Contacts of the helix formed by residues 230 - 234 (chain D) in PDB entry 2CUK
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 ARG 230 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77D ASP* 4.0 19.2 + - - +
201D THR 4.6 5.8 - - - +
202D PRO* 4.9 2.2 - - + -
203D LEU* 3.8 54.2 - - + +
227D ASN* 3.0 13.4 + - - -
229D ALA* 1.3 91.3 - - + +
231D GLY* 1.3 67.0 + - - +
232D ALA 4.5 3.6 - - - +
233D LEU* 3.1 23.2 + - + +
254D VAL* 3.5 5.2 - - - -
277D HIS* 6.4 1.1 - - - -
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Residues in contact with GLY 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227D ASN* 4.0 2.4 + - - -
230D ARG* 1.3 72.3 - - - +
232D ALA* 1.3 56.0 + - - +
233D LEU 3.1 5.4 + - - -
234D VAL* 3.2 22.7 + - - +
236D THR* 5.0 0.5 + - - -
254D VAL* 3.3 20.1 - - - +
255D THR* 3.6 27.5 + - - -
256D ASP* 3.5 12.7 + - - +
258D GLU* 4.7 1.4 + - - -
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Residues in contact with ALA 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203D LEU* 3.9 21.5 - - + -
208D HIS* 3.6 26.0 - - + +
209D ARG* 2.6 37.1 + - - +
230D ARG* 3.2 2.6 + - + +
231D GLY* 1.3 71.3 - - - +
233D LEU* 1.3 50.2 + - - +
234D VAL 3.1 6.9 + - - -
255D THR 4.7 0.2 + - - -
256D ASP* 4.0 23.1 - - - +
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Residues in contact with LEU 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199D LEU* 4.0 28.5 - - + -
201D THR* 3.5 26.9 - - + +
202D PRO 4.0 8.1 - - - +
203D LEU* 4.1 10.3 - - + -
207D THR* 3.3 42.4 - - - +
210D LEU* 3.0 11.4 + - + +
211D LEU* 2.8 29.1 + - - +
227D ASN* 4.2 1.1 - - - +
229D ALA* 3.8 18.6 - - + -
230D ARG* 3.1 23.6 + - + +
231D GLY 3.1 1.0 + - - -
232D ALA* 1.3 77.6 - - - +
234D VAL* 1.3 58.8 + - - +
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Residues in contact with VAL 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199D LEU* 3.7 16.4 - - + -
209D ARG* 4.7 3.6 - - - +
211D LEU* 3.8 15.0 - - + +
216D LEU* 4.8 1.6 - - + -
225D LEU* 4.2 16.4 - - + -
227D ASN* 3.6 24.7 - - + +
231D GLY 3.2 16.1 + - - +
232D ALA* 4.2 5.0 - - - -
233D LEU* 1.3 85.1 - - - +
235D ASP* 1.3 74.6 + - - +
236D THR* 3.1 13.8 + - - +
239D LEU* 4.2 25.1 - - + -
252D LEU* 5.3 3.8 - - + -
256D ASP* 4.4 6.2 - - - +
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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