Contacts of the helix formed by residues 606 - 619 (chain F) in PDB entry 6T8G
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 LYS 606 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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636A ASP* 5.9 0.4 + - - -
601F MET* 4.8 3.4 - - + -
604F VAL 4.2 0.4 - - - -
605F GLY* 1.3 74.5 - - - +
607F LYS* 1.3 63.5 + - - +
608F VAL 3.2 2.2 - - - +
609F GLU* 3.1 34.3 + - - +
610F GLU* 2.9 47.9 + - - +
641F LEU* 6.6 0.2 - - - -
3H A 4.7 17.5 - - - +
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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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525F ALA* 6.3 2.2 - - + -
529F ARG* 4.4 26.8 - - - +
604F VAL* 3.8 10.2 + - + +
606F LYS* 1.3 78.1 - - - +
608F VAL* 1.3 62.4 + - + +
610F GLU* 3.2 21.8 + - + +
611F LEU* 3.0 49.9 + - + +
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Residues in contact with VAL 608 (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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525F ALA* 5.2 12.3 - - + +
528F LEU* 3.8 8.3 - - + -
597F PHE* 5.5 0.9 - - + -
600F MET* 3.7 42.4 - - + +
601F MET* 5.2 5.6 - - - +
604F VAL* 3.7 36.0 + - + +
606F LYS* 3.2 1.0 - - - -
607F LYS* 1.3 78.4 - - + +
609F GLU* 1.3 57.1 + - - +
611F LEU* 3.3 8.6 + - + +
612F ILE* 2.9 48.4 + - + +
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Residues in contact with GLU 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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597F PHE* 5.5 1.1 - - - -
601F MET* 3.3 33.7 - - + +
606F LYS* 3.1 36.4 + - + +
608F VAL* 1.3 78.1 - - - +
610F GLU* 1.3 57.3 + - + +
612F ILE* 3.8 5.9 - - - +
613F ALA* 2.9 29.5 + - - +
639F THR* 2.3 39.0 + - - +
641F LEU* 4.2 18.0 - - + +
642F ILE* 3.9 19.1 - - + +
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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
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602A MET* 4.8 17.1 - - + +
606F LYS* 2.9 37.0 + - + +
607F LYS* 3.2 23.7 + - + +
609F GLU* 1.3 75.3 - - + +
611F LEU* 1.3 61.3 + - + +
613F ALA* 3.5 4.6 + - - +
614F ARG* 3.0 35.2 + - - +
641F LEU* 6.0 4.3 - - + -
3H A 5.1 4.9 + - - -
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Residues in contact with LEU 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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525F ALA* 4.7 6.5 - - + +
528F LEU* 4.1 26.5 - - + +
529F ARG* 3.9 33.9 - - + +
532F VAL* 4.4 18.5 - - + +
607F LYS* 3.0 36.6 + - + +
608F VAL* 3.7 10.5 - - + +
609F GLU 3.3 0.2 - - - -
610F GLU* 1.3 80.3 - - + +
612F ILE* 1.3 57.3 + - - +
614F ARG* 3.2 13.7 + - + +
615F ILE* 3.0 31.7 + - - +
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Residues in contact with ILE 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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528F LEU* 4.1 22.4 - - + -
594F VAL* 5.4 3.6 - - + -
597F PHE* 3.5 28.3 - - + -
600F MET* 5.1 3.8 - - + -
608F VAL* 2.9 36.3 + - + +
609F GLU* 4.0 4.3 - - - +
611F LEU* 1.3 72.1 - - - +
613F ALA* 1.3 61.7 + - - +
615F ILE* 3.3 7.6 + - + +
616F ALA* 2.9 29.3 + - + +
626F LEU* 3.8 14.3 - - + +
628F LEU* 3.7 33.4 - - + -
642F ILE* 4.2 11.9 - - + -
646F ILE* 5.7 0.4 - - + -
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Residues in contact with ALA 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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602A MET* 5.7 5.6 - - + -
609F GLU 2.9 18.5 + - - +
610F GLU* 3.9 4.9 - - - +
612F ILE* 1.3 77.0 - - - +
614F ARG* 1.3 57.0 + - - +
616F ALA* 3.8 5.0 - - - +
617F GLN* 2.9 40.6 + - - +
641F LEU* 4.1 40.2 - - + +
642F ILE* 4.8 4.4 - - + +
645F ASN* 4.7 4.4 - - - +
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Residues in contact with ARG 614 (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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599A ASP* 4.5 10.8 + - - +
602A MET* 3.5 43.0 - - - +
603A ILE* 4.4 24.4 - - - +
532F VAL* 4.4 26.8 - - + +
535F MET* 4.8 0.9 - - + -
610F GLU* 3.0 19.5 + - - +
611F LEU* 3.2 19.3 + - + +
613F ALA* 1.3 76.6 - - - +
615F ILE* 1.3 61.5 + - - +
617F GLN* 3.4 9.3 + - - +
618F LYS* 3.0 58.9 + - + +
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Residues in contact with ILE 615 (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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461F HIS* 5.1 1.3 - - + -
528F LEU* 3.9 28.5 - - + -
531F SER* 4.2 14.4 - - - -
532F VAL* 3.7 24.7 - - + +
535F MET* 4.1 13.5 - - + -
592F VAL* 5.9 2.7 - - + -
611F LEU 3.0 20.5 + - - +
612F ILE* 3.6 9.9 - - + +
614F ARG* 1.3 74.6 - - - +
616F ALA* 1.3 59.4 + - - +
618F LYS 3.0 2.8 + - - -
619F ALA* 2.8 46.7 + - + +
624F ILE* 5.1 11.9 - - + +
625F HIS 6.0 0.9 - - - +
626F LEU* 4.7 24.5 - - + -
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Residues in contact with ALA 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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468A THR* 4.3 8.3 - - - +
461F HIS* 4.3 19.6 + - + -
612F ILE* 2.9 18.0 + - + +
613F ALA* 4.1 4.7 - - - +
615F ILE* 1.3 77.5 - - - +
617F GLN* 1.3 61.9 + - - +
619F ALA 4.5 1.1 + - - -
620F ARG 5.6 0.5 + - - -
626F LEU* 4.9 5.8 - - + -
641F LEU 5.6 0.4 - - - +
642F ILE* 6.5 0.4 - - - -
645F ASN* 3.9 33.0 - - + +
646F ILE* 4.3 21.8 - - + -
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Residues in contact with GLN 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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468A THR* 4.2 5.2 - - - +
500A LYS* 5.5 1.2 - - - +
596A GLU* 4.2 10.7 - - - +
598A ALA* 4.7 9.2 - - - +
599A ASP* 5.2 4.2 + - - +
602A MET* 4.6 19.3 - - - +
631A GLN* 3.0 43.0 + - + +
632A ARG* 3.4 35.6 - - - +
613F ALA* 2.9 25.7 + - - +
614F ARG* 3.7 11.3 - - - +
616F ALA* 1.3 80.3 - - - +
618F LYS* 1.3 69.8 + - + +
620F ARG* 4.9 2.3 + - - +
641F LEU* 4.8 4.0 - - - +
645F ASN* 3.8 19.4 + - - +
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Residues in contact with LYS 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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499A PRO 5.3 5.0 + - - +
500A LYS* 5.0 13.0 - - + +
596A GLU* 4.7 18.6 - - - +
599A ASP* 3.1 38.7 + - - -
535F MET* 3.6 27.1 - - + -
536F GLU* 2.9 28.3 + - - +
539F TYR* 2.2 39.9 + - + +
614F ARG* 3.0 31.5 + - - +
615F ILE 3.0 2.8 + - - -
617F GLN* 1.3 85.1 - - + +
619F ALA* 1.3 55.5 + - - +
620F ARG* 2.9 10.4 + - - +
621F ALA 4.4 0.3 + - - -
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Residues in contact with ALA 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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461F HIS* 4.1 13.7 + - + -
535F MET* 3.7 10.5 - - - -
539F TYR* 4.3 1.3 - - - -
615F ILE* 2.8 29.0 + - + +
616F ALA 4.5 1.4 - - - -
617F GLN 3.6 1.4 - - - -
618F LYS* 1.3 69.4 - - - +
620F ARG* 1.3 63.2 + - - +
621F ALA 3.5 2.0 + - - -
622F ALA* 4.0 9.6 + - - -
623F GLY 4.4 0.9 + - - -
624F ILE* 3.0 46.2 - - + +
625F HIS* 5.1 1.9 + - - -
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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