Contacts of the helix formed by residues 558 - 583 (chain B) in PDB entry 3K5N
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 558 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556B ALA 4.0 3.1 + - - -
557B HIS* 1.3 82.5 + - - +
559B GLU* 1.3 61.1 + - - +
560B GLU* 3.2 7.6 - - - +
561B GLU* 4.1 9.6 + - - +
562B ALA* 2.5 34.8 + - - +
597B HIS* 4.8 6.5 - - - -
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Residues in contact with GLU 559 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558B SER* 1.3 75.2 - - - +
560B GLU* 1.3 69.2 + - + +
562B ALA* 5.0 0.7 - - - -
563B ALA* 2.7 37.7 + - + +
594B TYR* 5.2 5.7 + - - -
597B HIS* 4.9 11.5 + - - +
622B GLN 3.7 21.5 - - - +
623B GLU* 4.4 1.7 - - - -
624B GLY* 3.8 16.9 + - - -
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Residues in contact with GLU 560 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558B SER* 3.2 5.3 - - - +
559B GLU* 1.3 83.6 - - + +
561B GLU* 1.3 70.7 + - - +
563B ALA* 3.9 1.1 - - - +
564B LYS* 2.9 27.9 + - - +
567B ARG* 5.5 0.2 + - - -
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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
----------------------------------------------------------
557B HIS* 4.2 10.5 - - + +
558B SER* 3.2 19.2 + - - +
560B GLU* 1.3 91.4 - - - +
562B ALA* 1.3 57.4 + - - +
563B ALA 3.2 1.1 - - - -
564B LYS* 4.3 16.1 - - - +
565B ILE* 2.6 54.3 + - + +
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Residues in contact with ALA 562 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B LEU* 3.9 10.2 - - + +
553B LEU* 4.9 3.1 - - + -
557B HIS* 3.9 10.7 - - + +
558B SER 2.5 21.1 + - - +
559B GLU* 5.0 0.4 - - - -
561B GLU* 1.3 71.5 - - - +
563B ALA* 1.3 54.9 + - - +
565B ILE* 4.5 4.0 - - - -
566B GLY* 2.5 35.2 + - - -
594B TYR* 4.3 2.5 - - - -
597B HIS* 3.4 43.7 - - + +
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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
----------------------------------------------------------
559B GLU* 2.7 33.0 + - + +
560B GLU* 3.9 1.3 - - - +
562B ALA* 1.3 79.5 - - - +
564B LYS* 1.3 55.8 + - - +
567B ARG* 2.8 51.6 + - - +
594B TYR* 4.0 21.5 + - + +
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Residues in contact with LYS 564 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560B GLU 2.9 22.0 + - - +
561B GLU* 3.8 17.7 - - - +
563B ALA* 1.3 75.3 - - - +
565B ILE* 1.3 68.7 + - + +
566B GLY 3.2 0.5 + - - -
567B ARG* 3.8 25.7 - - - +
568B ALA* 3.3 22.7 + - - +
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Residues in contact with ILE 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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539B TYR* 2.4 55.2 - - + +
553B LEU* 4.6 9.0 - - + -
557B HIS* 3.9 28.3 - - + +
561B GLU* 2.6 37.1 + - + +
562B ALA* 4.0 3.6 - - - +
564B LYS* 1.3 75.7 - - + +
566B GLY* 1.3 61.9 + - - +
568B ALA* 3.7 4.5 + - - +
569B LEU* 3.3 23.1 + - + +
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Residues in contact with GLY 566 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B LEU* 3.8 19.0 - - - +
418B LEU* 5.7 1.3 - - - +
562B ALA 2.5 23.8 + - - -
563B ALA 3.5 0.2 - - - -
565B ILE* 1.3 72.0 - - - +
567B ARG* 1.3 66.0 + - - +
569B LEU* 3.1 18.6 + - - +
570B VAL* 3.1 16.3 + - - +
594B TYR* 3.9 11.4 - - - -
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Residues in contact with ARG 567 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560B GLU 5.5 0.2 + - - -
563B ALA* 2.8 30.8 + - - +
564B LYS* 3.8 30.7 - - - +
566B GLY* 1.3 72.7 - - - +
568B ALA* 1.3 59.2 + - - +
570B VAL* 2.7 37.5 - - + +
571B GLN* 3.5 8.5 + - - +
594B TYR* 4.3 21.1 - - + -
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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
----------------------------------------------------------
537B GLN* 5.4 2.9 - - - +
564B LYS 3.3 15.4 + - - +
565B ILE* 3.8 5.8 - - - +
566B GLY 3.1 0.6 - - - -
567B ARG* 1.3 76.8 - - - +
569B LEU* 1.3 66.3 + - + +
571B GLN* 3.1 34.4 - - - +
572B HIS* 3.2 9.5 + - - +
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Residues in contact with LEU 569 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B LEU* 5.1 4.7 - - + -
418B LEU* 4.9 11.2 - - + -
534B ILE* 3.4 36.1 - - + -
537B GLN* 3.2 30.5 - - + +
539B TYR* 3.6 32.3 - - + -
551B VAL* 4.7 13.2 - - + -
553B LEU* 6.1 0.7 - - + -
565B ILE* 3.3 17.5 + - + +
566B GLY* 3.1 14.1 + - - +
568B ALA* 1.3 79.3 - - + +
570B VAL* 1.3 59.2 + - + +
572B HIS* 3.2 4.0 + - - +
573B VAL* 2.8 33.8 + - + +
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Residues in contact with VAL 570 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418B LEU* 5.0 4.7 - - + -
566B GLY 3.1 18.6 - - - +
567B ARG* 2.7 15.3 - - + +
569B LEU* 1.3 76.5 - - + +
571B GLN* 1.3 71.8 + - + +
573B VAL* 3.0 8.3 + - - +
574B ASN* 2.5 46.4 + - - +
592B LEU* 3.3 34.1 - - + +
593B GLU* 5.3 0.4 - - - -
594B TYR* 3.7 27.1 - - + +
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Residues in contact with GLN 571 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567B ARG* 3.8 8.1 - - - +
568B ALA* 3.1 33.9 - - - +
570B VAL* 1.3 82.3 - - + +
572B HIS* 1.3 61.1 + - + +
574B ASN* 2.7 11.1 + - + +
575B ALA* 2.4 39.1 + - + +
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Residues in contact with HIS 572 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533B LEU* 4.0 34.9 - - + -
534B ILE* 5.8 1.6 - - - +
536B ALA* 5.8 1.3 - - + -
537B GLN* 4.2 37.2 + - + +
568B ALA 3.2 7.9 + - - +
569B LEU* 3.5 11.3 + - - +
571B GLN* 1.3 82.4 - - + +
573B VAL* 1.3 60.6 + - - +
575B ALA* 4.7 3.6 - - - -
576B TRP* 2.7 55.9 + + + +
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Residues in contact with VAL 573 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418B LEU* 6.3 0.7 - - + -
420B TYR* 3.8 22.7 - - - +
530B THR* 4.0 13.7 - - + -
533B LEU* 4.5 15.5 - - + -
534B ILE* 4.7 16.4 - - + -
569B LEU 2.8 21.4 + - - +
570B VAL* 3.1 10.8 - - - +
572B HIS* 1.3 89.2 - - - +
574B ASN* 1.3 62.8 + - - +
576B TRP* 3.5 5.5 - - - +
577B TRP* 3.0 35.7 + - + +
592B LEU* 3.9 17.5 - - + -
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Residues in contact with ASN 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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420B TYR* 5.1 0.3 - - - -
570B VAL* 2.5 26.1 + - - +
571B GLN* 2.7 17.3 + - + +
573B VAL* 1.3 69.2 - - - +
575B ALA* 1.3 67.5 + - - +
577B TRP* 3.0 18.6 + - - +
578B ALA* 3.1 13.1 + - - +
590B LEU* 4.8 8.3 + - - +
591B GLU* 4.2 13.3 - - - +
592B LEU* 3.3 43.9 + - - +
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Residues in contact with ALA 575 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571B GLN* 2.4 27.9 + - + +
572B HIS* 4.1 2.9 - - - +
574B ASN* 1.3 71.8 - - - +
576B TRP* 1.3 66.5 + - - +
578B ALA* 3.1 7.8 + - - +
579B GLU* 2.8 37.4 + - + +
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Residues in contact with TRP 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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529B GLN* 3.1 42.4 - - + -
533B LEU* 3.4 29.6 - - + +
572B HIS* 2.7 40.9 + + + +
573B VAL 3.5 4.0 - - - +
575B ALA* 1.3 72.9 - - - +
577B TRP* 1.3 75.5 + + - +
579B GLU* 4.0 3.6 - - - +
580B THR* 2.4 62.2 + - + +
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Residues in contact with TRP 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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420B TYR* 3.0 24.7 + + - -
431B PHE* 6.0 1.8 - + - -
525B GLN* 4.5 15.5 - - - -
526B ILE* 3.5 45.8 - - + -
529B GLN* 4.0 26.9 - - + -
530B THR* 4.4 3.5 + - - +
533B LEU* 5.5 0.9 - - + -
573B VAL* 3.0 28.8 + - + +
574B ASN* 3.0 11.0 + - - +
576B TRP* 1.3 94.6 - + - +
578B ALA* 1.3 56.9 + - - +
580B THR* 2.7 35.9 - - + +
581B LEU* 2.8 41.4 + - + +
588B SER* 4.2 11.2 - - - +
590B LEU* 4.1 23.1 - - + +
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Residues in contact with ALA 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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574B ASN 3.1 8.5 + - - +
575B ALA* 3.1 10.9 + - - +
577B TRP* 1.3 79.9 - - - +
579B GLU* 1.3 58.6 + - + +
581B LEU* 3.4 1.6 + - - +
582B GLN* 3.0 33.1 + - - +
586B LEU 5.3 0.2 - - - +
588B SER* 3.8 22.6 + - - +
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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 ALA* 2.8 27.2 + - + +
576B TRP* 4.1 3.6 - - - +
578B ALA* 1.3 73.6 - - + +
580B THR* 1.3 65.6 + - - +
581B LEU 3.0 1.2 + - - -
582B GLN* 3.2 28.6 + - - +
583B LYS* 3.3 25.2 + - - +
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Residues in contact with THR 580 (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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576B TRP* 2.4 66.7 + - + +
577B TRP* 2.7 37.2 - - + +
579B GLU* 1.3 73.4 - - - +
581B LEU* 1.3 61.0 + - + +
583B LYS* 4.0 25.8 - - - +
584B GLN* 4.2 8.7 - - - +
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Residues in contact with LEU 581 (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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430B THR* 4.5 13.7 - - + -
431B PHE* 4.8 16.6 - - + -
577B TRP* 2.8 33.9 + - + +
578B ALA 4.1 2.0 - - - +
580B THR* 1.3 85.9 - - + +
582B GLN* 1.3 63.4 + - - +
583B LYS 3.0 2.5 - - - -
584B GLN* 3.2 31.0 + - + +
586B LEU* 2.8 35.6 + - + +
588B SER* 3.4 28.3 - - - +
590B LEU* 4.2 17.3 - - + -
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Residues in contact with GLN 582 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578B ALA 3.0 19.0 + - - +
579B GLU* 3.2 24.3 + - - +
581B LEU* 1.3 77.3 - - - +
583B LYS* 1.3 60.4 + - + +
585B ARG* 2.7 27.3 + - - -
586B LEU 4.1 6.7 - - - +
587B THR* 5.9 1.1 - - - +
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Residues in contact with LYS 583 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579B GLU* 3.3 28.0 + - - +
580B THR* 4.0 19.0 - - - +
582B GLN* 1.3 79.6 - - + +
584B GLN* 1.3 59.4 + - - +
585B ARG* 2.9 15.6 + - - +
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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