Contacts of the helix formed by residues 559 - 578 (chain B) in PDB entry 3ODX
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 PRO 559 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519B GLN* 3.2 28.7 - - - +
523B LEU* 5.0 7.0 - - + -
555B LYS 2.8 29.4 - - - +
556B ASP* 3.5 10.1 - - - +
557B MET 3.4 2.7 - - - -
558B ILE* 1.3 87.6 - - + +
560B THR* 1.3 64.5 + - - +
562B MET* 2.8 20.8 + - - +
563B GLN* 3.3 21.7 + - - +
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Residues in contact with THR 560 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431B HIS* 3.7 24.0 + - + +
434B MET* 3.6 31.3 - - + +
435B LEU* 5.3 2.9 - - + -
552B LEU* 4.7 3.1 - - - +
556B ASP 3.2 13.5 + - - -
557B MET* 2.8 23.2 + - - +
559B PRO* 1.3 77.0 - - - +
561B GLU* 1.3 61.3 + - - +
563B GLN* 3.1 21.1 + - - +
564B ARG* 3.0 20.8 + - - +
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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
----------------------------------------------------------
431B HIS* 2.7 32.0 + - + -
435B LEU* 3.9 5.5 - - + +
467B LEU* 3.2 24.1 - - + +
471B HIS* 2.7 27.7 + - - -
512B SER* 2.8 26.9 + - - +
515B PHE* 3.8 29.8 - - + -
516B CYS* 3.6 12.1 - - - -
557B MET 4.3 0.4 + - - -
558B ILE 3.7 2.7 + - - +
559B PRO 2.9 4.8 + - - -
560B THR* 1.3 73.6 - - - +
562B MET* 1.3 65.0 + - - +
564B ARG* 3.4 3.3 + - - +
565B LEU* 3.2 23.0 + - - +
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Residues in contact with MET 562 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516B CYS* 3.9 21.5 - - + -
519B GLN* 3.8 21.1 + - - +
558B ILE 4.8 0.6 + - - -
559B PRO 2.8 14.9 + - - +
561B GLU* 1.3 71.2 - - - +
563B GLN* 1.3 67.7 + - - +
565B LEU* 3.0 15.4 + - - +
566B THR* 3.1 18.2 + - + +
599B LEU* 4.7 10.3 - - - -
602B VAL* 4.1 13.0 - - + -
603B ASN* 3.6 24.0 - - - +
606B VAL* 3.8 32.3 - - + -
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Residues in contact with GLN 563 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556B ASP 5.0 1.8 + - - +
559B PRO* 3.3 20.3 + - - +
560B THR* 3.1 31.1 + - - +
562B MET* 1.3 78.1 - - - +
564B ARG* 1.3 58.5 + - - +
566B THR* 2.5 33.8 + - - +
567B LYS* 3.2 25.2 + - - +
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Residues in contact with ARG 564 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424B LEU* 3.4 10.7 + - - +
427B THR* 2.7 36.6 + - - -
428B GLU* 2.5 49.1 + - - +
431B HIS* 3.6 37.6 - - + +
471B HIS* 4.2 2.5 - - + -
560B THR 3.0 2.9 + - - +
561B GLU 3.4 9.6 - - - +
563B GLN* 1.3 78.1 - - - +
565B LEU* 1.3 59.5 + - + +
567B LYS* 2.7 37.9 + - - +
568B TYR* 3.2 38.1 + - + +
571B LEU* 4.2 12.6 - - - +
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Residues in contact with LEU 565 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471B HIS* 4.8 1.1 - - + -
508B PHE* 4.1 12.6 - - + -
512B SER* 3.5 28.3 - - - +
516B CYS* 4.5 5.6 - - - -
561B GLU* 3.2 15.1 + - - +
562B MET* 3.0 11.7 + - - +
564B ARG* 1.3 77.5 - - - +
566B THR* 1.3 58.6 + - - +
567B LYS 3.1 0.8 + - - -
568B TYR* 3.7 24.0 + - + +
569B PRO* 3.6 17.2 - - - +
595B CYS 4.9 1.4 - - - +
598B ILE* 4.4 14.8 - - + -
599B LEU* 3.7 20.9 - - + +
602B VAL* 3.7 39.5 - - + -
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Residues in contact with THR 566 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562B MET* 3.1 24.6 + - + +
563B GLN* 2.5 26.6 + - - +
565B LEU* 1.3 75.1 - - - +
567B LYS* 1.3 68.3 + - - +
568B TYR 3.5 0.4 - - - -
569B PRO* 4.2 4.1 - - - +
570B LEU* 3.8 23.4 - - - +
599B LEU* 3.7 31.5 - - + +
603B ASN* 5.6 2.7 - - - +
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Residues in contact with LYS 567 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563B GLN* 3.4 28.3 + - - +
564B ARG* 2.7 28.7 + - - +
566B THR* 1.3 88.7 - - - +
568B TYR* 1.3 57.3 + - - +
569B PRO 3.7 0.4 - - - -
570B LEU* 3.3 23.5 + - + +
571B LEU* 3.1 34.6 + - + +
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Residues in contact with TYR 568 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424B LEU* 4.1 13.0 - - + -
428B GLU* 2.5 30.2 + - - -
471B HIS* 3.1 23.6 + + - -
474B PHE* 4.1 5.6 - + - -
499B ARG* 3.7 37.1 + - - -
500B PHE* 4.1 6.1 - + - -
508B PHE* 4.2 0.4 - + - -
564B ARG* 3.2 46.7 + - + -
565B LEU* 3.8 25.1 - - + +
567B LYS* 1.3 74.6 - - - +
569B PRO* 1.3 68.8 - - + +
571B LEU* 3.2 3.5 + - + -
572B LEU* 2.9 36.3 + - + +
595B CYS* 4.0 17.0 - - + -
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Residues in contact with PRO 569 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565B LEU 3.6 13.7 - - - +
566B THR 4.2 4.5 - - - +
567B LYS 4.1 0.7 - - - -
568B TYR* 1.3 94.3 - - + +
570B LEU* 1.3 63.2 + - + +
572B LEU* 4.7 3.1 - - + -
573B GLN* 2.8 48.3 + - + +
592B ALA 4.9 0.9 - - - +
595B CYS* 3.7 11.6 - - + +
596B ARG* 3.4 48.5 - - + +
599B LEU* 4.8 9.6 - - + -
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Residues in contact with LEU 570 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566B THR 3.8 20.0 - - - +
567B LYS* 3.3 25.5 + - + +
568B TYR 3.2 1.4 - - - -
569B PRO* 1.3 85.5 - - + +
571B LEU* 1.3 63.0 + - + +
573B GLN* 3.5 18.5 - - - +
574B SER* 3.4 22.5 + - - -
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Residues in contact with LEU 571 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B VAL* 3.4 27.7 - - + +
423B GLU* 3.5 36.6 - - + +
424B LEU* 3.9 35.7 - - + +
427B THR* 4.3 2.7 - - + +
564B ARG* 4.2 18.6 - - - +
567B LYS* 3.1 21.7 + - + +
568B TYR* 3.2 5.1 + - - +
570B LEU* 1.3 78.6 - - + +
572B LEU* 1.3 67.4 + - + +
574B SER* 3.1 2.5 + - - -
575B ILE* 3.1 25.2 + - - +
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Residues in contact with LEU 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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424B LEU* 4.4 22.2 - - + -
496B LEU* 3.6 36.6 - - + -
499B ARG* 5.2 0.4 - - - +
500B PHE* 4.2 5.6 - - + -
568B TYR* 2.9 30.1 + - + +
571B LEU* 1.3 79.0 - - + +
573B GLN* 1.3 64.7 + - - +
575B ILE* 4.5 6.5 - - + +
576B GLY* 3.1 18.5 + - - -
588B VAL* 3.4 11.1 - - - +
589B GLU* 5.7 0.2 - - - -
591B ALA* 3.7 18.6 - - + -
592B ALA* 3.6 16.8 - - + +
595B CYS* 3.5 28.0 - - - -
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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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569B PRO* 2.8 33.3 + - - +
570B LEU* 3.5 21.7 - - - +
572B LEU* 1.3 73.6 - - - +
574B SER* 1.3 58.7 + - - +
576B GLY* 4.0 0.8 - - - -
577B GLN* 3.1 38.2 + - - +
592B ALA* 4.1 3.5 - - + +
596B ARG* 3.3 46.8 - - - +
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Residues in contact with SER 574 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B LYS* 5.4 0.7 - - - +
417B ARG* 5.6 0.2 - - - -
420B VAL* 3.5 25.3 - - - +
570B LEU 3.4 16.3 + - - -
571B LEU* 3.1 6.6 + - - -
573B GLN* 1.3 78.7 - - - +
575B ILE* 1.3 64.4 + - - +
577B GLN* 3.1 31.3 + - - +
578B ASN* 3.5 18.7 + - - +
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Residues in contact with ILE 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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417B ARG* 4.2 8.9 - - + +
420B VAL* 3.5 26.2 - - + +
421B ILE* 3.6 43.5 - - + +
424B LEU* 4.5 18.2 - - + -
492B ILE* 4.4 4.7 - - + -
496B LEU* 5.6 3.1 - - + -
571B LEU 3.1 17.2 + - - +
572B LEU* 3.9 10.3 - - + +
573B GLN 3.4 0.2 - - - -
574B SER* 1.3 73.7 - - - +
576B GLY* 1.3 65.0 + - - +
578B ASN* 3.0 16.5 + - - +
579B THR* 3.1 24.5 + - - +
588B VAL* 3.8 19.7 - - + -
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Residues in contact with GLY 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 LEU 3.1 11.0 + - - -
573B GLN 4.0 1.3 - - - -
574B SER 3.6 0.2 - - - -
575B ILE* 1.3 77.7 - - - +
577B GLN* 1.3 56.3 + - - +
579B THR* 2.9 26.2 + - - -
585B ARG* 3.6 22.5 - - - +
588B VAL* 3.4 20.6 - - - +
589B GLU* 4.9 11.2 - - - -
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Residues in contact with GLN 577 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573B GLN* 3.1 26.3 + - - +
574B SER* 3.1 38.4 + - - +
576B GLY* 1.3 73.3 - - - +
578B ASN* 1.3 66.7 + - - +
579B THR 3.5 1.8 + - - +
585B ARG* 5.5 3.2 - - - +
589B GLU* 5.6 1.7 - - - +
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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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413B SER* 3.2 48.2 - - - +
414B GLN* 4.0 3.8 - - - +
416B LYS* 3.4 28.3 - - - +
417B ARG* 3.3 22.6 - - + +
574B SER* 3.5 22.4 + - - +
575B ILE 3.0 8.6 + - - +
577B GLN* 1.3 87.4 - - - +
579B THR* 1.4 56.7 + - - +
580B GLU 3.7 2.5 + - - -
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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