Contacts of the helix formed by residues 353 - 366 (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 ASN 353 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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350V ILE 2.9 12.7 + - - -
351V GLN 2.9 5.2 - - - +
352V LEU* 1.3 83.7 - - - +
354V VAL* 1.3 55.2 + - - +
355V PHE* 3.1 4.5 - - - +
356V GLN* 3.2 16.7 + - + +
357V TYR* 2.8 32.8 + - - +
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Residues in contact with VAL 354 (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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320V ALA* 4.0 27.8 - - + +
321V PRO* 4.8 7.7 - - + +
324V LEU* 5.4 4.7 - - + -
349V ALA* 3.3 22.6 + - + +
350V ILE* 4.1 3.4 + - - +
352V LEU 3.3 0.8 - - - -
353V ASN* 1.3 76.3 - - - +
355V PHE* 1.3 54.6 + - - +
357V TYR* 3.0 7.9 + - - +
358V LEU* 2.8 36.0 + - - +
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Residues in contact with PHE 355 (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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350V ILE* 5.3 1.6 + - - +
353V ASN* 3.1 2.2 - - - +
354V VAL* 1.3 80.2 - - - +
356V GLN* 1.3 61.2 + - - +
358V LEU* 3.2 6.4 + - - +
359V THR* 3.1 17.7 + - - -
402V ASP* 4.4 23.3 - - + +
403V ILE* 5.6 1.1 - - - -
406V THR* 3.8 27.4 - - - -
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Residues in contact with GLN 356 (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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353V ASN* 3.2 19.8 + - + +
355V PHE* 1.3 75.3 - - - +
357V TYR* 1.3 67.7 + - - +
359V THR* 3.1 15.3 + - - +
360V ARG* 3.2 12.3 + - - +
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Residues in contact with TYR 357 (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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317V PRO 5.7 2.5 - - - +
318V HIS 6.0 1.6 - - - +
320V ALA* 5.6 5.8 - - + -
352V LEU 5.8 0.2 - - - +
353V ASN 2.8 17.9 + - - +
354V VAL* 3.0 9.4 + - - +
356V GLN* 1.3 76.6 - - - +
358V LEU* 1.3 62.0 + - - +
360V ARG* 3.1 9.3 + - - +
361V LEU* 2.9 22.8 + - - +
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Residues in contact with LEU 358 (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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321V PRO* 6.1 5.6 - - + -
354V VAL 2.8 13.1 + - - +
355V PHE* 3.4 12.6 - - - +
357V TYR* 1.3 75.4 - - - +
359V THR* 1.4 58.0 + - - +
361V LEU* 3.2 8.4 + - - +
362V LEU* 2.8 31.4 + - - +
381V VAL* 5.4 11.7 - - + -
406V THR* 5.1 8.1 - - - +
410V VAL* 6.4 2.2 - - + -
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Residues in contact with THR 359 (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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355V PHE 3.1 9.5 + - - -
356V GLN* 3.1 10.7 + - - -
358V LEU* 1.4 80.0 - - - +
360V ARG* 1.3 56.6 + - - +
362V LEU* 3.1 10.1 + - - +
363V GLN* 2.8 26.3 + - - +
406V THR* 5.2 7.8 - - - -
409V GLU* 4.0 25.6 - - - +
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Residues in contact with ARG 360 (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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263V ASP* 5.8 3.0 - - + +
356V GLN 3.2 8.0 + - - +
357V TYR* 3.1 10.6 + - - +
359V THR* 1.3 76.2 - - - +
361V LEU* 1.3 65.8 + - - +
363V GLN* 3.0 9.5 + - - +
364V SER* 2.9 21.3 + - - -
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Residues in contact with LEU 361 (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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263V ASP* 5.8 3.8 - - - -
267V TYR* 4.4 24.4 - - + +
270V ALA* 6.3 2.5 - - + -
357V TYR 2.9 12.4 + - - +
358V LEU* 3.2 11.4 + - - +
360V ARG* 1.3 75.5 - - - +
362V LEU* 1.3 57.7 + - - +
364V SER* 3.1 9.1 + - - -
365V LEU* 2.9 28.3 + - - +
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Residues in contact with LEU 362 (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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358V LEU 2.8 17.2 + - - +
359V THR* 3.1 11.7 - - - +
361V LEU* 1.3 73.9 - - - +
363V GLN* 1.3 52.6 + - - +
365V LEU* 3.4 5.3 + - - +
366V ALA* 2.6 34.3 + - - +
378V CYS* 5.9 7.2 - - + -
409V GLU* 4.5 4.7 - - + +
410V VAL* 3.9 32.3 - - + +
413V ASP* 4.3 6.1 - - + +
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Residues in contact with GLN 363 (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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359V THR 2.8 12.5 + - - +
360V ARG* 3.0 11.6 + - - +
362V LEU* 1.3 71.9 - - - +
364V SER* 1.4 61.4 + - - +
366V ALA* 2.7 37.4 + - + +
413V ASP* 5.4 0.2 - - - +
414V PRO* 5.3 5.2 - - + -
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Residues in contact with SER 364 (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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263V ASP* 4.7 19.1 - - - -
264V ARG* 4.9 15.3 - - - -
267V TYR* 5.1 3.6 - - - -
360V ARG 2.9 12.6 + - - -
361V LEU* 3.1 12.5 + - - -
363V GLN* 1.4 76.2 - - - +
365V LEU* 1.3 63.3 + - - +
366V ALA 3.1 5.9 - - - +
368V GLY* 4.7 0.3 - - - -
369V GLY* 3.3 18.5 + - - -
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Residues in contact with LEU 365 (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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267V TYR* 5.7 6.0 - - + +
361V LEU 2.9 14.6 + - - +
362V LEU* 4.0 5.6 - - - +
364V SER* 1.3 72.6 - - - +
366V ALA* 1.3 68.5 + - - +
367V SER 3.5 0.3 + - - -
369V GLY* 5.0 2.7 - - - +
370V ASN 3.8 7.8 + - - +
374V THR* 2.7 47.9 - - - +
377V ALA* 5.1 6.7 - - + -
378V CYS* 5.6 5.4 - - + +
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Residues in contact with ALA 366 (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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362V LEU 2.6 18.1 + - - +
363V GLN* 2.7 22.9 + - + +
364V SER 3.1 7.8 - - - +
365V LEU* 1.3 79.1 - - - +
367V SER* 1.4 54.6 + - - +
368V GLY* 2.7 18.0 + - - -
374V THR* 4.9 0.9 - - - -
413V ASP* 3.2 40.6 - - - +
414V PRO* 3.4 11.0 - - + +
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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