Contacts of the helix formed by residues 468 - 472 (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 TYR 468 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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426K GLY* 3.0 18.4 + - - +
447K GLN* 3.6 33.4 - - + +
448K ALA 3.5 14.6 - - - -
449K GLY* 3.6 23.6 - - - -
467K GLY* 1.3 77.4 - - - -
469K LYS* 1.3 82.9 + - + +
471K SER* 3.0 18.9 + - - -
475K ARG* 3.6 16.2 - - - -
157L GLU* 2.7 30.1 + - - +
487L LYS* 4.1 38.1 - - + +
488L VAL 4.2 3.8 - - - -
489L LYS* 3.1 23.5 + - - +
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Residues in contact with LYS 469 (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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421K ASN* 2.9 28.5 + - - +
423K SER 3.3 19.9 + - - +
424K THR* 3.4 8.1 - - - +
425K TYR 3.9 13.6 + - - +
447K GLN* 3.1 39.2 + - - +
468K TYR* 1.3 79.8 - - + +
470K MET* 1.3 65.0 + - + +
471K SER 3.1 4.5 + - - -
472K GLY* 3.5 14.8 + - - +
239L ASP* 5.6 6.7 - - - +
261L ASN 4.6 6.9 - - - +
262L LEU* 4.7 6.4 - - - +
487L LYS* 4.4 13.5 - - - +
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Residues in contact with MET 470 (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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247K THR* 3.8 20.3 + - + +
251K ARG* 3.5 24.2 - - - +
269K LEU* 3.3 19.3 - - - +
424K THR* 3.1 43.4 + - + +
425K TYR* 3.9 6.4 - - + -
469K LYS* 1.3 78.8 - - + +
471K SER* 1.3 54.1 + - - +
472K GLY 3.2 5.4 - - - +
236L GLU* 4.7 6.1 - - - +
260L SER 3.5 25.1 - - - +
261L ASN* 3.5 31.6 - - + +
262L LEU* 4.7 9.2 - - + -
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Residues in contact with SER 471 (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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267K LEU 3.8 2.3 - - - +
268K GLU* 3.9 1.2 - - - -
269K LEU* 2.9 33.6 + - - +
270K GLY 3.2 17.1 + - - -
425K TYR* 3.4 4.9 - - - +
426K GLY 2.7 26.4 + - - -
427K LEU* 3.2 18.7 + - - +
467K GLY* 3.8 15.3 + - - -
468K TYR 3.0 15.2 + - - -
470K MET* 1.3 76.2 - - - +
472K GLY* 1.3 57.2 + - - +
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Residues in contact with GLY 472 (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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267K LEU* 3.1 19.7 - - - -
269K LEU* 3.7 9.6 - - - +
467K GLY 3.0 22.0 - - - +
468K TYR 4.4 0.5 - - - -
469K LYS 3.5 13.0 + - - +
470K MET* 3.2 4.8 - - - +
471K SER* 1.3 81.4 - - - +
473K SER* 1.3 61.5 + - - -
262L LEU* 5.5 5.8 - - - -
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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