Contacts of the helix formed by residues 600 - 631 (chain F) in PDB entry 5KHU
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 TYR 600 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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599F ASN* 3.8 28.9 - - - +
601F ALA* 3.8 28.9 - - - +
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Residues in contact with ALA 601 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600F TYR* 3.8 29.8 - - - +
602F TYR* 3.8 29.4 - - - +
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Residues in contact with TYR 602 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601F ALA* 3.8 25.6 - - - +
603F ALA* 3.8 29.2 - - - +
605F THR* 4.6 16.4 - - - +
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Residues in contact with ALA 603 (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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602F TYR* 3.8 29.2 - - - +
604F TYR* 3.8 26.0 - - - +
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Residues in contact with TYR 604 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603F ALA* 3.8 24.7 - - - +
605F THR* 3.8 29.2 - - - +
607F LEU* 4.4 15.9 - - - +
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Residues in contact with THR 605 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602F TYR* 4.6 15.9 - - - +
604F TYR* 3.8 26.2 - - - +
606F LEU* 3.8 29.2 - - - +
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Residues in contact with LEU 606 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605F THR* 3.8 29.2 - - - +
607F LEU* 3.8 25.4 - - - +
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Residues in contact with LEU 607 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604F TYR* 4.4 15.7 - - - +
606F LEU* 3.8 29.4 - - - +
608F GLY* 3.8 26.0 - - - +
610F GLU* 4.6 16.4 - - - +
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Residues in contact with GLY 608 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607F LEU* 3.8 25.6 - - - +
609F HIS* 3.8 28.7 - - - +
620F ALA* 4.3 24.2 - - - +
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Residues in contact with HIS 609 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608F GLY* 3.8 29.6 - - - +
610F GLU* 3.8 26.0 - - - +
612F VAL* 4.6 14.8 - - - +
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Residues in contact with GLU 610 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607F LEU* 4.6 16.8 - - - +
609F HIS* 3.8 28.3 - - - +
611F PHE* 3.8 29.2 - - - +
613F LEU* 4.4 17.0 - - - +
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Residues in contact with PHE 611 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610F GLU* 3.8 24.2 - - - +
612F VAL* 3.8 29.2 - - - +
614F THR* 4.5 15.7 - - - +
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Residues in contact with VAL 612 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609F HIS* 4.6 17.0 - - - +
611F PHE* 3.8 29.8 - - - +
613F LEU* 3.8 24.5 - - - +
615F GLU* 4.1 19.3 - - - +
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Residues in contact with LEU 613 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610F GLU* 4.4 16.4 - - - +
612F VAL* 3.8 24.9 - - - +
614F THR* 3.8 28.9 - - - +
----------------------------------------------------------
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Residues in contact with THR 614 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611F PHE* 4.5 15.0 - - - +
613F LEU* 3.8 30.1 - - - +
615F GLU* 3.8 25.4 - - - +
----------------------------------------------------------
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Residues in contact with GLU 615 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612F VAL* 4.1 20.0 - - - +
614F THR* 3.8 25.8 - - - +
616F GLU* 3.8 29.8 - - - +
----------------------------------------------------------
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Residues in contact with GLU 616 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615F GLU* 3.8 27.6 - - - +
617F LEU* 3.7 30.1 - - - +
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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
----------------------------------------------------------
616F GLU* 3.7 30.1 - - - +
618F ASP* 3.8 29.8 - - - +
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Residues in contact with ASP 618 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617F LEU* 3.8 29.2 - - - +
619F LYS* 3.8 26.7 - - - +
621F LEU* 4.6 15.5 - - - +
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Residues in contact with LYS 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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618F ASP* 3.8 27.1 - - - +
620F ALA* 3.8 29.2 - - - +
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Residues in contact with ALA 620 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608F GLY* 4.3 24.0 - - - +
619F LYS* 3.8 29.2 - - - +
621F LEU* 3.8 24.7 - - - +
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Residues in contact with LEU 621 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618F ASP* 4.6 17.7 - - - +
620F ALA* 3.8 26.2 - - - +
622F ALA* 3.8 28.9 - - - +
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Residues in contact with ALA 622 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621F LEU* 3.8 28.3 - - - +
623F CYS* 3.8 26.2 - - - +
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Residues in contact with CYS 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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622F ALA* 3.8 25.1 - - - +
624F PHE* 3.8 30.5 - - - +
626F ASN* 4.6 14.4 - - - +
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Residues in contact with PHE 624 (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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623F CYS* 3.8 29.2 - - - +
625F ARG* 3.8 26.5 - - - +
627F ALA* 4.5 16.2 - - - +
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Residues in contact with ARG 625 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624F PHE* 3.8 24.5 - - - +
626F ASN* 3.8 29.4 - - - +
628F ILE* 4.6 14.1 - - - +
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Residues in contact with ASN 626 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623F CYS* 4.6 15.5 - - - +
625F ARG* 3.8 29.2 - - - +
627F ALA* 3.8 26.2 - - - +
629F ARG* 4.3 17.0 - - - +
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Residues in contact with ALA 627 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624F PHE* 4.5 15.3 - - - +
626F ASN* 3.8 29.2 - - - +
628F ILE* 3.8 25.4 - - - +
630F VAL* 4.5 15.7 - - - +
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Residues in contact with ILE 628 (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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625F ARG* 4.6 15.3 - - - +
627F ALA* 3.8 25.1 - - - +
629F ARG* 3.8 28.9 - - - +
631F ASN* 4.6 6.3 - - - +
632F PRO* 3.9 28.3 - - - -
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Residues in contact with ARG 629 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626F ASN* 4.3 17.3 - - - +
628F ILE* 3.8 29.8 - - - +
630F VAL* 3.8 24.9 - - - +
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Residues in contact with VAL 630 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
627F ALA* 4.5 15.3 - - - +
629F ARG* 3.8 26.7 - - - +
631F ASN* 3.7 30.5 - - - +
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Residues in contact with ASN 631 (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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628F ILE* 4.6 7.0 - - - +
630F VAL* 3.7 30.5 - - - +
632F PRO* 3.8 29.2 - - - -
----------------------------------------------------------
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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