Contacts of the helix formed by residues 412 - 422 (chain K) in PDB entry 2ONM
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 412 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311K GLN* 4.5 0.9 - - - +
410K PHE* 3.3 12.5 - - - -
411K LYS* 1.3 96.8 - - + +
413K ILE* 1.3 64.8 + - - +
414K GLU* 3.6 15.7 + - - +
415K GLU* 3.0 26.8 + - - +
416K VAL 3.2 18.5 + - - -
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Residues in contact with ILE 413 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278K MET* 3.8 31.0 - - + -
311K GLN* 4.7 2.4 - - - +
410K PHE* 4.7 0.2 - - - -
412K THR* 1.3 71.4 - - - +
414K GLU* 1.3 87.3 + - - +
416K VAL* 3.2 15.5 - - + +
417K VAL* 3.1 21.9 - - - +
438K LYS* 4.1 24.9 - - + -
441K TYR* 3.6 33.0 - - + -
442K LEU* 4.0 21.3 - - + -
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Residues in contact with GLU 414 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412K THR* 3.6 17.6 + - - +
413K ILE* 1.3 95.9 - - - +
415K GLU* 1.3 63.7 + - - +
417K VAL* 3.6 5.4 + - - +
418K GLY* 3.5 13.9 + - - -
441K TYR* 4.0 23.3 + - - +
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Residues in contact with GLU 415 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410K PHE* 3.8 9.2 - - - +
411K LYS* 2.7 34.7 + - - +
412K THR* 3.0 23.7 + - - +
414K GLU* 1.3 75.5 - - - +
416K VAL* 1.3 64.6 + - - +
418K GLY* 3.2 4.9 + - - -
419K ARG* 3.0 56.1 + - + +
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Residues in contact with VAL 416 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276K ILE* 3.8 30.7 - - + -
278K MET* 5.2 0.2 - - - -
309K PHE* 3.7 40.6 - - + -
410K PHE* 3.5 33.9 - - + -
412K THR 3.2 3.0 + - - -
413K ILE* 3.2 17.3 - - + +
415K GLU* 1.3 77.7 - - - +
417K VAL* 1.3 61.0 + - - +
419K ARG* 4.4 4.3 - - - +
420K ALA* 2.7 38.2 + - - +
442K LEU* 4.3 7.0 - - + -
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Residues in contact with VAL 417 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413K ILE 3.1 16.1 + - - +
414K GLU* 3.7 8.5 - - - +
415K GLU 3.2 0.4 - - - -
416K VAL* 1.3 78.2 - - - +
418K GLY* 1.3 58.4 + - - +
420K ALA* 3.8 3.3 - - - +
421K ASN* 2.9 54.1 + - - +
441K TYR* 3.9 19.7 - - + +
442K LEU* 3.5 24.7 - - + -
445K ALA* 3.8 21.5 - - + +
446K LEU* 4.7 4.7 - - + +
72L LEU* 5.2 6.5 - - + -
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Residues in contact with GLY 418 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414K GLU 3.5 6.0 + - - -
415K GLU 3.2 7.3 + - - -
417K VAL* 1.3 81.0 - - - +
419K ARG* 1.3 58.2 + - - +
421K ASN* 3.8 4.4 - - - +
422K ASN* 3.0 29.3 + - - +
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Residues in contact with ARG 419 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307K ARG* 3.0 19.5 + - - -
309K PHE* 3.8 19.4 - - + -
389K VAL 4.7 3.2 + - - -
390K GLN* 5.3 2.6 + - - +
391K ASP* 2.7 47.2 + - - +
408K LEU* 3.7 17.6 - - - +
409K LYS 2.7 29.9 + - - -
410K PHE* 3.6 8.7 - - - +
415K GLU* 3.0 48.9 + - + +
416K VAL* 3.8 4.0 - - - +
418K GLY* 1.3 74.6 - - - +
420K ALA* 1.3 64.9 + - - +
422K ASN* 3.3 16.6 + - - +
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Residues in contact with ALA 420 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274K PRO* 3.8 25.4 - - + +
276K ILE* 4.1 7.4 - - + -
307K ARG* 2.8 30.0 + - - +
309K PHE* 4.3 4.9 - - + -
416K VAL 2.7 21.7 + - - +
417K VAL 3.8 0.2 - - - +
419K ARG* 1.3 71.8 - - - +
421K ASN* 1.3 60.9 + - - +
423K SER* 4.3 1.9 - - - -
425K TYR 5.6 0.5 - - - +
446K LEU* 3.7 26.0 - - + -
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Residues in contact with ASN 421 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417K VAL* 2.9 29.9 + - - +
418K GLY* 4.1 4.2 - - - +
420K ALA* 1.3 75.7 - - - +
422K ASN* 1.3 58.1 + - - +
423K SER* 2.8 10.8 + - - -
425K TYR 5.2 0.3 - - - +
445K ALA 2.9 24.0 + - - -
446K LEU* 3.5 12.4 - - - +
447K GLN* 3.0 52.6 + - - +
469K LYS* 2.9 24.0 + - - +
72L LEU* 6.0 1.0 - - - +
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Residues in contact with ASN 422 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307K ARG* 4.2 4.7 + - - -
391K ASP* 5.7 7.9 + - - +
418K GLY 3.0 19.3 + - - +
419K ARG* 3.3 17.4 + - - +
421K ASN* 1.3 71.8 - - - +
423K SER* 1.3 63.5 + - - +
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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