Contacts of the strand formed by residues 258 - 263 (chain D) in PDB entry 3QKJ
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 MET 258 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308A LYS* 5.1 13.9 - - + -
217D TYR* 3.5 10.6 - - - -
254D ALA* 4.0 5.4 - - + +
255D MET* 3.0 26.4 + - + +
256D SER 3.7 8.1 - - - +
257D GLY* 1.4 80.6 + - - +
259D ARG* 1.3 78.0 + - - +
271D GLU* 3.7 44.6 - - + +
272D VAL* 3.5 6.3 - - - -
273D SER* 3.7 35.0 - - - +
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Residues in contact with ARG 259 (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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217D TYR* 3.5 40.8 + - - +
219D ASP* 2.8 43.2 + - - -
221D LYS* 3.3 13.5 + - - +
222D GLU 3.0 19.4 + - - -
223D PHE* 2.8 27.6 + - + -
243D VAL* 4.3 7.6 - - + -
254D ALA* 4.7 1.6 - - - -
257D GLY 4.1 0.4 - - - -
258D MET* 1.3 91.4 + - - +
260D TRP* 1.3 67.0 + - - +
261D VAL* 3.8 1.0 + - + +
270D SER 3.7 0.2 - - - +
271D GLU* 3.5 2.8 - - - -
272D VAL* 2.6 39.8 + - - +
274D ALA* 3.7 20.2 - - + +
277D LEU* 4.0 22.2 - - + -
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Residues in contact with TRP 260 (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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2D SO4 3.8 15.9 - - - -
217D TYR* 2.9 16.2 + - - +
243D VAL* 3.5 8.3 - - - +
244D VAL* 3.0 39.8 + - + +
245D SER 4.7 0.2 - - - +
246D TRP* 3.5 22.8 - - + +
249D THR* 3.8 17.9 - - + -
251D LYS* 3.5 40.4 - - + -
252D ARG* 2.8 43.8 + - + -
254D ALA* 3.5 24.8 - - + +
259D ARG* 1.3 73.0 - - - +
261D VAL* 1.3 60.6 + - - +
269D PHE* 4.2 3.4 - - + -
270D SER* 3.4 30.1 - - - -
271D GLU* 3.5 28.3 - - + -
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Residues in contact with VAL 261 (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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229D VAL* 4.3 3.8 - - + -
241D ALA* 3.9 14.8 - - + -
242D MET 3.3 8.7 - - - +
243D VAL* 4.2 13.0 - - + -
244D VAL* 4.4 3.6 - - - +
259D ARG* 4.4 5.2 - - + +
260D TRP* 1.3 79.5 - - - +
262D GLN* 1.3 58.3 + - - +
263D TRP* 3.9 30.7 - - + -
268D LYS 3.9 0.5 - - - +
269D PHE* 3.3 5.5 - - - +
270D SER* 2.9 40.2 + - - +
272D VAL* 3.9 9.2 - - + -
277D LEU* 4.1 34.5 - - + -
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Residues in contact with GLN 262 (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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241D ALA* 3.2 4.1 - - - -
242D MET* 2.8 35.6 + - + +
244D VAL* 4.0 17.0 - - + +
261D VAL* 1.3 72.2 - - - +
263D TRP* 1.3 63.8 + - - +
264D PHE* 3.7 1.4 + - - -
267D GLY* 3.0 38.7 + - - +
268D LYS 3.3 4.3 - - - +
269D PHE* 3.4 34.9 - - + -
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Residues in contact with TRP 263 (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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231D GLY* 3.6 32.8 - - - -
233D ILE* 3.8 25.1 - - + -
239D TRP* 3.4 40.6 - - + -
240D PRO 3.8 7.0 - - - -
241D ALA* 3.7 18.2 - - + -
261D VAL* 3.9 17.9 - - + -
262D GLN* 1.3 72.4 - - - +
264D PHE* 1.3 64.2 + - - +
266D ASP* 3.5 15.7 - - - +
267D GLY* 2.9 32.2 + - - -
268D LYS* 2.9 33.7 + - + -
270D SER* 2.8 32.7 + - - +
272D VAL* 4.4 2.7 - - + -
356D BTB 3.6 34.0 - - - -
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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