Contacts of the strand formed by residues 265 - 271 (chain T) in PDB entry 5K0Y
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 PHE 265 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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248T GLY 4.6 4.9 - - - +
249T GLY 3.5 25.6 - - - -
251T GLU* 3.6 42.2 - - + -
252T ALA 4.0 9.6 - - - -
253T MET* 3.9 18.8 - - + -
262T ILE* 4.3 7.6 - - + -
264T LYS* 1.4 92.1 - - - +
266T GLU* 1.4 59.3 + - - +
282T LYS* 3.6 8.5 - - - -
284T HIS* 3.2 32.9 + - + +
285T PHE 3.5 31.9 - - - -
286T GLY* 3.4 17.9 - - - +
287T PRO* 3.6 19.7 - - + -
288T ILE* 4.9 1.8 - - + +
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Residues in contact with GLU 266 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230T PRO* 4.4 0.5 - - - +
232T ARG* 4.3 8.8 + - - -
247T GLY* 4.6 0.3 - - - -
248T GLY 4.2 13.5 + - - +
251T GLU* 3.6 26.6 - - - +
264T LYS 3.6 8.0 - - - +
265T PHE* 1.4 73.0 - - - +
267T ALA* 1.4 58.6 + - - +
268T ARG* 3.5 45.2 + - + +
280T ARG* 4.0 20.1 - - + -
281T VAL 3.3 24.0 - - - +
282T LYS* 4.0 15.3 - - + +
288T ILE* 3.3 17.1 - - - +
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Residues in contact with ALA 267 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245T VAL* 4.5 4.9 - - + -
246T VAL 3.8 10.8 - - - +
247T GLY* 4.6 1.1 - - - -
266T GLU* 1.4 73.0 - - - +
268T ARG* 1.3 60.7 + - - +
269T PHE* 4.2 1.0 + - - -
279T GLY 4.0 0.5 - - - +
280T ARG* 3.4 3.1 - - - -
281T VAL* 3.0 34.0 + - - +
284T HIS* 5.7 0.9 - - - +
288T ILE* 3.5 17.5 - - + +
291T VAL* 5.2 1.1 - - + -
300T TYR* 3.7 34.1 - - + +
302T SER* 3.9 4.7 - - - +
312T HIS* 5.9 0.2 - - - +
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Residues in contact with ARG 268 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227T ARG 5.3 0.2 + - - -
228T THR* 3.8 22.9 - - - +
229T GLU* 3.8 11.1 + - - +
230T PRO* 3.5 33.5 - - - +
232T ARG* 3.7 22.4 - - - +
245T VAL* 3.6 2.7 - - - -
246T VAL* 3.0 37.0 + - + +
251T GLU* 4.1 6.1 + - - -
266T GLU* 3.5 32.2 + - + +
267T ALA* 1.3 75.9 - - - +
269T PHE* 1.4 60.9 + - - +
270T PHE* 3.8 17.9 + - + -
277T GLU* 3.6 17.7 + - - +
279T GLY 3.5 4.0 - - - -
280T ARG* 3.4 37.5 - - + +
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Residues in contact with PHE 269 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134M LYS* 5.5 0.2 - - - -
1T MET* 3.9 13.0 - - + -
238T SER* 4.8 1.8 - - - -
241T TYR* 3.8 15.7 - + - -
243T HIS* 4.6 13.2 - - + -
244T VAL 3.6 6.1 - - - +
245T VAL* 3.8 25.8 - - + -
267T ALA 4.8 1.6 - - - -
268T ARG* 1.4 72.2 - - - +
270T PHE* 1.4 60.4 + - - +
277T GLU* 3.4 11.8 - - - +
278T PHE* 3.0 30.8 + - + -
279T GLY* 3.1 23.9 + - - +
281T VAL* 4.0 12.1 - - + -
300T TYR* 3.6 45.8 - + - -
314T PHE* 4.3 4.7 - + - -
318T TYR* 3.4 26.2 - + - +
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Residues in contact with PHE 270 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226T PHE* 3.8 35.9 - + + -
227T ARG 4.4 12.8 - - - -
228T THR* 3.8 30.7 - - + -
243T HIS* 3.4 6.1 - - - +
244T VAL* 2.9 39.3 + - + +
246T VAL* 3.8 17.0 - - + -
268T ARG* 3.8 19.5 - - + -
269T PHE* 1.4 75.7 - - - +
271T HIS* 1.4 60.5 + - - +
275T GLU 4.1 12.3 - - - -
276T GLU 3.6 4.3 - - - -
277T GLU* 3.8 40.6 - - + -
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Residues in contact with HIS 271 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226T PHE* 3.8 3.1 - - - -
242T GLU* 3.2 32.2 + - + +
243T HIS* 3.3 36.0 - + - +
270T PHE* 1.4 71.8 - - - +
272T LEU* 1.3 64.3 + - - +
273T ALA* 3.3 16.0 + - + -
274T PHE* 3.7 21.9 - + + -
275T GLU* 2.9 29.8 + - - -
276T GLU 2.9 14.4 + - - +
322T GLU* 3.8 19.7 + - - -
326T ARG* 3.3 37.0 - - - +
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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