Contacts of the helix formed by residues 332 - 346 (chain O) in PDB entry 3H1I
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 HIS 332 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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303O THR* 3.5 19.7 + - - +
304O THR* 3.9 13.6 + - + -
305O GLN* 3.3 43.0 - - + +
306O PRO 5.8 1.3 - - - +
328O SER* 4.2 0.9 - - - -
329O GLN* 3.4 25.0 + - + +
331O ALA* 1.3 82.8 + - + +
333O ALA* 1.3 57.4 + - - +
334O GLY 3.2 2.2 - - - -
335O GLU* 3.7 25.0 + - - +
336O VAL* 2.7 39.4 + - + +
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Residues in contact with ALA 333 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253O VAL* 3.9 13.2 - - + -
328O SER* 3.2 17.0 - - - +
329O GLN 3.1 14.3 + - - +
330O ALA 3.5 12.1 - - - +
331O ALA 3.2 0.8 - - - -
332O HIS* 1.3 76.4 - - - +
334O GLY* 1.3 72.2 + - - +
337O ILE* 3.0 28.7 + - + +
432O SER 4.5 0.4 - - - -
433O THR* 3.6 23.3 - - - +
434O PRO* 4.7 0.4 - - - -
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Residues in contact with GLY 334 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331O ALA 3.9 6.0 + - - -
332O HIS 3.2 0.8 - - - -
333O ALA* 1.3 87.3 - - - +
335O GLU* 1.3 64.4 + - - +
337O ILE* 3.1 8.3 + - - +
338O ARG* 3.3 26.6 + - - +
432O SER 3.4 22.9 + - - -
434O PRO* 4.1 9.0 - - - +
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Residues in contact with GLU 335 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302O ALA* 3.7 29.4 - - + +
303O THR* 4.3 6.1 - - - -
304O THR* 5.2 0.9 + - - +
331O ALA 5.1 3.1 - - - +
332O HIS* 3.7 36.6 + - + +
334O GLY* 1.3 70.5 - - - -
336O VAL* 1.3 57.1 + - + +
338O ARG* 3.6 26.1 + - - +
339O ALA* 2.7 38.9 + - + +
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Residues in contact with VAL 336 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299O VAL* 3.9 25.3 - - + +
302O ALA* 6.0 0.7 - - - -
303O THR* 4.0 27.1 - - + +
307O PHE* 4.7 6.7 - - + -
308O ASP 5.4 0.2 - - - +
309O ALA* 5.4 0.4 - - + -
326O THR* 3.7 28.5 - - + +
327O ILE 5.1 2.2 - - - +
328O SER* 3.6 24.0 - - - +
332O HIS* 2.7 26.1 + - + +
333O ALA 3.9 3.4 - - - +
334O GLY 2.9 4.4 + - - -
335O GLU* 1.3 74.5 - - - +
337O ILE* 1.3 58.5 + - - +
339O ALA* 3.8 2.5 - - - +
340O ALA* 3.0 25.8 + - - +
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Residues in contact with ILE 337 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253O VAL* 5.4 0.7 - - + -
255O ALA* 4.1 16.8 - - + -
257O VAL* 4.3 12.8 - - + -
324O PHE* 3.6 26.0 - - + -
326O THR* 3.6 17.0 - - - +
328O SER* 5.3 0.7 - - - +
333O ALA* 3.0 23.1 - - + +
334O GLY 3.1 2.1 + - - +
336O VAL* 1.3 74.7 - - + +
338O ARG* 1.3 65.8 + - - +
340O ALA* 2.9 20.8 + - - +
341O MET* 3.1 10.8 + - - +
424O MET* 4.4 7.4 - - + -
433O THR* 3.6 16.6 - - + -
434O PRO* 3.6 25.8 - - + -
439O LEU* 4.9 8.3 - - + -
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Residues in contact with ARG 338 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334O GLY* 3.3 15.6 + - - +
335O GLU* 3.2 38.0 + - - +
337O ILE* 1.3 78.4 - - - +
339O ALA* 1.3 57.4 + - - +
341O MET* 3.0 28.3 + - - +
342O ASN* 3.2 15.5 + - - +
432O SER 5.5 1.4 + - - -
434O PRO* 4.6 15.5 - - + +
438O GLU* 4.9 9.8 - - - +
439O LEU* 4.2 21.5 - - + -
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Residues in contact with ALA 339 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298O GLY 4.9 5.4 - - - +
299O VAL* 4.8 12.9 - - - +
302O ALA* 3.9 25.8 - - + -
335O GLU* 2.7 20.7 + - - +
336O VAL* 4.0 3.4 - - - +
338O ARG* 1.3 68.5 - - - +
340O ALA* 1.3 63.2 + - - +
341O MET 3.1 2.2 - - - -
342O ASN* 3.3 16.5 + - - +
343O GLN* 3.3 23.4 + - - +
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Residues in contact with ALA 340 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295O LEU* 3.3 31.1 - - + +
299O VAL* 4.4 8.5 - - + -
309O ALA* 5.4 0.4 - - + -
324O PHE* 3.8 29.1 - - + -
326O THR* 4.1 7.2 - - + -
336O VAL 3.0 14.6 + - - +
337O ILE* 2.9 16.7 + - - +
339O ALA* 1.3 77.6 - - - +
341O MET* 1.3 59.8 + - - +
343O GLN 4.2 0.2 - - - -
344O LEU* 3.6 12.6 + - - +
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Residues in contact with MET 341 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257O VAL* 5.0 2.0 - - + -
324O PHE* 4.0 15.3 - - + -
337O ILE 3.1 10.9 + - - +
338O ARG* 3.0 12.4 + - - +
340O ALA* 1.3 75.7 - - - +
342O ASN* 1.3 56.8 + - - +
343O GLN 2.9 1.3 - - - -
344O LEU* 2.3 30.7 + - - +
345O LYS* 2.7 33.7 + - + +
417O PHE* 3.7 26.0 - - + -
418O VAL* 5.7 2.5 - - + -
422O LYS* 4.0 33.7 - - + +
439O LEU* 4.0 45.1 - - + +
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Residues in contact with ASN 342 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338O ARG* 3.2 20.2 + - - +
339O ALA* 3.3 17.9 - - - +
341O MET* 1.3 74.7 - - - +
343O GLN* 1.3 54.4 - - - +
345O LYS* 3.2 27.3 + - - +
346O ALA* 2.6 40.0 + - + +
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Residues in contact with GLN 343 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279O LEU* 4.1 4.6 - - + +
294O LYS* 3.4 38.8 + - + +
295O LEU* 3.6 30.3 - - + +
298O GLY* 3.2 20.0 - - - -
339O ALA 3.3 18.2 + - - +
340O ALA 3.9 6.3 - - - +
341O MET 2.9 0.2 - - - -
342O ASN* 1.3 80.3 - - - +
344O LEU* 1.3 56.0 + - - +
346O ALA* 4.3 5.6 - - - +
347O ALA* 3.0 20.4 + - - +
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Residues in contact with LEU 344 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275O LEU* 5.1 4.0 - - + -
279O LEU* 3.3 42.6 - - + -
295O LEU* 5.4 3.6 - - + -
322O PHE* 5.1 5.2 - - + -
323O GLY* 5.0 4.3 - - - -
324O PHE* 4.2 14.8 - - + -
340O ALA 3.6 10.3 + - - +
341O MET* 2.3 30.3 + - - +
343O GLN* 1.3 68.7 - - - +
345O LYS* 1.3 60.7 + - + -
347O ALA* 3.3 13.1 - - + +
348O ALA* 3.3 12.1 + - - +
414O ALA* 4.4 5.4 - - + +
417O PHE* 3.2 56.1 - - + -
418O VAL* 4.1 3.7 - - - +
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Residues in contact with LYS 345 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341O MET* 2.7 25.1 + - + +
342O ASN* 3.2 43.4 + - - +
344O LEU* 1.3 76.0 - - + +
346O ALA* 1.3 54.1 + - - +
347O ALA 2.5 4.9 + - - -
348O ALA* 2.4 32.3 + - - +
349O GLN* 3.0 21.0 + - - +
418O VAL* 4.0 29.2 - - + -
439O LEU 6.2 2.0 - - - -
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Residues in contact with ALA 346 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342O ASN* 2.6 20.5 + - + +
343O GLN* 4.4 5.4 - - - +
345O LYS* 1.3 71.7 - - - +
347O ALA* 1.3 56.9 + - - +
349O GLN* 4.1 18.1 + - - +
351O GLY* 3.4 24.0 + - - +
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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