Contacts of the helix formed by residues 468 - 470 (chain C) in PDB entry 1O04
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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426C GLY* 2.9 18.6 + - - +
447C GLN* 3.8 25.1 - - + +
448C ALA 3.4 24.0 - - - -
449C GLY* 3.4 14.4 - - - -
467C GLY* 1.3 73.5 - - - -
469C LYS* 1.3 77.7 + - + +
471C SER* 3.0 20.1 + - - -
475C ARG* 3.4 22.7 - - - -
157D GLU* 2.7 34.4 + - - +
264D ARG* 3.7 4.9 - - - +
487D GLU* 3.5 20.6 + - + -
488D VAL 3.7 4.9 - - - -
489D LYS* 3.5 11.4 - - - +
6804D GAI 3.7 32.5 - - - -
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Residues in contact with LYS 469 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421C ASN* 2.8 31.3 + - - +
423C SER 3.1 21.1 + - - +
424C THR* 3.3 10.5 - - - +
425C TYR 3.9 12.7 + - - +
447C GLN* 2.9 39.4 + - - +
468C TYR* 1.3 81.6 - - + +
470C MET* 1.3 64.7 + - + +
471C SER 3.3 2.3 + - - -
472C GLY 3.4 13.9 + - - +
239D ASP* 5.7 6.3 - - - +
261D ASN 4.8 5.4 - - - +
262D LEU* 4.8 2.4 - - - +
264D ARG* 3.4 18.0 + - - +
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Residues in contact with MET 470 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247C THR* 2.8 37.0 + - + +
251C ARG* 3.9 28.9 - - - +
269C LEU* 3.6 5.7 - - - +
424C THR* 2.9 43.3 + - + +
425C TYR* 4.5 4.0 - - + -
469C LYS* 1.3 79.0 - - + +
471C SER* 1.3 59.6 + - - +
472C GLY 3.2 2.4 + - - -
236D GLU* 5.2 4.5 - - - +
260D SER 5.2 1.1 - - - +
261D ASN* 3.7 41.3 - - + +
262D LEU* 4.5 13.5 - - + -
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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