Contacts of the helix formed by residues 367 - 378 (chain V) in PDB entry 5IY6
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 SER 367 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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365V GLY* 3.6 2.5 + - - -
366V ASN* 1.3 93.8 + - - +
368V ALA* 1.3 59.2 + - - +
369V VAL* 3.3 14.7 + - - +
370V SER* 3.5 5.5 + - - -
371V VAL* 3.3 27.4 + - - +
409V THR* 4.7 5.6 - - - +
613V THR* 5.7 0.2 - - - -
614V SER* 3.5 26.1 + - - -
40Y T 4.8 6.3 - - - -
41Y T 5.7 2.5 - - - -
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Residues in contact with ALA 368 (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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367V SER* 1.3 67.7 + - - +
369V VAL* 1.3 65.2 + - - +
370V SER 3.3 0.2 - - - -
371V VAL* 2.9 31.5 + - + +
372V GLU* 2.9 9.8 + - - +
391V ARG* 4.1 25.4 - - - +
393V THR* 6.4 1.3 - - + -
409V THR* 5.4 1.6 + - - -
41Y T 5.3 8.6 + - - +
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Residues in contact with VAL 369 (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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367V SER* 3.3 10.6 + - - +
368V ALA* 1.3 76.2 - - + +
370V SER* 1.4 57.2 + - - +
372V GLU* 3.2 10.5 + - + +
373V GLN* 2.9 44.1 + - + +
614V SER* 4.3 20.4 - - - +
615V PHE* 5.5 0.9 - - - +
616V ASP* 6.0 1.8 - - - +
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Residues in contact with SER 370 (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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365V GLY* 6.0 2.0 - - - -
366V ASN* 3.6 12.5 + - - -
367V SER 3.5 11.8 + - - -
368V ALA 3.3 0.2 - - - -
369V VAL* 1.4 71.8 - - - +
371V VAL* 1.3 56.8 + - - +
373V GLN* 3.3 14.3 + - - +
374V TRP* 2.7 43.9 + - - -
407V ILE* 5.5 0.4 - - - -
441V ASP* 4.4 16.7 + - - -
442V GLU* 4.8 4.0 + - - -
614V SER* 2.1 32.1 + - - -
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Residues in contact with VAL 371 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365V GLY* 5.8 3.1 - - - -
367V SER 3.3 14.8 + - - +
368V ALA* 2.9 25.5 + - - +
370V SER* 1.3 76.9 - - - +
372V GLU* 1.3 55.4 + - - +
374V TRP* 3.1 2.9 + - - +
375V LYS 2.9 24.9 + - - -
391V ARG* 3.7 30.5 - - + +
403V CYS* 3.2 27.3 - - + -
407V ILE* 3.5 40.2 - - + -
408V SER* 5.7 2.0 - - - +
409V THR* 5.6 5.4 - - - +
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Residues in contact with GLU 372 (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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368V ALA 2.9 10.8 + - - +
369V VAL* 3.2 13.2 + - + +
371V VAL* 1.3 77.6 - - - +
373V GLN* 1.3 59.8 + - - +
375V LYS* 2.7 44.3 + - - +
376V ALA* 3.2 21.8 + - - +
391V ARG* 2.9 34.6 + - - +
403V CYS* 4.7 2.8 - - - -
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Residues in contact with GLN 373 (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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347V SER* 4.9 7.3 + - - -
369V VAL* 2.9 30.7 + - + +
370V SER* 3.6 23.5 + - - +
372V GLU* 1.3 70.1 - - - +
374V TRP* 1.3 66.7 + - + +
376V ALA* 3.4 9.1 + - - +
377V GLN* 3.1 20.8 + - - +
614V SER* 4.6 3.6 + - - -
615V PHE 5.6 4.4 - - - +
616V ASP* 5.2 14.3 + - - +
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Residues in contact with TRP 374 (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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346V LYS 5.1 1.6 - - - -
347V SER* 4.3 26.6 - - - +
350V GLY* 4.0 29.2 - - - -
351V VAL* 4.4 9.6 - - + +
363V VAL* 3.4 30.7 - - + -
370V SER* 2.7 40.3 + - - -
371V VAL* 3.3 10.1 - - - +
373V GLN* 1.3 73.4 - - + +
375V LYS* 1.3 54.6 + - - +
377V GLN* 2.8 13.3 + - - +
378V PHE* 2.8 36.8 + - - +
403V CYS* 4.1 11.7 - - + -
404V SER* 3.8 24.7 - - - +
407V ILE* 4.6 6.9 - - + +
439V ILE* 4.2 11.9 - - + -
441V ASP* 3.5 44.9 + - + -
466V LEU* 4.9 2.9 - - + -
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Residues in contact with LYS 375 (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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371V VAL 2.9 11.9 + - - +
372V GLU* 2.7 42.2 + - - +
374V TRP* 1.3 77.0 - - - +
376V ALA* 1.3 60.3 + - - +
378V PHE* 3.4 8.0 + - + +
379V LYS* 3.4 20.6 + - - +
386V ASP* 5.9 1.3 - - - +
389V ILE* 4.1 33.5 - - + +
402V GLY 4.6 7.6 - - - +
403V CYS* 3.7 21.6 - - - +
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Residues in contact with ALA 376 (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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372V GLU 3.2 9.7 + - - +
373V GLN* 3.5 13.2 - - - +
374V TRP 3.2 0.4 - - - -
375V LYS* 1.3 77.9 - - - +
377V GLN* 1.3 64.6 + - - +
378V PHE 3.5 0.5 + - - -
379V LYS* 3.6 16.7 + - - +
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Residues in contact with GLN 377 (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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345V GLY* 5.4 3.4 - - - -
347V SER* 3.1 28.9 + - - +
348V LEU* 3.6 45.8 - - + +
351V VAL* 4.0 11.0 - - + -
373V GLN 3.1 11.7 + - - +
374V TRP* 2.8 15.9 + - - +
376V ALA* 1.3 73.7 - - - +
378V PHE* 1.3 59.7 + - - +
379V LYS* 3.3 1.7 + - - +
380V MET* 4.4 2.8 + - - +
381V TRP* 3.4 16.8 - - - -
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Residues in contact with PHE 378 (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 LEU* 4.1 25.8 - - + -
351V VAL* 3.5 29.4 - - + -
354V ALA* 6.3 0.4 - - + -
355V CYS* 4.5 5.6 - - - -
374V TRP 2.8 18.8 + - - +
375V LYS* 3.4 6.7 + - + +
376V ALA 3.4 0.4 - - - -
377V GLN* 1.3 71.7 - - - +
379V LYS* 1.4 57.0 + - - +
380V MET 3.3 2.0 - - - -
381V TRP* 2.9 46.6 + + + -
382V SER* 3.0 26.8 + - - -
389V ILE* 4.4 7.9 - - + -
401V ILE* 4.6 7.9 - - + -
402V GLY 3.4 18.4 - - - -
404V SER* 3.3 42.0 - - - +
405V VAL* 5.6 0.2 - - + -
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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