Contacts of the helix formed by residues 459 - 473 (chain B) in PDB entry 5DO7
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 ILE 459 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424B ALA* 5.7 0.2 - - + -
427B MET* 4.6 13.7 - - - -
455B ILE 3.7 7.6 - - - +
456B GLY* 4.3 0.9 - - - +
458B LEU* 1.3 72.7 - - - +
460B PRO* 1.3 73.8 - - + +
462B ASN* 2.8 13.5 + - + +
463B VAL* 2.8 17.8 + - + -
507B TYR* 3.6 35.9 - - + +
508B ILE* 5.9 2.0 - - + -
511B TYR* 3.0 58.1 - - + +
535B VAL* 4.5 3.6 - - + -
539B VAL* 3.4 33.9 - - + -
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Residues in contact with PRO 460 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456B GLY 3.1 19.7 - - - +
457B ALA* 4.2 1.1 - - - -
458B LEU 3.3 0.7 - - - -
459B ILE* 1.3 90.2 - - + +
461B PHE* 1.3 55.2 + - - +
462B ASN 2.7 13.0 + - - -
463B VAL* 2.8 14.6 + - + -
464B ILE* 2.8 31.7 + - + +
538B VAL* 6.3 0.7 - - + -
539B VAL* 5.6 4.7 - - + -
542B CYS* 4.3 17.9 - - + -
567B TYR* 3.2 35.9 - - + -
595B PHE* 4.5 1.8 - - + -
596B LEU* 3.9 14.4 - - + -
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Residues in contact with PHE 461 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A TYR* 5.4 6.7 - + - -
532A SER* 4.2 12.3 - - - -
535A ALA* 3.6 33.2 - - + -
536A LEU* 3.7 35.0 - - + -
539A ILE* 4.8 19.3 - - + -
427B MET* 5.1 3.1 - - + -
458B LEU 2.8 17.5 + - - +
460B PRO* 1.3 74.7 - - - +
462B ASN* 1.3 64.2 + - + +
464B ILE* 4.8 5.5 - - - +
465B LEU* 4.5 13.9 + - + +
564B ASN* 4.7 17.2 - - - +
567B TYR* 4.2 20.4 - + + +
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Residues in contact with ASN 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B GLU* 1.9 47.6 + - - +
427B MET* 3.7 26.1 - - + +
458B LEU 4.1 0.6 + - - -
459B ILE 2.8 8.9 + - - +
460B PRO 2.7 4.8 + - - -
461B PHE* 1.3 79.4 - - + +
463B VAL* 1.3 65.5 + - - +
465B LEU* 2.8 20.2 + - - +
466B ASP* 2.8 12.4 + - - +
507B TYR* 2.5 28.8 + - - +
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Residues in contact with VAL 463 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459B ILE* 2.8 11.1 + - + +
460B PRO* 2.8 27.7 + - + +
462B ASN* 1.3 72.6 - - - +
464B ILE* 1.3 71.0 + - + +
466B ASP* 2.9 12.1 + - + +
467B VAL* 2.8 24.8 + - + +
507B TYR* 4.4 10.1 + - + +
539B VAL* 4.5 16.6 - - + +
542B CYS* 4.1 21.3 - - + -
543B ARG* 3.8 49.4 - - + +
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Residues in contact with ILE 464 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460B PRO* 2.8 30.8 + - + +
461B PHE* 4.8 2.0 - - - -
463B VAL* 1.3 78.2 - - + +
465B LEU* 1.3 59.5 + - + +
467B VAL* 3.8 1.2 - - - +
468B ILE* 2.8 41.4 + - + +
542B CYS* 3.3 39.3 - - - +
545B MET* 4.5 16.8 - - + -
546B ALA* 4.6 9.0 - - + -
560B SER* 4.9 3.8 - - - +
563B SER* 3.6 26.9 - - - +
564B ASN* 4.6 23.3 - - - +
567B TYR* 5.3 8.3 - - + -
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Residues in contact with LEU 465 (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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528A ASN* 4.9 4.3 - - - +
531A ASN* 6.3 1.1 - - - +
532A SER* 4.2 25.4 - - - +
461B PHE* 4.5 13.5 - - + +
462B ASN* 2.8 12.0 + - - +
464B ILE* 1.3 75.7 - - + +
466B ASP* 1.3 68.3 + - - +
468B ILE* 4.4 3.8 - - - -
469B SER* 2.8 29.4 + - - -
556B PHE* 4.1 25.1 - - + -
560B SER* 3.7 19.1 - - - +
564B ASN* 5.1 7.6 - - - +
673B TRP* 4.4 17.9 - - + -
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Residues in contact with ASP 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B HIS* 2.3 50.0 + - - -
423B GLU* 4.6 7.4 - - - +
462B ASN* 2.8 8.5 + - - +
463B VAL* 2.9 24.0 + - + +
465B LEU* 1.3 80.0 - - - +
467B VAL* 1.3 55.9 + - - +
469B SER* 3.3 15.6 - - - -
470B LYS* 3.5 17.3 + - - +
503B GLU* 4.1 0.4 - - - +
507B TYR* 3.5 15.9 - - - -
543B ARG* 3.9 13.0 + - - -
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Residues in contact with VAL 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463B VAL* 2.8 20.1 + - + +
466B ASP* 1.3 70.9 - - + +
468B ILE* 1.3 65.3 + - - +
469B SER 3.3 1.1 - - - -
470B LYS* 3.4 9.6 + - + +
471B CYS* 3.2 22.2 + - - +
496B LYS* 5.3 0.2 - - + -
500B GLU* 3.8 27.4 - - - +
543B ARG* 4.1 33.0 - - + +
546B ALA* 3.3 31.2 - - + -
547B LEU* 3.6 24.6 - - + +
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Residues in contact with ILE 468 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464B ILE* 2.8 37.1 + - + +
465B LEU* 4.0 4.3 - - - +
467B VAL* 1.3 73.8 - - - +
469B SER* 1.3 69.6 + - - +
470B LYS 3.1 0.3 + - - -
471B CYS* 4.1 0.3 - - - +
472B TYR* 2.8 33.8 + - + +
546B ALA* 3.4 35.9 - - + +
550B ALA* 3.4 20.4 - - + +
556B PHE* 3.6 35.0 - - + +
559B ALA* 4.4 4.3 - - + -
560B SER* 4.4 9.4 - - - +
563B SER* 4.2 10.1 - - - +
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Residues in contact with SER 469 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465B LEU* 2.8 20.9 + - - -
466B ASP* 3.3 8.5 - - - -
468B ILE* 1.3 77.0 - - - +
470B LYS* 1.3 57.7 + - - +
472B TYR* 3.9 0.9 - - - +
473B SER* 2.9 32.3 + - - -
556B PHE* 3.7 14.8 - - - -
673B TRP* 3.1 37.8 + - - +
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Residues in contact with LYS 470 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410B ASP* 4.0 12.4 + - - +
416B THR* 5.9 2.2 - - - -
420B HIS* 4.2 8.5 - - - -
466B ASP* 3.5 25.7 + - - +
467B VAL* 3.4 11.3 + - + +
468B ILE 3.2 1.0 - - - -
469B SER* 1.3 76.1 - - - +
471B CYS* 1.3 69.1 + - - +
473B SER* 2.8 23.0 + - - -
474B GLU* 2.8 26.0 + - - +
496B LYS* 5.8 1.3 - - - -
500B GLU* 3.8 32.1 - - - +
503B GLU* 2.7 36.6 + - - -
543B ARG* 4.0 5.1 - - - +
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Residues in contact with CYS 471 (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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467B VAL* 3.2 14.6 + - - +
468B ILE 4.1 1.6 - - - +
470B LYS* 1.3 76.0 - - - +
472B TYR* 1.3 59.0 + - - +
474B GLU* 2.9 40.6 + - - +
477B MET* 3.7 22.0 - - - +
496B LYS* 4.4 5.3 - - - +
547B LEU* 4.1 18.2 - - + -
550B ALA* 4.0 22.7 - - + -
551B ALA* 4.4 10.1 - - - -
658B TYR* 4.3 14.4 - - - -
667B GLN* 4.4 6.7 - - - -
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Residues in contact with TYR 472 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468B ILE* 2.8 25.8 + - + +
469B SER 4.2 1.6 - - - +
471B CYS* 1.3 71.1 - - - +
473B SER* 1.3 55.4 + - - +
474B GLU 2.9 16.5 + - - +
475B ARG* 4.4 0.7 + - - +
550B ALA* 3.0 42.4 - - + -
553B LEU* 3.0 10.6 + - - +
554B PRO* 2.8 16.5 - - - +
555B THR* 2.5 32.8 + - - -
556B PHE* 3.2 40.6 - - + -
559B ALA* 3.6 9.4 - - + -
667B GLN* 3.3 20.6 - - - -
668B LYS 5.2 2.0 - - - -
670B SER* 4.6 18.9 + - - +
673B TRP 5.5 3.6 - - - -
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Residues in contact with SER 473 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469B SER* 2.9 16.5 + - - -
470B LYS* 2.8 20.7 + - - -
472B TYR* 1.3 70.0 - - - +
474B GLU* 1.3 61.9 + - - +
475B ARG* 3.9 3.7 + - - +
673B TRP 4.4 17.8 - - - -
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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
------------------------------------------------------------
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