Contacts of the helix formed by residues 548 - 569 (chain B) in PDB entry 3II5
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 GLU 548 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546B LYS 4.2 1.1 + - - +
547B PHE* 1.3 76.5 - - - +
549B MET* 1.3 66.7 + - - +
550B ILE* 3.7 24.7 - - + +
551B LYS* 2.8 17.4 + - + +
552B LEU* 3.0 12.9 + - - +
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Residues in contact with MET 549 (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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547B PHE 4.0 0.8 + - - -
548B GLU* 1.3 72.5 - - - +
550B ILE* 1.3 58.2 + - - +
552B LEU* 3.1 22.3 + - + +
553B ILE* 2.8 54.3 + - + +
649B MET* 3.9 27.1 - - - +
681B ARG* 3.8 9.8 - - + +
683B ASN* 3.4 63.4 - - + +
684B CYS* 4.2 9.4 - - + +
685B PRO* 4.1 3.4 - - + -
720B LEU* 5.2 7.0 - - + -
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Residues in contact with ILE 550 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548B GLU* 3.7 26.0 - - + +
549B MET* 1.3 78.5 - - - +
551B LYS* 1.3 64.0 + - + +
553B ILE* 3.8 3.6 + - - +
554B ASP* 3.1 25.3 + - - +
720B LEU* 4.1 27.9 - - + +
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Residues in contact with LYS 551 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547B PHE* 3.6 29.6 - - + -
548B GLU* 2.8 21.5 + - + +
550B ILE* 1.3 81.4 - - + +
552B LEU* 1.3 59.4 + - - +
554B ASP* 3.0 18.5 + - + +
555B ILE* 2.8 38.6 + - + +
583B LEU* 5.8 0.7 - - - -
586B ASP 3.2 27.6 + - - -
587B LEU* 3.8 26.5 + - - +
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Residues in contact with LEU 552 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540B LEU* 4.9 3.8 - - + -
547B PHE* 3.5 35.9 - - + +
548B GLU 3.0 16.1 + - - +
549B MET* 3.5 25.6 - - + +
551B LYS* 1.3 74.6 - - - +
553B ILE* 1.3 59.2 + - - +
555B ILE* 3.0 10.8 + - + +
556B ALA* 2.8 28.6 + - - +
648B LEU* 3.7 37.4 - - + +
649B MET* 3.6 17.3 - - + -
681B ARG* 3.2 30.1 - - - +
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Residues in contact with ILE 553 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549B MET* 2.8 35.0 + - + +
550B ILE* 3.8 5.4 - - + +
552B LEU* 1.3 73.4 - - - +
554B ASP* 1.3 58.4 + - - +
556B ALA* 3.4 9.6 - - - +
557B ARG* 3.0 25.3 + - - +
649B MET* 4.9 1.5 - - + +
685B PRO* 3.9 17.7 - - + -
688B MET* 4.4 13.9 - - + -
713B ILE* 4.3 7.0 - - + +
716B LEU* 3.7 30.3 - - + -
717B ALA* 4.3 21.5 - - + -
720B LEU* 3.7 27.4 - - + -
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Residues in contact with ASP 554 (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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550B ILE 3.1 14.7 + - - +
551B LYS* 3.0 25.4 + - + +
553B ILE* 1.3 75.4 - - - +
555B ILE* 1.3 61.6 + - - +
557B ARG* 2.6 48.2 + - - +
558B GLN* 2.8 50.6 + - - +
587B LEU 4.4 3.8 - - - +
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Residues in contact with ILE 555 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536B LEU* 4.3 28.3 - - + -
547B PHE* 4.4 17.0 - - + -
551B LYS* 2.8 44.3 + - + +
552B LEU* 3.4 11.0 - - - +
554B ASP* 1.3 75.7 - - - +
556B ALA* 1.3 60.2 + - - +
558B GLN* 3.5 3.6 + - - +
559B THR* 2.9 32.4 + - - +
581B ILE* 5.2 1.1 - - + -
583B LEU* 4.1 34.1 - - + -
587B LEU 5.4 0.7 - - - +
589B VAL* 4.0 18.4 - - + -
644B VAL* 6.2 0.2 - - + -
648B LEU* 4.3 10.8 - - + -
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Residues in contact with ALA 556 (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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552B LEU 2.8 12.3 + - - +
553B ILE* 3.4 13.7 - - - +
555B ILE* 1.3 76.7 - - - +
557B ARG* 1.3 57.1 + - - +
559B THR* 3.1 7.4 + - - -
560B ALA* 2.9 28.2 + - - +
641B PHE* 3.7 6.9 - - - -
645B LEU* 3.9 26.5 - - + -
648B LEU* 4.0 11.4 - - + +
649B MET* 6.0 0.2 - - + -
688B MET* 4.3 11.0 - - + -
713B ILE* 4.4 5.8 - - + -
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Residues in contact with ARG 557 (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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474A LYS* 6.1 1.9 - - - +
553B ILE* 3.0 14.4 + - + +
554B ASP* 2.6 45.8 + - - +
556B ALA* 1.3 74.4 - - - +
558B GLN* 1.3 71.6 + - - +
560B ALA* 3.2 6.3 + - - +
561B GLN* 3.0 54.7 + - - +
710B LEU* 4.2 11.9 - - + -
713B ILE* 4.0 21.0 - - + +
714B GLU* 4.4 16.2 - - + +
717B ALA* 4.8 18.4 - - - +
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Residues in contact with GLN 558 (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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511B ASN* 3.3 28.3 + - - +
554B ASP* 2.8 49.1 + - - +
555B ILE* 3.9 1.2 - - - +
557B ARG* 1.3 87.3 - - - +
559B THR* 1.3 60.4 + - - +
561B GLN* 3.3 12.8 + - - +
562B GLY 3.3 16.6 + - - -
587B LEU 3.4 16.2 + - - -
588B THR* 3.4 8.6 - - - +
589B VAL* 2.7 48.9 + - + +
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Residues in contact with THR 559 (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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555B ILE* 2.9 17.1 + - - +
556B ALA* 3.1 9.0 + - - -
558B GLN* 1.3 74.7 - - - +
560B ALA* 1.3 65.4 + - - +
562B GLY 3.4 0.7 + - - -
563B MET* 3.0 27.1 + - + +
576B LEU* 4.8 5.2 - - + -
581B ILE* 3.8 30.9 - - + +
589B VAL* 3.7 17.5 - - - +
591B ILE* 3.8 17.0 - - + +
641B PHE* 3.7 23.8 - - + -
644B VAL* 5.4 2.3 - - + +
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Residues in contact with ALA 560 (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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556B ALA 2.9 13.6 + - - +
557B ARG 3.2 9.6 + - - +
559B THR* 1.3 75.5 - - - +
561B GLN* 1.3 58.0 + - - +
564B ASP* 3.0 32.2 + - - +
641B PHE* 3.9 13.4 - - + -
706B PHE* 3.9 19.0 - - + -
709B ILE* 4.6 1.1 - - + -
710B LEU* 3.7 23.6 - - + +
713B ILE* 4.2 11.7 - - + -
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Residues in contact with GLN 561 (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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474A LYS* 5.4 2.4 + - - -
476A HIS* 3.5 20.7 + - - +
477A GLY* 3.6 22.4 - - - -
478A ASP* 4.7 2.9 + - - +
509B HIS* 3.9 5.5 + - - -
510B VAL* 5.9 1.8 - - - +
511B ASN* 2.7 34.4 + - - +
557B ARG* 3.0 43.3 + - - +
558B GLN* 3.5 13.2 - - - +
559B THR 3.1 0.2 - - - -
560B ALA* 1.3 75.5 - - - +
562B GLY* 1.3 66.3 + - - +
564B ASP* 3.7 1.7 - - - +
565B TYR* 3.0 23.7 + - - +
710B LEU* 3.7 18.6 - - + +
714B GLU* 5.1 2.3 - - - +
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Residues in contact with GLY 562 (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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509B HIS* 4.3 0.2 - - - -
511B ASN* 4.0 7.7 - - - +
512B ILE* 3.6 24.2 - - - +
558B GLN 3.3 8.1 + - - -
559B THR 3.4 0.4 + - - -
561B GLN* 1.3 78.9 - - - +
563B MET* 1.3 55.3 + - - +
565B TYR* 3.1 4.0 + - - +
566B LEU* 2.9 32.6 + - - +
591B ILE* 3.8 17.0 - - - -
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Residues in contact with MET 563 (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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559B THR* 3.0 22.4 + - + +
562B GLY* 1.3 72.9 - - - +
564B ASP* 1.3 68.2 + - - +
566B LEU* 3.3 13.8 + - + +
567B HIS* 3.0 44.3 + - + +
573B HIS* 4.2 11.0 - - + -
576B LEU* 4.0 30.3 - - + -
591B ILE* 4.0 15.5 - - + -
637B ASP* 3.5 35.4 - - + +
706B PHE* 3.3 35.2 - - + -
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Residues in contact with ASP 564 (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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476A HIS* 2.8 25.7 + - - +
560B ALA 3.0 21.4 + - - +
561B GLN 3.7 4.3 - - - +
563B MET* 1.3 75.5 - - - +
565B TYR* 1.3 56.6 + - - +
567B HIS* 3.6 3.5 + - - +
568B ALA* 3.1 26.9 + - - +
706B PHE* 3.7 14.2 - - + -
707B PRO* 3.1 42.2 - - - +
710B LEU* 3.7 20.7 - - + +
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Residues in contact with TYR 565 (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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449A TRP* 3.9 5.2 - - - -
475A TRP* 3.9 24.5 - + - -
476A HIS* 4.0 22.9 + + + -
516A MET 5.0 1.4 + - - -
506B LYS 3.5 8.7 + - - -
507B THR* 4.0 16.2 - - + -
508B ARG* 2.8 37.3 + - - -
509B HIS* 3.4 40.2 - + + -
512B ILE* 3.9 8.7 - - + -
561B GLN 3.0 15.2 + - - +
562B GLY 3.3 8.1 - - - +
563B MET 3.1 0.2 - - - -
564B ASP* 1.3 74.1 - - - +
566B LEU* 1.3 72.8 + - + +
568B ALA* 3.1 13.4 + - + +
569B LYS* 3.2 35.0 + - + +
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Residues in contact with LEU 566 (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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1B 831 3.9 28.7 - - - -
507B THR* 4.2 20.6 - - + -
512B ILE* 3.9 22.4 - - + -
562B GLY 2.9 16.3 + - - +
563B MET* 3.7 23.1 - - + +
565B TYR* 1.3 79.1 - - + +
567B HIS* 1.3 63.8 + - + +
569B LYS* 3.0 12.5 + - - -
571B ILE* 2.9 47.1 + - + +
573B HIS* 4.1 21.1 - - + -
591B ILE* 4.8 6.1 - - + -
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Residues in contact with HIS 567 (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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563B MET* 3.0 25.9 + - + +
564B ASP* 3.9 6.7 - - - +
566B LEU* 1.3 76.6 - - + +
568B ALA* 1.3 58.8 + - - +
570B SER* 2.8 20.1 + - - -
571B ILE 3.2 20.9 - - - -
572B ILE* 4.6 0.2 - - - -
634B PHE* 3.4 72.8 - + + +
637B ASP* 3.1 26.7 + - + +
638B VAL* 4.8 0.4 - - + +
705B LEU* 5.6 0.4 - - - +
706B PHE* 3.6 29.6 + + + +
707B PRO* 6.1 2.0 - - + +
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Residues in contact with ALA 568 (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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455A GLN* 5.8 2.0 - - - +
475A TRP* 6.1 0.4 - - + -
476A HIS* 3.5 27.4 - - + +
564B ASP* 3.1 14.8 + - - +
565B TYR* 3.1 10.5 + - + +
567B HIS* 1.3 78.1 - - - +
569B LYS* 1.3 61.5 + - + +
570B SER* 3.1 4.9 + - - -
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Residues in contact with LYS 569 (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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448A ASP 3.6 22.0 + - - -
449A TRP* 3.7 22.8 - - - +
450A GLU 5.6 1.8 + - - -
475A TRP* 4.9 11.2 - - - -
516A MET 5.4 1.0 + - - -
506B LYS* 3.6 23.5 + - + +
565B TYR* 3.2 46.4 + - + +
566B LEU 3.0 9.2 + - - +
568B ALA* 1.3 77.6 - - + +
570B SER* 1.3 70.2 + - - +
571B ILE* 3.2 19.6 + - + +
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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