Contacts of the strand formed by residues 272 - 281 (chain B) in PDB entry 5DVX
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 LEU 272 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220B TYR* 4.0 3.1 - - - -
223B LEU* 4.8 3.4 - - + -
253B VAL* 5.4 3.8 - - + -
254B HIS 3.3 17.3 - - - +
255B LEU* 3.9 20.6 - - + -
262B VAL* 4.6 17.3 - - + -
265B ALA* 4.1 11.0 + - + +
266B LEU* 4.0 30.3 - - + -
267B GLY 5.7 0.4 - - - +
268B ARG 4.8 0.4 + - - -
270B GLY 4.1 4.2 - - - +
271B GLY* 1.3 83.7 - - - +
273B ALA* 1.3 62.8 + - - +
331B LEU* 4.1 23.3 - - + -
337B ALA* 5.8 0.4 - - + -
339B GLY 4.1 3.2 + - - +
340B VAL* 3.5 21.2 - - + -
341B ILE* 3.0 22.2 + - - +
402B GOL 4.8 5.4 - - - -
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Residues in contact with ALA 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B MET* 4.2 11.9 - - + -
214B LEU* 4.4 3.1 - - + -
220B TYR* 3.6 37.2 - - + -
253B VAL* 4.5 0.2 - - - +
254B HIS* 2.7 41.4 + - + -
272B LEU* 1.3 76.0 - - - +
274B VAL* 1.3 65.5 + - - +
340B VAL* 4.3 0.4 - - - -
341B ILE* 3.2 16.4 - - + +
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Residues in contact with VAL 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B MET* 5.8 1.6 - - - -
251B HIS* 3.8 17.5 - - + +
252B VAL 3.4 9.9 - - - +
253B VAL* 4.3 20.0 - - + -
254B HIS* 4.9 0.2 - - - -
272B LEU* 5.9 0.4 - - + -
273B ALA* 1.3 80.4 - - - +
275B LEU* 1.3 71.3 + - - +
276B ALA 4.1 0.2 + - - -
331B LEU* 4.9 6.7 - - + -
340B VAL* 3.8 18.1 - - + +
341B ILE 3.0 8.3 + - - +
342B TRP* 3.4 45.3 - - + -
343B THR* 3.0 28.6 + - - +
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Residues in contact with LEU 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B LEU* 3.7 20.4 - - + -
182B LEU* 4.4 22.2 - - + -
185B PHE* 5.6 0.9 - - + -
212B MET* 4.5 15.3 - - + -
250B ILE 3.6 0.7 - - - +
251B HIS* 3.4 3.8 - - - -
252B VAL* 2.9 43.4 + - + +
254B HIS* 4.1 12.2 + - + +
273B ALA 4.2 0.2 - - - -
274B VAL* 1.3 72.9 - - - +
276B ALA* 1.3 59.3 + - - +
317B LEU* 3.8 27.9 - - + +
343B THR* 3.6 22.2 - - + +
345B PHE* 3.4 31.4 - - + -
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Residues in contact with ALA 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B GLU* 3.8 12.1 - - - +
250B ILE 3.2 4.3 - - - -
251B HIS* 3.7 22.9 - - + -
275B LEU* 1.3 75.9 - - - +
277B ALA* 1.3 60.9 + - - +
317B LEU* 5.9 0.7 - - - -
342B TRP* 4.1 11.7 - - + -
343B THR 2.8 14.5 + - - +
344B VAL* 3.3 17.5 - - + +
345B PHE* 2.9 31.8 + - - -
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Residues in contact with ALA 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B GLU* 3.3 6.3 - - - +
250B ILE* 2.9 46.9 + - + +
276B ALA* 1.3 74.8 - - - +
278B PHE* 1.3 67.3 - - - +
279B LEU* 5.2 0.2 - - + -
317B LEU* 4.7 1.3 - - + +
318B PRO* 3.6 37.0 - - + -
344B VAL* 5.3 1.6 - - - -
345B PHE* 3.8 10.1 - - + +
347B GLN 4.7 0.2 - - - +
349B VAL* 4.9 2.9 - - + -
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Residues in contact with PHE 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B ILE* 4.6 2.2 - - + -
237B SER* 3.9 8.3 - - - -
239B HIS* 3.3 43.1 - - + -
241B VAL* 3.8 24.7 - - + -
246B PHE* 3.6 52.0 - + + -
248B ALA 3.6 2.2 - - - -
249B GLU* 3.5 18.2 - - - -
277B ALA* 1.3 75.4 - - - +
279B LEU* 1.3 59.9 + - - +
280B GLU 4.2 0.2 - - - -
344B VAL* 4.1 19.7 - - + -
345B PHE 4.7 10.9 + - - -
346B ASN 5.7 0.9 - - - -
347B GLN 5.1 0.8 + - - -
348B THR* 3.5 19.1 - - + +
349B VAL* 3.0 26.9 + - - +
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Residues in contact with LEU 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227B LEU* 4.3 12.1 - - + -
246B PHE* 4.2 0.9 - - - +
247B PRO* 3.3 12.5 - - - +
248B ALA* 2.9 55.0 + - + +
249B GLU 3.9 0.9 - - - +
250B ILE* 3.8 11.9 - - + +
277B ALA 3.7 11.7 - - - +
278B PHE* 1.3 77.9 - - - +
280B GLU* 1.3 61.1 + - - +
289B TYR* 3.6 32.5 - - + +
349B VAL* 3.3 27.6 - - + +
351B LEU* 4.0 22.9 - - + -
356B LEU* 4.7 4.7 - - + -
359B LEU* 4.6 5.6 - - + -
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Residues in contact with GLU 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246B PHE* 3.5 40.4 - - + -
247B PRO* 4.1 10.6 - - + +
279B LEU* 1.3 73.4 - - - +
281B GLU* 1.3 65.6 + - - +
348B THR* 2.9 30.0 + - - +
349B VAL 2.8 10.5 + - - +
350B SER* 3.2 8.0 + - - +
351B LEU* 2.8 25.6 + - - +
356B LEU* 4.1 7.1 - - - +
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Residues in contact with GLU 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B PRO* 4.3 6.4 - - + +
280B GLU* 1.3 78.8 - - - +
282B GLY* 1.3 72.4 + - - +
350B SER* 4.4 3.1 + - - -
351B LEU 3.3 8.3 - - - +
353B ALA* 3.7 32.6 + - - +
356B LEU* 3.8 14.2 - - + +
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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