Contacts of the helix formed by residues 263 - 270 (chain D) in PDB entry 3RIK
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 ASP 263 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201D PRO* 3.5 8.7 - - - +
202D GLY* 2.9 38.8 + - - -
206D HIS* 3.2 25.2 - - - +
207D GLN* 2.7 32.5 + - - +
210D ALA* 3.9 2.5 - - + -
259D PHE* 3.0 26.6 + - + +
261D ALA 3.5 0.6 - - - -
262D ARG* 1.3 77.2 - - - +
264D LEU* 1.3 60.0 + - - +
265D GLY 3.4 1.3 - - - -
266D PRO* 3.3 1.7 - - - +
267D THR* 2.7 38.6 + - - -
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Residues in contact with LEU 264 (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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210D ALA* 4.0 13.9 - - + +
213D PHE* 3.6 42.8 - - + -
232D ALA* 4.0 17.0 - - + -
259D PHE* 2.9 43.2 + - + +
260D ILE* 4.3 4.7 - - + -
263D ASP* 1.3 70.5 - - - +
265D GLY* 1.3 69.4 + - - +
267D THR* 5.6 0.2 - - - -
268D LEU* 3.0 42.1 + - + +
278D LEU* 3.8 28.0 - - + -
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Residues in contact with GLY 265 (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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260D ILE* 2.7 23.5 + - - +
264D LEU* 1.3 76.9 - - - +
266D PRO* 1.4 65.2 - - - +
268D LEU* 3.6 2.6 - - - +
269D ALA* 2.9 21.1 + - - +
278D LEU* 4.9 3.3 - - - +
304D TYR* 3.3 34.8 - - - -
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Residues in contact with PRO 266 (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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207D GLN* 6.3 0.2 - - - +
260D ILE 3.6 1.1 - - - +
261D ALA 3.2 27.8 - - - +
262D ARG 3.4 12.1 - - - +
263D ASP 3.3 11.2 - - - +
265D GLY* 1.4 84.9 - - - +
267D THR* 1.3 68.2 + - - +
269D ALA* 3.4 4.8 + - + +
270D ASN* 3.0 25.5 + - - +
304D TYR* 3.7 19.2 - - + +
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Residues in contact with THR 267 (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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207D GLN* 4.0 14.0 + - - -
210D ALA* 3.4 31.5 - - - +
211D ARG* 4.1 15.2 - - + +
214D VAL* 3.8 21.5 - - + +
263D ASP 2.7 29.1 + - - -
264D LEU* 4.3 1.1 - - - -
266D PRO* 1.3 76.6 - - - +
268D LEU* 1.3 63.7 + - - +
270D ASN* 3.3 10.2 + - - +
271D SER* 3.4 11.3 + - - -
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Residues in contact with LEU 268 (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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210D ALA 5.8 0.2 - - - +
213D PHE* 4.5 9.0 - - + -
214D VAL* 4.5 13.9 - - + -
217D LEU* 3.8 28.7 - - + -
230D VAL* 4.3 20.0 - - + -
264D LEU* 3.0 44.8 + - + +
265D GLY* 3.6 2.2 - - - +
267D THR* 1.3 75.3 - - - +
269D ALA* 1.3 62.2 + - - +
271D SER* 2.5 27.3 + - - +
273D HIS* 4.9 7.4 - - + +
274D HIS* 3.6 11.9 - - - -
276D VAL* 5.5 10.8 - - + +
278D LEU* 4.7 14.6 - - + -
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Residues in contact with ALA 269 (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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265D GLY 2.9 18.5 + - - +
266D PRO* 3.8 5.2 - - + +
268D LEU* 1.3 72.2 - - - +
270D ASN* 1.3 57.3 - - - +
271D SER 3.3 0.8 - - - +
274D HIS* 3.3 27.2 - - + +
304D TYR* 3.9 21.1 - - + +
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Residues in contact with ASN 270 (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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266D PRO 3.0 18.2 + - - +
267D THR* 3.9 4.3 - - - +
269D ALA* 1.3 72.7 - - - +
271D SER* 1.3 61.3 + - - +
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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