Contacts of the strand formed by residues 278 - 284 (chain N) in PDB entry 5X22
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 PRO 278 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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271N VAL* 4.0 20.6 - - + -
272N LEU 3.5 10.5 - - - +
273N ARG* 3.6 27.4 - - + +
276N ASP 3.3 0.6 - - - -
277N GLU* 1.3 93.0 - - + +
279N VAL* 1.3 60.9 + - - +
280N ALA 3.5 3.4 - - - +
281N THR* 5.2 3.8 - - - +
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Residues in contact with VAL 279 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255N GLU* 3.5 38.9 - - + +
256N GLU 3.8 17.3 - - - +
272N LEU* 2.8 19.1 + - + +
273N ARG* 3.8 0.6 - - - +
274N ARG* 3.3 38.8 - - + +
277N GLU 3.4 3.3 + - - +
278N PRO* 1.3 72.6 - - - +
280N ALA* 1.3 63.1 + - - +
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Residues in contact with ALA 280 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255N GLU* 3.9 17.0 - - + -
270N LEU 4.8 0.2 - - - -
271N VAL* 3.4 7.3 - - - +
272N LEU* 2.9 44.6 + - + +
278N PRO* 3.5 2.4 - - - +
279N VAL* 1.3 82.3 - - - +
281N THR* 1.3 67.0 + - - +
282N TYR* 3.9 21.1 - - + +
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Residues in contact with THR 281 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219N GLU* 5.8 3.4 - - + +
220N ARG 3.6 23.6 + - - +
221N ALA* 3.7 12.5 - - + -
222N GLY* 3.0 18.7 + - - -
269N PHE* 4.1 20.4 - - + -
270N LEU 3.8 2.5 - - - -
271N VAL* 4.2 16.7 - - + +
278N PRO* 5.2 3.6 - - - +
280N ALA* 1.3 78.4 + - - +
282N TYR* 1.3 70.4 + - - +
332N TYR* 4.9 1.6 + - - -
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Residues in contact with TYR 282 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221N ALA* 4.2 3.6 - - - -
222N GLY 3.3 11.7 - - - +
251N PHE* 3.5 34.5 - + + -
253N ALA* 4.6 0.2 - - - -
254N GLU* 2.9 39.7 + - + +
255N GLU* 3.6 6.9 + - - +
269N PHE* 3.6 8.5 - - - -
270N LEU* 2.9 48.9 + - + +
272N LEU* 4.0 14.8 - - + -
280N ALA* 3.9 24.4 - - + +
281N THR* 1.3 80.6 - - - +
283N PHE* 1.3 60.8 + - - +
284N LEU* 5.2 1.1 - - + -
304N LEU* 3.7 27.4 - - + -
332N TYR* 3.9 20.4 - + - -
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Residues in contact with PHE 283 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221N ALA* 3.7 18.6 - - + +
222N GLY 2.9 10.7 + - - +
223N LEU* 3.3 27.2 - - + +
242N LEU* 4.9 3.1 - - + -
264N LEU* 4.8 3.1 - - + -
268N ALA 3.2 21.5 - - - -
269N PHE* 3.8 13.0 - + - +
282N TYR* 1.3 74.8 - - - +
284N LEU* 1.3 69.2 + - - +
285N PRO* 3.3 25.4 - - + +
313N MET* 3.7 25.8 - - + -
314N PRO* 3.7 29.4 - - + -
317N VAL* 4.1 13.9 - - + -
335N LEU* 4.6 15.5 - - + -
337N LEU* 3.5 23.6 - - + -
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Residues in contact with LEU 284 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251N PHE* 4.3 16.8 - - + -
261N LEU* 4.9 1.1 - - + -
267N GLY* 3.4 2.6 - - - -
268N ALA* 2.9 55.4 + - + +
270N LEU* 3.7 36.6 - - + -
282N TYR* 5.2 0.2 - - + -
283N PHE* 1.3 84.2 - - - +
285N PRO* 1.3 68.5 - - - +
288N MET* 3.9 33.8 - - + +
290N PRO* 4.0 24.7 - - + -
305N ALA* 4.1 11.7 - - + -
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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