Contacts of the strand formed by residues 290 - 295 (chain D) in PDB entry 3BUW
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 SER 290 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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281D LEU* 4.2 4.1 - - - +
284D PHE* 3.5 29.0 - - - +
287D LYS* 2.8 39.9 + - - +
288D PRO 3.6 0.2 + - - -
289D GLY* 1.3 78.4 - - - +
291D TYR* 1.3 59.0 + - - +
307D TYR* 3.2 2.6 - - - -
308D VAL* 2.9 33.4 + - - +
339D PHE* 3.3 11.9 - - - +
342D GLY* 3.8 8.7 - - - -
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Residues in contact with TYR 291 (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 HIS* 3.2 16.5 + + - -
267D GLY* 4.4 0.3 - - - -
281D LEU* 4.2 3.9 - - - +
289D GLY 3.6 4.3 - - - +
290D SER* 1.3 75.6 - - - +
292D ILE* 1.3 66.4 + - - +
293D PHE* 3.8 19.5 - + - -
305D ILE* 4.2 8.5 - - + -
306D GLY 3.1 15.5 - - - +
307D TYR* 3.8 10.3 - - + -
328D LEU* 3.8 23.6 - - + +
337D TYR* 3.4 47.1 - - + -
338D LEU 3.8 0.2 - - - -
339D PHE 2.9 10.5 + - - -
340D PRO* 3.3 25.8 - - + +
341D ASP 2.7 30.7 + - - +
346D ASN* 2.6 27.5 + - - -
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Residues in contact with ILE 292 (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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267D GLY 3.4 14.4 - - - +
269D MET* 4.0 13.2 - - + -
272D LEU* 4.8 0.4 - - + -
277D VAL* 3.7 45.2 - - + +
280D ARG* 4.0 22.2 - - - -
281D LEU* 3.9 20.9 - - + -
291D TYR* 1.3 87.9 - - - +
293D PHE* 1.3 65.2 + - - +
305D ILE* 3.6 2.1 - - - +
306D GLY 2.8 28.0 + - - +
341D ASP* 3.6 31.9 - - + +
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Residues in contact with PHE 293 (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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261D LEU* 3.3 28.0 - - - -
265D HIS* 3.6 30.1 - + - -
267D GLY* 2.8 22.5 + - - +
268D TYR* 3.6 20.1 - + + -
269D MET* 2.8 28.8 + - - +
277D VAL* 5.8 1.1 - - - -
291D TYR* 3.8 17.9 - + - -
292D ILE* 1.3 77.1 - - - +
294D ARG* 1.3 63.0 + - - +
303D TRP* 3.7 19.3 - + + -
304D ALA 3.4 5.8 - - - +
305D ILE* 3.0 32.5 - - + -
324D LEU* 3.8 16.4 - - + -
328D LEU* 4.1 11.2 - - + -
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Residues in contact with ARG 294 (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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323C PTR 2.9 41.6 + - - -
268D TYR* 4.8 1.3 - - - -
269D MET* 3.4 22.9 - - + +
270D ALA 4.3 2.7 - - - +
272D LEU 3.2 23.8 + - - +
273D THR* 3.8 1.8 + - - +
274D TYR* 3.4 19.2 - - - +
277D VAL* 3.5 22.8 - - + +
293D PHE* 1.3 79.5 - - - +
295D LEU* 1.3 79.7 + - - +
296D SER* 3.8 3.6 - - - +
297D CYS* 4.0 2.0 - - - +
303D TRP* 3.4 17.4 - - - -
304D ALA* 2.9 40.7 + - - +
316D GLN* 2.9 32.9 - - - +
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Residues in contact with LEU 295 (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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160D HIS* 5.0 9.1 - - + +
227D THR* 5.3 5.2 - - + +
230D LEU* 4.0 31.0 - - + -
243D ILE* 4.6 2.0 - - + -
247D LEU* 3.4 37.9 - - + -
248D PHE* 5.5 1.8 - - + -
268D TYR* 4.1 20.0 - - + +
269D MET 4.8 1.0 + - - -
270D ALA 4.9 5.0 + - - +
272D LEU 4.3 3.8 - - - +
294D ARG* 1.3 93.6 + - - +
296D SER* 1.3 67.1 + - - +
297D CYS* 3.5 2.1 + - - +
300D LEU* 4.7 7.2 - - + -
301D GLY 5.8 0.9 - - - +
302D GLN 3.9 4.9 - - - +
303D TRP* 4.0 19.3 - - + -
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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