Contacts of the helix formed by residues 319 - 337 (chain V) in PDB entry 5IJO
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 319 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244V PHE* 5.0 14.8 - - + -
270V ALA* 5.7 5.8 - - - +
313V PHE* 4.1 25.4 - - + +
316V ILE* 4.5 5.5 + - + +
317V PRO 3.4 1.0 - - - -
318V HIS* 1.3 74.5 - - + +
320V ALA* 1.3 57.8 + - - +
321V PRO 3.2 2.7 - - - -
322V VAL* 3.1 16.8 + - + +
323V LEU* 2.8 27.4 + - - +
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Residues in contact with ALA 320 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316V ILE 5.0 2.7 - - - +
317V PRO* 3.2 19.1 + - + +
318V HIS 2.9 4.5 + - - +
319V HIS* 1.3 78.2 - - - +
321V PRO* 1.3 59.5 - - - +
323V LEU* 3.0 9.3 + - - +
324V LEU* 2.9 28.4 + - - +
349V ALA* 3.9 5.6 - - + +
352V LEU* 4.3 18.8 - - + -
354V VAL* 4.0 24.2 - - + -
357V TYR* 5.6 4.0 - - + -
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Residues in contact with PRO 321 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270V ALA* 4.8 18.6 - - + +
274V VAL* 5.7 6.8 - - + +
318V HIS 4.2 2.3 - - - +
319V HIS 3.2 0.4 - - - -
320V ALA* 1.3 80.9 - - - +
322V VAL* 1.3 60.6 + - - +
324V LEU* 3.4 7.0 + - + +
325V ALA* 3.0 24.8 + - - +
354V VAL* 4.8 8.9 - - + +
358V LEU* 6.1 5.2 - - + -
384V LEU* 5.6 3.1 - - - +
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Residues in contact with VAL 322 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270V ALA* 5.7 5.7 + - - +
273V LEU* 4.7 20.4 - - + -
274V VAL* 5.6 7.8 - - - +
310V MET* 5.9 7.2 - - + -
319V HIS* 3.1 20.3 + - + +
321V PRO* 1.3 75.2 - - - +
323V LEU* 1.3 61.3 + - - +
325V ALA* 3.2 5.9 + - - +
326V TRP* 2.8 33.6 + - + +
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Residues in contact with LEU 323 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310V MET* 5.7 8.5 - - - +
313V PHE* 6.1 1.8 - - + -
314V GLY* 5.2 14.8 - - - +
319V HIS 2.8 13.3 + - - +
320V ALA* 3.3 13.2 - - - +
322V VAL* 1.3 77.7 - - - +
324V LEU* 1.3 62.6 + - - +
326V TRP* 3.9 4.3 - - - +
327V ALA* 3.0 24.1 + - - +
345V ILE* 4.7 15.4 - - + +
349V ALA* 4.5 10.3 - - + -
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Residues in contact with LEU 324 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320V ALA 2.9 13.0 + - - +
321V PRO* 3.8 9.6 - - + +
323V LEU* 1.3 76.8 - - - +
325V ALA* 1.3 64.3 + - - +
327V ALA* 3.1 16.9 + - - +
328V LEU* 3.2 11.6 + - - +
346V GLY* 5.2 3.1 - - - -
349V ALA* 4.0 18.1 - - + +
354V VAL* 5.4 4.7 - - + -
384V LEU* 6.3 2.2 - - + -
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Residues in contact with ALA 325 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274V VAL* 5.4 10.1 - - + -
277V MET* 5.3 10.5 - - + -
279V ILE* 4.5 23.7 - - + +
321V PRO 3.0 17.6 + - - +
322V VAL* 3.7 5.8 - - - +
324V LEU* 1.3 75.8 - - - +
326V TRP* 1.3 63.9 + - - +
328V LEU* 3.1 17.4 + - - +
329V LEU* 3.2 10.6 + - - +
384V LEU* 5.2 14.1 - - + +
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Residues in contact with TRP 326 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277V MET* 6.2 2.2 - - - -
310V MET* 5.1 14.1 - - + -
322V VAL* 2.8 17.6 + - + +
323V LEU* 4.0 4.0 - - - +
325V ALA* 1.3 75.1 - - - +
327V ALA* 1.3 55.4 + - - +
329V LEU* 2.9 11.0 + - + +
330V ARG* 2.7 35.8 + - - +
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Residues in contact with ALA 327 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323V LEU 3.0 15.9 + - - +
324V LEU 3.1 9.2 + - - +
326V TRP* 1.3 74.7 - - - +
328V LEU* 1.3 58.4 + - - +
330V ARG* 3.3 3.8 + - - +
331V HIS* 2.8 29.3 + - - +
342V VAL* 3.8 32.2 - - + +
345V ILE* 4.4 5.2 - - + -
346V GLY* 3.9 18.2 - - - +
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Residues in contact with LEU 328 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279V ILE* 5.9 3.8 - - + -
324V LEU 3.2 6.6 + - - +
325V ALA* 3.1 13.3 + - - +
326V TRP 3.1 0.6 - - - -
327V ALA* 1.3 80.4 - - - +
329V LEU* 1.3 51.7 + - - +
331V HIS* 3.1 7.3 + - - +
332V THR* 2.8 34.4 + - - -
387V PHE* 5.3 14.4 - - + -
388V VAL* 6.4 1.1 - - - -
396V THR* 5.6 14.4 - - - +
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Residues in contact with LEU 329 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279V ILE* 6.2 4.0 - - + -
282V LEU* 5.9 7.9 - - + -
283V HIS* 6.3 2.9 - - - +
325V ALA 3.2 4.6 + - - +
326V TRP* 2.9 18.3 + - + +
328V LEU* 1.3 75.8 - - - +
330V ARG* 1.3 68.2 + - - +
332V THR* 3.1 16.4 + - - -
333V LEU* 3.2 10.7 + - - +
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Residues in contact with ARG 330 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326V TRP 2.7 18.9 + - - +
327V ALA* 3.7 5.4 - - - +
329V LEU* 1.3 73.5 - - - +
331V HIS* 1.3 58.4 + - - +
333V LEU* 2.8 30.6 - - - +
334V ASN* 2.9 6.9 + - - +
338V THR 5.4 0.2 - - - +
339V SER* 4.7 5.2 - - - -
342V VAL* 3.9 18.4 - - + -
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Residues in contact with HIS 331 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327V ALA 2.8 18.4 + - - +
328V LEU* 3.4 8.1 - - - +
330V ARG* 1.3 73.1 - - - +
332V THR* 1.3 58.7 + - - +
333V LEU 3.0 1.8 - - - -
334V ASN* 2.6 38.2 + - + +
335V PRO* 3.7 2.6 - - - +
339V SER* 4.8 4.3 - - - -
342V VAL* 4.7 4.4 - - + +
396V THR* 6.3 3.6 - - - -
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Residues in contact with THR 332 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283V HIS* 5.1 14.8 - - - -
286V ALA* 4.5 23.7 - - - +
328V LEU 2.8 12.8 + - - -
329V LEU* 3.1 11.2 + - - -
331V HIS* 1.3 76.4 - - - +
333V LEU* 1.3 61.1 + - - +
334V ASN 3.4 0.3 + - - -
335V PRO* 3.9 9.9 - - - +
336V GLU* 4.4 4.0 + - - +
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Residues in contact with LEU 333 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286V ALA* 6.3 0.2 - - - -
329V LEU 3.2 6.4 + - - +
330V ARG* 2.8 19.7 + - - +
332V THR* 1.3 80.0 - - - +
334V ASN* 1.3 51.5 + - - -
336V GLU* 2.7 14.4 + - + +
337V GLU* 2.7 35.8 + - + +
338V THR 6.0 0.7 - - - +
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Residues in contact with ASN 334 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330V ARG 2.9 6.1 + - - -
331V HIS* 2.6 29.7 + - + +
333V LEU* 1.3 75.8 - - - +
335V PRO* 1.3 54.1 - - - +
337V GLU 2.5 38.9 + - - +
338V THR* 4.1 3.8 - - - +
339V SER* 3.8 22.0 - - - +
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Residues in contact with PRO 335 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331V HIS 3.7 3.6 - - - +
332V THR 3.9 7.2 - - - +
333V LEU 3.4 0.8 - - - -
334V ASN* 1.3 77.0 - - - +
336V GLU* 1.3 60.9 + - - +
337V GLU 4.2 2.1 - - - +
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Residues in contact with GLU 336 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332V THR 4.4 2.5 + - - +
333V LEU* 2.7 18.6 + - + +
335V PRO* 1.3 80.1 - - - +
337V GLU* 1.3 56.6 + - + +
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Residues in contact with GLU 337 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333V LEU* 2.7 13.7 + - + +
334V ASN 2.5 22.8 + - - +
335V PRO 4.2 2.1 - - - +
336V GLU* 1.3 75.7 - - + +
338V THR* 1.4 67.0 + - - +
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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