Contacts of the helix formed by residues 606 - 623 (chain F) in PDB entry 4OQB
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 606 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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604F MET* 3.3 14.5 - - - +
605F PRO* 1.3 80.6 - - - +
607F LYS* 1.3 74.8 + - - +
608F GLU* 3.5 8.2 + - - +
609F ASP* 3.5 19.2 + - - +
610F ALA* 3.4 15.1 + - - +
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Residues in contact with LYS 607 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546F LEU* 5.0 20.6 - - + -
574F LEU* 5.7 0.2 - - - +
575F LEU 4.7 7.4 + - - -
584F TRP* 3.5 39.9 - - - +
604F MET* 6.5 0.2 - - + -
606F SER* 1.3 82.8 + - - +
608F GLU* 1.3 62.2 + - + +
609F ASP 3.3 0.4 - - - -
610F ALA* 3.3 21.2 - - + +
611F ILE* 3.7 10.9 + - - +
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Residues in contact with GLU 608 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606F SER* 3.5 7.0 + - - +
607F LYS* 1.3 75.7 - - + +
609F ASP* 1.3 66.1 + - - +
610F ALA 3.2 0.4 - - - -
611F ILE* 3.6 25.2 + - - +
612F GLU* 3.4 18.2 + - - +
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Residues in contact with ASP 609 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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604F MET* 4.0 3.7 - - - +
605F PRO* 3.6 23.8 - - + +
606F SER* 3.5 34.8 + - - +
607F LYS 3.3 0.4 - - - -
608F GLU* 1.3 77.6 - - - +
610F ALA* 1.3 59.6 + - - +
611F ILE 3.4 0.2 - - - -
612F GLU* 3.4 8.9 + - - +
613F HIS* 2.9 30.7 + - - +
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Residues in contact with ALA 610 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574F LEU* 3.4 32.3 - - + -
584F TRP 5.6 1.6 - - - +
585F ILE* 4.1 2.0 - - - +
604F MET* 4.0 18.1 - - + -
606F SER 3.4 11.0 + - - +
607F LYS* 3.3 19.7 - - + +
608F GLU 3.2 0.4 - - - -
609F ASP* 1.3 76.3 - - - +
611F ILE* 1.3 55.6 + - - +
613F HIS* 3.2 1.6 + - - +
614F PHE* 2.7 39.3 + - - +
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Residues in contact with ILE 611 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546F LEU* 6.4 1.3 - - + -
548F LYS* 5.8 10.3 - - + -
553F PHE* 3.9 24.7 - - + -
574F LEU* 4.8 4.2 - - + +
607F LYS 3.7 9.8 + - - +
608F GLU* 3.6 29.1 + - - +
609F ASP 3.4 0.4 - - - -
610F ALA* 1.3 76.2 - - - +
612F GLU* 1.3 61.3 + - - +
614F PHE* 4.4 4.9 - - - -
615F MET* 3.0 59.3 + - + +
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Residues in contact with GLU 612 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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608F GLU 3.4 10.4 + - - +
609F ASP* 3.4 13.9 + - - +
610F ALA 3.2 0.4 - - - -
611F ILE* 1.3 82.5 - - - +
613F HIS* 1.3 57.4 + - - +
615F MET* 4.8 1.0 - - - +
616F LYS* 3.1 34.7 + - + +
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Residues in contact with HIS 613 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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585F ILE* 3.8 20.6 - - + -
587F ARG* 3.9 8.7 + - - -
602F GLU* 3.9 17.9 + - - -
604F MET* 3.8 21.6 - - + +
609F ASP 2.9 18.1 + - - +
610F ALA 3.8 1.1 - - - +
612F GLU* 1.3 74.5 - - - +
614F PHE* 1.3 59.8 + - - +
616F LYS* 4.0 6.7 - - - +
617F LEU* 3.1 68.9 + - + +
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Residues in contact with PHE 614 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553F PHE* 3.5 49.8 - + + -
554F SER* 3.9 3.6 - - - -
555F ALA 4.9 0.9 - - - -
572F LEU* 3.6 33.5 - - + +
573F GLN* 4.1 7.4 - - - -
574F LEU* 4.1 15.7 - - + -
585F ILE* 3.5 15.2 - - + +
610F ALA 2.7 22.9 + - - +
611F ILE* 3.9 4.9 - - - +
613F HIS* 1.3 71.5 - - - +
615F MET* 1.3 67.5 + - + +
616F LYS 3.3 0.2 + - - -
617F LEU* 3.3 3.7 + - - +
618F TYR* 2.8 32.5 + + + +
626F TRP* 3.5 46.0 - + - -
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Residues in contact with MET 615 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553F PHE* 3.8 15.5 - - + -
611F ILE* 3.0 43.3 + - + +
612F GLU* 4.8 1.3 - - - +
614F PHE* 1.3 84.3 - - + +
616F LYS* 1.3 57.3 + - - +
618F TYR* 3.7 8.4 - - - +
619F GLU* 3.2 29.3 + - - +
626F TRP* 3.8 44.0 + - + +
627F HIS* 4.7 11.4 - - + +
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Residues in contact with LYS 616 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612F GLU* 3.1 26.4 + - + +
613F HIS* 4.0 6.5 - - - +
614F PHE 3.2 0.4 - - - -
615F MET* 1.3 75.8 - - - +
617F LEU* 1.3 60.8 + - + +
619F GLU* 3.5 3.7 + - - +
620F GLU* 2.9 41.1 + - + +
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Residues in contact with LEU 617 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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570F TYR* 4.2 8.6 + - - +
572F LEU* 4.4 11.0 - - + -
585F ILE* 4.2 10.5 - - + -
587F ARG* 3.5 47.8 - - + +
613F HIS* 3.1 51.5 + - + +
614F PHE 3.7 2.7 - - - +
616F LYS* 1.3 73.3 - - - +
618F TYR* 1.3 69.7 + - - +
620F GLU* 3.4 16.5 + - - +
621F LYS* 3.1 34.3 + - - +
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Residues in contact with TYR 618 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551F LYS* 5.9 0.9 + - - -
555F ALA* 4.0 16.8 - - + +
557F LEU* 4.3 14.8 - - + -
570F TYR* 6.3 0.2 - - - -
572F LEU* 4.0 18.5 - - + +
614F PHE* 2.8 18.1 + - + +
615F MET* 3.7 9.2 - - - +
616F LYS 3.3 0.2 - - - -
617F LEU* 1.3 75.1 - - - +
619F GLU* 1.3 54.4 + - - +
621F LYS* 2.9 6.7 + - - +
622F THR* 2.7 63.8 + - + +
624F ASN* 3.8 6.1 - - + -
625F ALA 3.5 21.0 + - - -
626F TRP* 3.5 49.9 + + + -
631F PHE* 4.4 5.5 - - - -
640F PRO* 4.0 20.1 - - - +
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Residues in contact with GLU 619 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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615F MET 3.2 16.3 + - - +
616F LYS* 4.1 3.1 - - - +
618F TYR* 1.3 78.9 - - - +
620F GLU* 1.3 59.3 + - - +
623F GLY* 2.8 41.0 + - - +
624F ASN 3.3 27.0 - - - +
625F ALA* 4.3 12.9 - - - +
637F LYS* 5.0 1.9 - - - -
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Residues in contact with GLU 620 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616F LYS* 2.9 29.3 + - + +
617F LEU* 3.6 17.0 - - - +
619F GLU* 1.3 77.6 - - - +
621F LYS* 1.3 82.7 + - - +
637F LYS* 4.1 16.0 - - - +
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Residues in contact with LYS 621 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557F LEU* 4.1 10.3 - - + -
570F TYR* 3.8 43.5 - - + -
617F LEU* 3.1 23.5 + - - +
618F TYR* 2.9 3.8 + - - +
620F GLU* 1.3 109.0 + - - +
622F THR* 1.3 59.6 + - - +
637F LYS* 3.3 9.8 - - - +
638F PHE* 2.8 53.2 + - + +
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Residues in contact with THR 622 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557F LEU* 4.2 13.9 - - - -
618F TYR* 2.7 62.2 + - + +
621F LYS* 1.3 74.2 - - - +
623F GLY* 1.3 58.2 + - - +
624F ASN* 3.4 23.1 - - + +
631F PHE* 3.2 22.3 - - - -
634F TYR* 4.1 4.2 + - - +
637F LYS* 3.5 9.4 - - - +
638F PHE* 3.3 22.5 + - - +
640F PRO* 3.6 9.4 - - - +
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Residues in contact with GLY 623 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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619F GLU* 2.8 29.9 + - - +
621F LYS 3.6 1.2 - - - -
622F THR* 1.3 76.9 - - - +
624F ASN* 1.3 61.8 + - - +
634F TYR* 3.8 20.7 - - - -
637F LYS* 3.8 14.8 - - - +
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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
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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