.6 + - - +
395M GLY 2.9 12.0 + - - -
400M PRO* 3.2 44.0 - - + +
401M GLY* 3.3 21.0 - - - +
402M ALA* 3.8 5.2 + - + -
432M VAL* 5.3 0.4 - - + -
434M ARG* 4.2 22.0 - - + -
437M MET* 4.4 12.3 - - - -
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Residues in contact with VAL 392 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388M LEU 2.9 11.8 + - - +
389M THR* 3.7 10.8 - - + +
391M LEU* 1.3 76.0 - - - +
393M ARG* 1.3 66.4 + - - +
395M GLY* 3.2 11.1 + - - -
402M ALA* 4.3 1.8 - - - -
405M VAL* 3.4 28.7 - - + -
415M LEU* 3.4 38.2 - - + +
421M ALA* 4.3 12.6 - - - +
423M ASP 5.5 0.9 - - - +
424M ILE* 4.3 15.9 - - + +
426M LEU* 4.4 5.8 - - + -
432M VAL* 3.6 26.9 - - + -
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Residues in contact with ARG 393 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389M THR* 2.8 38.8 + - + +
390M GLN* 3.7 29.0 + - - +
392M VAL* 1.3 79.4 - - - +
394M ASN* 1.3 65.8 + - - +
395M GLY* 3.3 1.2 + - - -
421M ALA 4.9 6.7 - - - -
422M GLY* 4.5 19.7 + - - +
423M ASP 5.9 0.9 - - - +
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Residues in contact with ASN 394 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390M GLN* 2.6 49.8 + - - +
391M LEU* 3.0 11.2 - - - +
393M ARG* 1.3 76.1 - - - +
395M GLY* 1.3 57.1 + - - +
398M GLU* 2.9 59.5 + - - +
400M PRO* 3.2 27.9 + - - +
401M GLY* 4.2 0.7 - - - -
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Residues in contact with GLY 395 (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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391M LEU 2.9 8.5 + - - -
392M VAL 3.2 9.9 + - - -
393M ARG 4.2 0.7 - - - -
394M ASN* 1.3 81.9 - - - +
396M PRO* 1.3 70.2 - - - +
397M ASN* 3.1 7.8 + - - -
398M GLU* 3.9 4.6 - - - +
401M GLY* 3.2 9.0 - - - -
402M ALA 3.2 20.0 + - - -
415M LEU* 5.8 0.2 - - - -
435M HIS* 3.7 0.9 + - - -
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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