Contacts of the helix formed by residues 557 - 581 (chain B) in PDB entry 3V4R
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 THR 557 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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522B ALA 4.5 2.4 + - - -
523B ASP* 3.5 40.4 - - + +
525B GLU* 4.2 16.2 + - + +
529B ARG 5.1 0.3 + - - -
555B LYS* 4.5 4.7 - - + +
556B ILE* 1.3 75.2 - - - +
558B LYS* 1.3 64.8 + - - +
559B SER* 3.7 8.1 - - - -
560B MET* 3.1 30.3 + - - +
561B GLU* 2.9 23.3 + - - +
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Residues in contact with LYS 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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557B THR* 1.3 72.5 - - - +
559B SER* 1.4 63.6 + - - +
561B GLU* 3.2 10.2 + - + +
562B ILE* 3.1 51.4 + - + +
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Residues in contact with SER 559 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525B GLU* 3.3 17.4 + - - -
529B ARG 3.5 22.9 + - - -
530B SER* 4.0 3.1 - - - -
531B GLU* 3.6 30.5 + - - +
534B LEU* 4.1 2.9 - - - -
557B THR* 3.7 8.2 + - - -
558B LYS* 1.4 77.9 - - - +
560B MET* 1.4 61.1 + - - -
562B ILE* 3.5 4.7 + - - +
563B ALA* 3.3 22.7 + - - +
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Residues in contact with MET 560 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424B VAL* 3.9 13.5 - - + -
522B ALA* 3.8 28.7 - - + +
523B ASP* 4.0 2.5 - - - -
534B LEU* 3.9 15.9 - - + +
551B MET* 3.9 20.9 - - - -
553B ALA* 3.8 16.8 - - + -
555B LYS 3.7 7.4 - - - +
556B ILE* 3.7 31.4 - - + -
557B THR* 3.1 36.0 + - - +
559B SER* 1.4 71.9 - - - +
561B GLU* 1.4 55.7 + - - +
563B ALA* 3.4 2.6 + - - +
564B ILE* 2.9 45.0 + - + +
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Residues in contact with GLU 561 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556B ILE* 4.2 13.6 - - + +
557B THR 2.9 12.5 + - - +
558B LYS* 3.5 17.9 - - + +
560B MET* 1.4 75.1 - - - +
562B ILE* 1.3 52.8 + - + +
564B ILE* 3.4 5.8 + - - +
565B ASN* 2.8 49.7 + - - +
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Residues in contact with ILE 562 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531B GLU* 4.1 24.2 - - + -
535B ILE* 4.8 8.7 - - + -
558B LYS* 3.1 46.8 + - + +
559B SER* 3.7 4.3 - - - +
561B GLU* 1.3 74.9 - - + +
563B ALA* 1.3 53.0 + - - +
565B ASN* 3.3 7.2 + - - +
566B GLU* 2.8 36.0 + - + +
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Residues in contact with ALA 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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531B GLU 4.2 1.8 - - - +
534B LEU* 3.9 23.8 - - + -
535B ILE* 3.8 27.5 - - + +
538B ILE* 4.0 10.5 - - + -
551B MET* 4.8 2.0 - - + -
559B SER 3.3 11.8 + - - +
560B MET* 3.4 8.0 + - - +
562B ILE* 1.3 74.8 - - - +
564B ILE* 1.3 62.3 + - - +
566B GLU* 4.0 1.4 - - - +
567B THR* 2.8 34.4 + - - -
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Residues in contact with ILE 564 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422B ILE* 3.9 33.0 - - + +
424B VAL* 3.8 26.7 - - + -
551B MET* 4.0 15.3 - - + -
556B ILE* 5.0 5.6 - - + -
560B MET* 2.9 36.7 + - + +
561B GLU* 3.7 6.1 - - - +
563B ALA* 1.3 71.4 - - - +
565B ASN* 1.4 67.5 + - - +
567B THR* 3.6 2.9 + - - -
568B LYS* 3.1 26.7 + - + +
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Residues in contact with ASN 565 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561B GLU* 2.8 34.3 + - - +
562B ILE* 3.7 6.3 - - - +
564B ILE* 1.4 79.5 - - - +
566B GLU* 1.4 58.6 + - - +
568B LYS* 3.1 9.1 + - - +
569B ARG* 3.0 28.2 + - - +
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Residues in contact with GLU 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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38B LEU* 4.4 6.8 - - - +
535B ILE* 4.2 19.1 - - + -
562B ILE* 2.8 23.0 + - + +
563B ALA 4.0 3.8 - - - +
565B ASN* 1.4 71.2 - - - +
567B THR* 1.3 56.4 + - - +
569B ARG* 2.7 51.2 + - - +
570B ARG* 3.0 64.5 + - - +
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Residues in contact with THR 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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419B ASP* 4.0 18.0 - - + +
420B PRO 3.4 25.6 - - - +
422B ILE* 3.7 23.8 - - + +
535B ILE* 5.2 6.9 - - - +
538B ILE* 4.0 21.1 - - + +
563B ALA 2.8 22.2 + - - -
564B ILE 3.8 1.1 - - - -
566B GLU* 1.3 73.9 - - - +
568B LYS* 1.4 55.6 - - - +
570B ARG* 3.3 6.0 + - - +
571B ARG* 2.8 37.1 + - - +
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Residues in contact with LYS 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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564B ILE* 3.1 15.9 + - + +
565B ASN* 3.1 13.9 + - - +
567B THR* 1.4 74.5 - - - +
569B ARG* 1.4 55.9 + - - +
571B ARG* 3.4 6.2 + - - +
572B GLU* 3.0 33.6 + - - +
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Residues in contact with ARG 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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38B LEU* 4.4 15.2 - - - +
409B GLU* 5.3 8.3 - - - +
411B ILE* 3.6 25.2 - - - +
565B ASN 3.0 12.7 + - - +
566B GLU* 2.7 47.4 + - - +
568B LYS* 1.4 75.6 - - - +
570B ARG* 1.4 68.3 + - - +
572B GLU* 3.3 5.1 + - - +
573B GLN* 3.1 45.5 + - - +
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Residues in contact with ARG 570 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B LEU* 4.0 7.4 - - - +
40B ALA* 4.0 21.7 - - - +
41B THR 5.5 0.2 - - - +
394B ALA* 2.8 36.0 + - - +
395B THR* 4.1 10.1 - - - +
411B ILE* 4.0 34.0 - - + +
413B ARG* 5.9 0.7 + - - -
419B ASP* 3.4 29.2 + - - +
535B ILE* 4.2 11.6 - - - +
566B GLU* 3.0 53.1 + - - +
567B THR* 3.9 3.4 - - - +
569B ARG* 1.4 86.4 - - - +
571B ARG* 1.4 61.8 + - - +
573B GLN* 3.9 1.9 + - - +
574B GLN* 3.4 22.9 + - - +
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Residues in contact with ARG 571 (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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418B LEU* 4.0 32.9 + - + +
419B ASP* 2.8 50.4 + - + +
420B PRO* 3.8 20.1 - - - +
421B LEU* 3.5 40.2 - - - +
547B GLY 4.7 3.0 + - - -
548B ARG* 5.2 1.2 - - - +
567B THR 2.8 21.9 + - - +
568B LYS* 3.8 5.2 - - - +
570B ARG* 1.4 71.5 - - - +
572B GLU* 1.4 57.8 + - - +
574B GLN* 3.7 4.1 + - - +
575B GLU* 3.0 29.5 + - + +
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Residues in contact with GLU 572 (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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568B LYS 3.0 18.1 + - - +
569B ARG* 3.5 6.3 - - - +
571B ARG* 1.4 72.8 - - - +
573B GLN* 1.4 65.0 + - - +
575B GLU* 3.0 8.9 + - - +
576B ARG* 2.9 30.9 + - - +
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Residues in contact with GLN 573 (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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411B ILE* 3.7 31.4 - - + -
569B ARG* 3.1 41.1 + - - +
570B ARG 4.2 1.1 - - - +
571B ARG 3.6 0.2 - - - -
572B GLU* 1.4 78.5 - - - +
574B GLN* 1.3 56.6 + - - +
576B ARG* 3.5 6.9 + - - +
577B PHE* 3.1 27.3 + - - +
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Residues in contact with GLN 574 (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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411B ILE* 5.4 7.8 - - - +
412B ILE* 5.7 8.1 - - - +
413B ARG* 5.6 4.9 - - - +
416B GLY 5.2 2.0 - - - +
417B LEU 4.9 4.9 - - - +
418B LEU* 3.7 26.0 - - + -
419B ASP 5.5 0.2 - - - +
570B ARG 3.4 16.7 + - - +
571B ARG* 3.7 2.7 - - - +
572B GLU 3.2 0.4 - - - -
573B GLN* 1.3 76.2 - - - +
575B GLU* 1.4 59.2 + - - +
577B PHE* 3.2 9.4 + - - +
578B ASN* 2.9 33.5 + - - +
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Residues in contact with GLU 575 (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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418B LEU* 3.6 17.0 - - + +
571B ARG* 3.0 20.5 + - + +
572B GLU* 3.0 7.8 + - - +
574B GLN* 1.4 74.2 - - - +
576B ARG* 1.4 55.9 + - - +
578B ASN* 3.4 6.7 + - - +
579B GLU* 3.1 26.2 + - - +
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Residues in contact with ARG 576 (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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572B GLU 2.9 14.5 + - - +
573B GLN* 3.6 11.2 - - - +
574B GLN 3.3 0.2 - - - -
575B GLU* 1.4 72.3 - - - +
577B PHE* 1.3 62.3 + - - +
579B GLU* 3.6 8.0 - - - +
580B GLU* 3.3 22.0 + - - +
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Residues in contact with PHE 577 (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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15B GLY* 4.3 28.3 - - - -
412B ILE* 4.6 18.4 - - + -
413B ARG 4.8 13.2 - - - -
414B PRO* 6.1 0.7 - - + -
573B GLN 3.1 13.9 + - - +
574B GLN* 3.5 11.0 - - - +
576B ARG* 1.3 72.8 - - - +
578B ASN* 1.3 71.7 + - - +
579B GLU 3.2 0.4 - - - -
580B GLU* 3.5 2.8 + - - -
581B HIS* 3.0 71.7 + + - +
583B ILE* 3.6 20.6 - - + -
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Residues in contact with ASN 578 (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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416B GLY* 2.8 36.9 + - - -
418B LEU* 3.7 11.5 - - - +
574B GLN* 2.9 18.4 + - - +
575B GLU* 3.6 8.5 - - - +
576B ARG 3.4 0.2 - - - -
577B PHE* 1.3 81.0 - - - +
579B GLU* 1.4 56.6 + - - +
582B GLY* 3.0 8.6 + - - -
583B ILE* 2.9 63.6 + - - +
585B PRO* 3.5 18.8 - - - +
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Residues in contact with GLU 579 (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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575B GLU 3.1 13.1 + - - +
576B ARG* 3.6 12.8 - - - +
577B PHE 3.2 0.4 - - - -
578B ASN* 1.4 75.6 - - - +
580B GLU* 1.4 61.2 + - - +
581B HIS 3.3 1.0 + - - -
582B GLY* 3.3 11.7 + - - -
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Residues in contact with GLU 580 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576B ARG 3.3 13.3 + - - +
577B PHE* 3.5 2.2 + - - +
579B GLU* 1.4 77.4 - - - +
581B HIS* 1.4 76.8 + - + +
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Residues in contact with HIS 581 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577B PHE* 3.0 55.9 + + - +
580B GLU* 1.4 91.2 - - + +
582B GLY* 1.3 65.1 - - - +
583B ILE* 3.6 19.8 - - + +
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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
------------------------------------------------------------
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