Contacts of the strand formed by residues 298 - 305 (chain D) in PDB entry 5Y7K
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 HIS 298 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203D TYR* 4.1 3.1 + - - -
263D ASN* 6.1 0.3 - - - +
264D PRO 4.9 6.9 - - - +
265D THR* 6.0 0.5 - - - -
266D VAL* 4.4 16.6 + - + +
289D ALA* 4.4 4.8 - - - +
293D MET* 2.8 40.8 + - + +
294D LEU* 4.3 18.5 - - + +
296D GLY 3.1 12.4 + - - -
297D ASP* 1.3 76.7 - - - +
299D TYR* 1.3 73.0 + - - +
315D TRP* 3.5 35.7 - + - -
316D LEU 3.1 16.6 - - - +
317D ARG* 4.2 0.4 - - + -
318D ARG 4.0 2.2 - - - +
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Residues in contact with TYR 299 (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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202D VAL* 6.4 1.8 - - + -
203D TYR* 3.4 26.9 - + + +
207D VAL* 5.1 9.9 - - + -
263D ASN* 2.9 36.0 + - + -
264D PRO* 5.7 2.9 - - + -
266D VAL* 5.0 0.2 - - - -
298D HIS* 1.3 80.6 - - - +
300D LEU* 1.3 63.5 + - - +
301D CYS* 3.9 2.2 - - + +
315D TRP* 3.4 15.7 - - - -
316D LEU* 2.4 59.9 + - + +
317D ARG 3.8 7.2 - - - -
318D ARG* 3.7 30.2 - - + +
320D GLN* 3.9 16.4 + - - -
665D VAL* 3.8 33.1 + - + -
668D GLU* 3.9 4.7 + - - -
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Residues in contact with LEU 300 (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 TYR* 3.3 12.2 + - + +
207D VAL* 3.3 9.7 - - - +
208D PHE* 3.0 28.4 - - + -
226D ALA* 4.0 18.2 - - + -
266D VAL* 4.1 17.2 - - + +
268D PHE* 3.8 28.7 - - + -
299D TYR* 1.3 72.2 - - - +
301D CYS* 1.3 58.8 + - - +
302D ASP 4.2 4.7 - - - +
303D VAL* 4.1 11.4 - - + -
313D LEU* 4.1 16.2 - - + -
314D GLN 3.6 16.4 - - - +
315D TRP* 3.8 36.1 - - + -
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Residues in contact with CYS 301 (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 VAL* 3.9 11.4 - - + +
208D PHE* 4.0 3.1 - - - -
299D TYR* 5.2 2.2 - - + -
300D LEU* 1.3 74.3 - - - +
302D ASP* 1.3 56.4 + - - +
314D GLN* 3.1 34.0 + - - -
315D TRP 4.0 2.0 - - - -
316D LEU* 3.9 25.8 - - + -
358D ARG* 2.6 39.9 + - + +
359D PRO* 3.7 38.4 - - + +
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Residues in contact with ASP 302 (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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208D PHE* 4.0 2.4 - - - -
300D LEU* 3.7 3.3 - - - +
301D CYS* 1.3 80.7 - - - +
303D VAL* 1.3 70.4 + - - +
304D THR* 2.9 24.1 + - - -
312D SER* 5.0 1.9 + - - +
313D LEU* 3.7 3.5 - - - -
314D GLN* 3.1 65.4 + - + +
358D ARG* 3.8 16.6 + - - +
359D PRO 4.9 3.0 - - - +
360D SER 4.5 1.4 - - - +
361D GLU* 3.4 22.1 + - - +
362D PRO* 3.4 4.3 - - - +
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Residues in contact with VAL 303 (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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208D PHE* 4.6 3.2 - - + -
215D TRP* 3.5 69.1 + - + +
268D PHE* 3.6 33.4 - - + -
300D LEU* 4.1 12.3 - - + -
302D ASP* 1.3 82.3 + - - +
304D THR* 1.3 69.1 + - - +
305D TRP* 5.1 0.9 - - + +
311D ILE* 4.1 11.2 - - + -
312D SER 3.6 3.4 - - - -
313D LEU* 4.0 6.1 - - + -
358D ARG* 5.2 0.4 - - - +
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Residues in contact with THR 304 (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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302D ASP* 2.9 26.6 + - - -
303D VAL* 1.3 75.2 + - - +
305D TRP* 1.3 70.5 + - - +
311D ILE* 4.4 1.8 - - - -
312D SER* 2.7 42.9 + - - -
361D GLU* 4.3 5.4 - - + +
362D PRO* 3.6 34.1 - - - +
364D PHE* 4.1 9.0 - - + -
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Residues in contact with TRP 305 (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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215D TRP* 3.1 32.8 + + + +
216D TRP 3.3 14.7 + - - -
217D SER* 3.7 15.0 - - - -
218D PRO* 3.8 23.4 - - + +
222D PHE* 3.5 25.1 - - + -
224D ALA* 3.7 19.3 - - + -
270D VAL* 4.2 2.7 - - + -
303D VAL* 5.1 0.9 - - + -
304D THR* 1.3 85.3 - - - +
306D ALA* 1.3 60.0 + - - +
307D THR 3.7 9.9 - - - -
308D GLN 4.1 9.0 - - - -
310D ARG 3.4 20.9 - - - -
311D ILE* 3.7 26.3 - - + +
337D TRP* 3.5 36.8 - + - -
364D PHE* 4.2 2.3 - - - +
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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