Contacts of the helix formed by residues 378 - 392 (chain W) in PDB entry 5O9G
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 ASP 378 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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377W ARG* 1.3 79.2 - - - +
379W PHE* 1.3 75.0 + - - +
380W GLN 3.2 1.8 - - - -
381W LEU* 3.4 7.0 + - - +
382W THR* 2.7 37.2 + - - +
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Residues in contact with PHE 379 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377W ARG* 4.0 17.9 - - + -
378W ASP* 1.3 92.2 + - - +
380W GLN* 1.3 95.0 + - + +
382W THR* 3.7 7.6 - - - -
383W GLY 2.9 10.6 + - - -
405W LEU* 3.7 37.0 - - + -
597W ARG* 2.4 53.8 + - - +
601W ASP* 5.8 0.7 - - + -
602W VAL* 3.7 29.8 - - + -
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Residues in contact with GLN 380 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376W LEU* 3.7 29.6 - - + -
377W ARG* 3.0 60.6 + - - +
378W ASP 3.2 0.2 - - - -
379W PHE* 1.3 99.7 - - - +
381W LEU* 1.3 60.7 + - - +
383W GLY* 3.1 2.6 + - - -
384W ILE* 2.9 34.2 + - - +
405W LEU 4.0 10.9 + - - +
406W GLY* 5.1 2.0 - - - +
409W VAL* 6.3 1.3 - - + -
410W GLN* 3.3 27.7 - - + +
1501W ADP 4.5 6.6 + - - +
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Residues in contact with LEU 381 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365W SER 3.5 24.7 - - - +
366W VAL* 3.5 24.0 - - - +
367W GLN* 3.9 22.4 - - + +
368W PRO* 4.7 6.1 - - + -
376W LEU* 4.2 23.6 - - + +
377W ARG 4.0 18.2 - - - +
378W ASP* 3.4 7.9 + - - +
380W GLN* 1.3 76.1 - - - +
382W THR* 1.3 58.0 + - - +
384W ILE* 3.8 15.7 - - + +
385W ASN* 2.9 41.5 + - - +
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Residues in contact with THR 382 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378W ASP* 2.7 25.7 + - - +
379W PHE* 3.6 10.4 - - - -
381W LEU* 1.3 77.7 - - - +
383W GLY* 1.3 57.1 + - - +
385W ASN* 3.3 10.5 + - + +
386W TRP* 2.9 28.2 + - + +
597W ARG* 4.3 8.5 - - - +
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Residues in contact with GLY 383 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379W PHE 2.9 16.5 + - - -
380W GLN 3.1 3.1 + - - -
382W THR* 1.3 72.6 - - - +
384W ILE* 1.3 60.7 + - - +
386W TRP* 3.2 8.1 + - - +
387W MET* 2.9 38.3 + - - +
399W LEU* 6.2 0.2 - - - -
410W GLN* 4.6 7.6 - - - -
595W LEU* 4.8 6.7 - - - -
597W ARG* 3.6 15.4 - - - +
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Residues in contact with ILE 384 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368W PRO* 6.0 4.7 - - + -
376W LEU* 4.5 9.0 - - + -
380W GLN 2.9 21.2 + - - +
381W LEU* 3.8 24.0 - - + +
383W GLY* 1.3 75.8 - - - +
385W ASN* 1.3 63.6 + - - +
387W MET* 3.4 6.8 + - - +
388W ALA* 2.9 32.0 + - + +
410W GLN* 4.3 22.2 - - + +
413W ALA* 3.7 31.0 - - + +
414W PHE* 4.2 18.8 - - + -
417W TRP* 5.3 12.8 - - + -
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Residues in contact with ASN 385 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361W PHE* 4.1 6.6 - - - -
363W LYS* 4.9 11.3 - - + +
364W LEU* 2.6 51.4 + - - +
365W SER* 4.5 3.2 - - - +
366W VAL 5.8 0.2 + - - -
381W LEU* 2.9 29.7 + - - +
382W THR* 3.7 9.1 - - + +
384W ILE* 1.3 80.7 - - - +
386W TRP* 1.3 49.3 + - - +
388W ALA* 3.9 3.8 - - - +
389W PHE* 2.6 37.2 + - - +
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Residues in contact with TRP 386 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382W THR* 2.9 14.8 + - + +
383W GLY* 3.2 11.1 + - - +
385W ASN* 1.3 76.1 - - - +
387W MET* 1.3 79.0 + - + +
389W PHE* 3.5 11.9 - + - +
390W LEU* 2.9 45.4 + - + +
397W GLY* 3.6 30.1 - - - -
398W ILE 4.0 11.7 - - - -
399W LEU* 5.3 0.9 - - + -
538W MET* 4.5 9.9 - - + -
592W PRO 4.4 10.3 + - - -
593W PHE 4.3 1.6 - - - -
594W ILE 4.1 19.9 + - - -
595W LEU* 3.5 50.5 - - + +
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Residues in contact with MET 387 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383W GLY 2.9 22.6 + - - +
384W ILE* 4.0 1.3 - - - +
386W TRP* 1.3 92.9 - - + +
388W ALA* 1.3 57.5 + - - +
390W LEU* 3.6 2.1 + - - +
391W TRP* 2.9 29.5 + - - +
399W LEU* 3.9 25.1 - - + -
410W GLN* 4.7 11.2 - - - +
411W THR* 5.2 9.0 - - + +
414W PHE* 3.5 49.3 - - + -
509W PHE* 4.8 2.9 - - + -
538W MET* 3.7 43.5 - - + +
540W ILE* 5.8 0.2 - - + -
595W LEU* 5.5 0.7 - - + -
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Residues in contact with ALA 388 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361W PHE* 3.3 24.2 - - + -
384W ILE* 2.9 18.6 + - + +
385W ASN* 4.7 1.1 - - - +
387W MET* 1.3 74.7 - - - +
389W PHE* 1.3 63.9 + - - +
391W TRP* 3.8 8.4 - - + +
392W SER* 3.2 26.2 + - - -
414W PHE* 3.3 12.9 - - + -
417W TRP* 3.7 24.7 - - + -
418W LEU* 6.4 0.2 - - + -
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Residues in contact with PHE 389 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361W PHE* 3.6 26.6 - + + -
363W LYS* 3.8 27.8 - - + -
385W ASN 2.6 25.1 + - - +
386W TRP* 3.2 16.1 + + - +
388W ALA* 1.3 80.4 - - - +
390W LEU* 1.3 65.3 + - + +
392W SER* 3.9 8.3 + - - -
393W LYS* 3.2 52.3 + - + +
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Residues in contact with LEU 390 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386W TRP* 2.9 37.0 + - + +
387W MET* 4.3 2.9 - - - +
389W PHE* 1.3 79.5 - - + +
391W TRP* 1.3 65.2 + - - +
392W SER 3.2 0.9 - - - -
393W LYS* 3.3 21.0 + - + +
395W ASP* 3.4 42.0 + - + +
396W ASN* 3.6 31.6 - - - +
397W GLY* 3.6 11.4 - - - +
538W MET* 6.0 1.1 - - + -
592W PRO 5.0 5.4 - - - +
593W PHE* 4.5 17.5 - - + -
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Residues in contact with TRP 391 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354W TYR* 5.3 7.2 - + + -
358W ARG* 2.4 46.1 + - - -
359W PRO* 5.2 8.3 - - + -
361W PHE* 6.0 0.4 - + - -
387W MET 2.9 19.7 + - - +
388W ALA* 4.0 11.0 - - + +
389W PHE 3.4 0.4 - - - -
390W LEU* 1.3 78.6 - - - +
392W SER* 1.3 66.0 + - - +
393W LYS 3.3 0.3 + - - -
394W GLY* 3.4 4.0 + - - -
395W ASP 4.3 7.2 + - - -
414W PHE* 4.2 11.9 - + + -
417W TRP* 6.1 1.3 - + - -
418W LEU* 3.6 40.4 - - + +
422W ARG* 3.8 32.5 - - + -
424W GLN* 4.3 21.1 - - + -
509W PHE* 5.4 4.4 - + - -
536W ASN* 3.0 37.6 + - + +
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Residues in contact with SER 392 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358W ARG* 3.3 33.2 - - - +
359W PRO* 5.0 8.0 + - - +
361W PHE* 3.3 33.4 - - - +
388W ALA 3.2 16.8 + - - -
389W PHE 4.2 6.3 - - - -
390W LEU 3.2 1.0 - - - -
391W TRP* 1.3 90.7 - - - +
393W LYS* 1.3 59.6 + - - +
394W GLY 3.4 0.4 - - - -
422W ARG* 5.1 1.7 + - - -
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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