Contacts of the strand formed by residues 265 - 272 (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 THR 265 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203D TYR* 5.6 0.2 - - - -
228D PHE* 3.3 6.9 - - - +
229D ASN* 2.9 57.3 + - - +
263D ASN 4.5 5.4 - - - +
264D PRO* 1.3 76.6 - - - +
266D VAL* 1.3 63.3 + - - +
267D LYS* 6.1 0.8 - - - +
298D HIS 6.0 0.7 - - - -
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Residues in contact with VAL 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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203D TYR* 3.9 18.2 - - - +
226D ALA* 4.5 0.7 - - + -
227D GLN 3.2 10.3 - - - +
228D PHE* 3.7 23.6 - - + -
264D PRO 5.7 0.2 - - - +
265D THR* 1.3 77.8 - - - +
267D LYS* 1.3 82.3 + - - +
298D HIS* 4.4 19.9 + - + +
299D TYR 4.7 0.2 - - - -
300D LEU* 4.1 24.7 - - + +
315D TRP* 3.7 27.2 - - + -
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Residues in contact with LYS 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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226D ALA* 3.3 5.5 - - - +
227D GLN* 2.7 53.2 + - + +
265D THR* 6.1 1.1 - - - +
266D VAL* 1.3 83.0 - - - +
268D PHE* 1.3 61.3 + - - +
269D PHE* 3.7 24.2 - - + -
286D GLN* 3.8 26.2 - - - +
315D TRP* 5.3 3.1 - - - -
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Residues in contact with PHE 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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215D TRP* 3.7 14.6 - + - -
224D ALA* 3.4 21.5 - - + -
225D TYR 3.5 11.7 - - - -
226D ALA* 4.3 0.9 - - + -
267D LYS* 1.3 75.7 - - - +
269D PHE* 1.3 66.8 + - - +
270D VAL* 3.6 22.9 - - + -
286D GLN* 3.5 7.7 + - - +
287D ILE* 2.9 51.0 + - + +
300D LEU* 3.8 22.7 - - + -
303D VAL* 3.6 23.8 - - + -
311D ILE* 3.6 18.6 - - + -
313D LEU* 3.6 28.7 - - + -
315D TRP* 4.7 6.6 - - + -
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Residues in contact with PHE 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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224D ALA* 3.3 0.5 - - - -
225D TYR* 2.9 76.4 + + + +
227D GLN* 4.0 23.6 - - + -
267D LYS* 3.7 32.1 - - + -
268D PHE* 1.3 77.4 - - - +
270D VAL* 1.3 69.8 + - - +
271D VAL 4.3 0.2 - - - -
284D SER* 3.7 23.1 - - - -
285D ILE 3.2 5.8 - - - +
286D GLN* 3.7 39.3 - - + -
287D ILE 4.7 0.2 - - - +
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Residues in contact with VAL 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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222D PHE* 3.8 22.2 - - + -
223D LEU 3.5 5.8 - - - +
224D ALA* 3.8 7.6 - - + -
268D PHE* 3.6 20.9 - - + -
269D PHE* 1.3 81.3 - - - +
271D VAL* 1.3 62.2 + - - +
284D SER* 4.5 0.4 - - - -
285D ILE* 2.8 38.8 + - - +
287D ILE* 3.9 17.5 - - + -
305D TRP* 4.2 4.3 - - + -
311D ILE* 4.6 4.7 - - + -
337D TRP* 3.4 39.7 + - + +
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Residues in contact with VAL 271 (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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185D ILE* 4.1 28.3 - - + -
222D PHE* 3.3 7.0 - - - -
223D LEU* 2.7 64.8 + - + +
225D TYR* 4.4 3.6 - - + -
270D VAL* 1.3 74.1 - - - +
272D ASN* 1.3 67.4 + - - +
273D THR* 3.6 6.4 + - + -
276D LEU* 4.6 0.9 - - + -
282D ALA* 4.2 20.6 - - + +
283D THR 3.8 17.7 - - - +
284D SER* 3.7 19.1 - - - +
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Residues in contact with ASN 272 (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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221D THR* 3.4 18.7 - - - +
222D PHE* 3.9 22.9 - - + -
270D VAL 4.4 0.2 + - - -
271D VAL* 1.3 75.5 - - - +
273D THR* 1.3 60.5 + - - +
274D ASP* 2.9 25.9 + - - +
275D SER* 2.7 37.4 + - - +
276D LEU* 3.4 11.2 - - - +
283D THR 4.7 2.8 + - - +
330D TYR* 4.6 9.7 + - + -
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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