Contacts of the helix formed by residues 406 - 420 (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 THR 406 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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354O GLU* 5.5 0.2 - - - -
357O VAL* 4.9 0.7 - - - -
404O SER 4.5 6.7 - - - +
405O VAL* 1.3 75.6 - - - +
407O SER* 1.3 66.8 + - - +
408O ALA* 3.0 12.3 + - - +
409O ASP* 2.6 52.4 + - - +
410O VAL* 3.4 12.7 + - - +
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Residues in contact with SER 407 (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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352O VAL* 3.8 21.3 + - - +
354O GLU* 3.3 37.6 + - - -
357O VAL* 4.1 17.0 - - - +
405O VAL 4.1 0.2 + - - -
406O THR* 1.3 72.5 - - - +
408O ALA* 1.3 63.6 + - - +
410O VAL* 3.3 6.9 - - - +
411O VAL* 3.2 23.8 + - - +
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Residues in contact with ALA 408 (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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406O THR* 2.9 10.9 - - - +
407O SER* 1.3 74.5 - - - +
409O ASP* 1.3 54.7 + - - +
410O VAL 2.5 17.5 + - - -
411O VAL* 2.6 22.1 + - - +
412O ASN* 2.6 25.8 + - - +
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Residues in contact with ASP 409 (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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271O ALA* 4.0 15.2 - - + +
404O SER 4.4 1.9 - - - +
405O VAL* 3.8 16.1 - - + -
406O THR* 2.6 52.5 + - - +
408O ALA* 1.3 71.2 - - - +
410O VAL* 1.3 51.7 + - - +
412O ASN* 3.5 11.5 + - - +
413O ALA* 2.7 35.5 + - - +
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Residues in contact with VAL 410 (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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271O ALA 4.7 2.9 - - - +
274O VAL* 4.0 18.8 - - + -
275O LEU* 3.8 29.9 - - + +
278O VAL* 4.6 6.5 - - + -
352O VAL* 3.9 24.9 - - + -
357O VAL* 4.2 11.0 - - + -
405O VAL* 3.9 16.6 - - + -
406O THR 3.5 13.2 - - - +
407O SER 3.3 8.5 - - - +
408O ALA 2.5 4.4 + - - -
409O ASP* 1.3 69.5 - - - +
411O VAL* 1.3 64.5 + - - +
412O ASN 2.9 4.2 + - - -
413O ALA* 3.1 6.7 + - - +
414O ALA* 2.8 24.7 + - - +
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Residues in contact with VAL 411 (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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347O ALA 4.2 2.9 - - - +
348O ALA 3.2 30.2 - - - +
350O GLY* 3.8 18.8 - - - +
352O VAL* 3.8 24.5 - - + +
407O SER* 3.4 18.8 - - - +
408O ALA* 2.6 13.3 + - - +
410O VAL* 1.3 74.0 - - - +
412O ASN* 1.3 56.0 + - - +
414O ALA* 3.2 9.1 - - - +
415O LYS* 3.2 25.1 + - + +
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Residues in contact with ASN 412 (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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408O ALA* 2.6 35.4 + - - +
409O ASP* 3.5 15.1 + - - +
410O VAL 2.9 0.4 - - - -
411O VAL* 1.3 71.7 - - - +
413O ALA* 1.3 58.8 + - - +
414O ALA 2.8 1.1 - - - -
415O LYS* 2.5 37.4 + - - +
416O LYS* 2.9 12.5 + - - +
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Residues in contact with ALA 413 (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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271O ALA* 4.4 4.5 - - + -
272O PHE* 3.6 52.2 - - + +
275O LEU* 3.6 12.1 - - + +
322O PHE* 5.4 0.2 - - - -
409O ASP 2.7 22.0 + - - +
410O VAL* 3.7 4.5 - - - +
412O ASN* 1.3 72.7 - - - +
414O ALA* 1.3 62.4 - - - +
416O LYS* 3.3 15.1 + - - +
417O PHE* 3.4 9.5 + - - +
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Residues in contact with ALA 414 (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* 3.2 20.3 - - + +
344O LEU* 4.4 8.7 - - + +
347O ALA* 3.5 11.0 - - + +
348O ALA* 3.4 22.6 - - + +
410O VAL 2.8 12.7 + - - +
411O VAL 3.2 12.8 - - - +
412O ASN 2.8 0.6 + - - -
413O ALA* 1.3 78.8 - - - +
415O LYS* 1.3 59.6 + - - +
417O PHE* 3.5 10.7 - - - +
418O VAL* 3.3 19.9 - - - +
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Residues in contact with LYS 415 (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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348O ALA* 3.7 31.2 - - + +
349O GLN* 5.8 4.0 - - - -
411O VAL* 3.2 11.0 + - - +
412O ASN* 2.5 25.4 + - - +
414O ALA* 1.3 71.0 - - - +
416O LYS* 1.3 53.1 + - - +
417O PHE 2.7 16.6 + - - -
418O VAL* 2.8 16.1 + - + +
419O SER* 2.9 17.5 + - - -
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Residues in contact with LYS 416 (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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259O THR* 4.0 9.9 - - - +
260O GLU* 4.4 16.0 - - - +
261O GLY 3.6 18.4 + - - -
268O GLU* 2.7 43.2 + - - +
272O PHE* 3.7 18.4 - - + -
412O ASN 2.9 8.8 + - - +
413O ALA* 3.5 13.2 - - - +
415O LYS* 1.3 75.5 - - - +
417O PHE* 1.3 58.7 + - - +
419O SER* 3.4 15.7 + - - +
420O GLY* 3.6 7.6 + - - -
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Residues in contact with PHE 417 (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* 3.9 20.9 - - + -
258O VAL* 4.0 5.8 - - - -
259O THR* 3.6 25.4 + - - -
260O GLU 5.9 0.2 - - - -
272O PHE* 5.5 1.5 - - + -
322O PHE* 3.4 33.0 - + + -
323O GLY* 3.4 23.8 - - - -
324O PHE* 4.2 9.6 - + - -
341O MET* 3.7 25.6 - - + -
344O LEU* 3.2 33.4 - - + -
413O ALA 3.4 8.0 + - - +
414O ALA* 3.5 11.4 - - - +
415O LYS 2.7 4.9 + - - -
416O LYS* 1.3 74.7 - - - +
418O VAL* 1.3 69.3 + - + +
419O SER 3.1 5.5 + - - -
420O GLY 4.1 3.1 - - - +
422O LYS* 3.9 11.1 - - + -
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Residues in contact with VAL 418 (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* 5.7 2.5 - - + -
344O LEU 4.1 10.5 - - - +
345O LYS* 4.0 30.7 - - + -
348O ALA* 3.7 18.2 - - + -
414O ALA 3.3 17.7 - - - +
415O LYS* 2.8 9.1 + - + +
417O PHE* 1.3 82.2 - - + +
419O SER* 1.3 60.0 + - - +
422O LYS* 3.7 21.7 + - - +
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Residues in contact with SER 419 (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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415O LYS* 2.9 18.4 + - - -
416O LYS* 3.4 12.1 + - - +
417O PHE 3.1 1.0 - - - -
418O VAL* 1.3 79.6 - - - +
420O GLY* 1.3 78.3 + - - +
422O LYS* 4.9 0.9 - - - -
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Residues in contact with GLY 420 (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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259O THR* 4.2 15.0 - - - -
416O LYS 3.6 6.7 + - - -
417O PHE 4.1 1.5 + - - +
419O SER* 1.3 94.7 + - - +
421O LYS* 1.3 64.5 + - - -
422O LYS* 3.6 16.1 + - - +
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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