Contacts of the helix formed by residues 606 - 620 (chain O) in PDB entry 6R7H
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 ASN 606 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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525O SER* 4.8 13.0 - - - +
600O GLN* 6.2 0.7 - - - -
605O MET* 1.3 87.8 - - - +
607O GLU* 1.3 65.3 + - + +
608O LYS* 3.3 13.3 + - + +
609O GLU* 3.6 8.0 + - + +
610O LEU* 3.6 15.8 + - - +
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Residues in contact with GLU 607 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596O TYR* 4.0 8.4 + - - +
600O GLN* 3.5 29.4 + - - +
606O ASN* 1.3 73.2 - - + +
608O LYS* 1.3 74.8 + - + +
609O GLU 3.3 0.2 - - - -
610O LEU* 3.6 6.9 + - - -
611O THR* 2.7 33.8 + - - -
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Residues in contact with LYS 608 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606O ASN* 3.3 9.1 - - + -
607O GLU* 1.3 94.5 - - + +
609O GLU* 1.3 60.3 + - - +
611O THR* 3.8 10.7 + - - -
612O LYS* 3.8 20.3 + - - +
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Residues in contact with GLU 609 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525O SER* 3.0 22.3 + - - -
558O TYR* 3.1 26.6 + - + -
580O TYR* 2.9 40.6 + - + -
605O MET* 3.5 21.7 - - + +
606O ASN* 3.6 8.2 + - + +
607O GLU 3.3 0.2 - - - -
608O LYS* 1.3 77.7 - - - +
610O LEU* 1.3 64.0 + - - +
611O THR 3.2 0.7 - - - -
612O LYS* 3.6 7.1 + - + +
613O THR* 2.9 29.5 + - - +
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Residues in contact with LEU 610 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584O VAL* 4.7 4.3 - - + -
596O TYR* 4.4 16.6 - - + +
599O LEU* 3.6 50.5 - - + +
600O GLN* 3.8 26.2 - - + -
603O THR* 4.0 11.4 - - + +
605O MET* 3.7 21.2 - - + +
606O ASN 3.6 14.8 + - - +
607O GLU* 3.6 6.5 + - - +
608O LYS 3.4 0.4 - - - -
609O GLU* 1.3 76.7 - - - +
611O THR* 1.3 60.0 + - - +
613O THR* 4.3 9.9 - - - -
614O ILE* 3.0 31.8 + - + +
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Residues in contact with THR 611 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596O TYR* 3.6 11.7 + - - +
607O GLU 2.7 23.1 + - - -
608O LYS* 3.9 9.1 - - - -
609O GLU 3.2 0.6 - - - -
610O LEU* 1.3 76.6 - - - +
612O LYS* 1.3 74.7 + - + +
614O ILE* 3.4 10.7 - - + +
615O LYS* 3.2 24.1 + - + +
632O ILE* 5.2 10.9 - - + +
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Residues in contact with LYS 612 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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608O LYS 3.8 17.3 + - - +
609O GLU* 3.6 7.5 + - + +
610O LEU 3.4 0.2 - - - -
611O THR* 1.3 89.7 - - - +
613O THR* 1.3 61.9 + - - +
615O LYS* 3.7 6.1 + - - +
616O SER* 3.7 19.9 + - - -
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Residues in contact with THR 613 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580O TYR* 4.2 39.1 - - + +
581O GLN* 4.7 6.5 + - + +
584O VAL* 4.6 8.3 - - + -
605O MET* 4.4 7.4 - - + +
609O GLU* 2.9 22.1 + - - +
610O LEU* 3.8 11.8 - - + -
611O THR 3.2 1.0 - - - -
612O LYS* 1.3 76.8 - - - +
614O ILE* 1.3 64.0 + - - +
615O LYS 3.2 0.7 + - - -
616O SER* 3.5 6.1 + - - -
617O LEU* 3.4 33.5 + - + +
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Residues in contact with ILE 614 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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596O TYR* 4.6 9.0 - - + -
599O LEU* 4.2 20.4 - - + -
610O LEU* 3.0 25.9 + - + +
611O THR* 3.4 12.1 - - - +
613O THR* 1.3 74.9 - - - +
615O LYS* 1.3 66.5 + - - +
616O SER 3.4 0.2 - - - -
617O LEU* 3.9 8.1 - - + -
618O LEU* 3.2 22.2 + - + +
623O ILE* 3.8 29.6 - - + -
632O ILE* 4.2 25.1 - - + +
638O PHE* 3.7 37.7 - - + -
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Residues in contact with LYS 615 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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611O THR* 3.2 19.8 + - + +
612O LYS* 3.9 9.2 - - + +
613O THR 3.2 1.0 - - - -
614O ILE* 1.3 80.1 - - - +
616O SER* 1.3 62.0 + - - +
618O LEU* 3.4 16.1 + - + +
619O ASP* 3.0 43.3 + - - +
632O ILE* 3.9 23.0 - - + +
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Residues in contact with SER 616 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581O GLN* 4.9 13.0 - - - -
612O LYS 3.7 10.4 + - - -
613O THR* 3.5 8.8 + - - -
615O LYS* 1.3 78.9 - - - +
617O LEU* 1.3 62.0 + - - +
618O LEU 3.5 0.5 + - - -
619O ASP* 3.7 11.8 + - - +
620O VAL* 3.4 21.5 + - - +
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Residues in contact with LEU 617 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581O GLN* 3.4 38.1 - - + +
584O VAL* 4.3 14.1 - - + -
585O LEU* 5.7 3.4 - - + -
613O THR* 3.4 34.2 + - + +
614O ILE* 4.0 11.4 - - + +
615O LYS 3.3 0.6 - - - -
616O SER* 1.3 78.4 - - - +
618O LEU* 1.3 60.2 + - - +
619O ASP 3.5 0.2 - - - -
620O VAL* 3.4 12.9 - - - +
622O MET* 3.7 26.5 - - + -
623O ILE* 3.2 54.5 + - + +
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Residues in contact with LEU 618 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614O ILE* 3.2 17.0 + - + +
615O LYS* 3.9 12.1 - - + +
616O SER 3.3 0.4 - - - -
617O LEU* 1.3 77.2 - - - +
619O ASP* 1.3 68.4 + - - +
620O VAL 3.3 7.8 - - - +
623O ILE* 3.5 19.4 - - + +
624O ASN* 4.7 3.6 + - - +
625O HIS* 4.3 30.5 - - + +
630O GLU 4.9 9.6 - - - +
631O ASP* 5.3 1.6 - - - -
632O ILE* 3.9 30.7 - - + +
638O PHE* 4.4 21.1 - - + -
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Residues in contact with ASP 619 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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615O LYS* 3.0 42.2 + - - +
616O SER* 3.7 8.1 + - - +
617O LEU 3.5 0.2 - - - -
618O LEU* 1.3 79.2 - - - +
620O VAL* 1.3 62.7 + - + +
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Residues in contact with VAL 620 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616O SER 3.4 20.6 - - - +
617O LEU* 3.4 18.4 - - - +
618O LEU 3.3 10.2 - - - +
619O ASP* 1.3 85.5 - - + +
621O LYS* 1.3 65.5 + - - +
622O MET* 3.4 25.6 + - + +
623O ILE 4.4 3.3 - - - +
624O ASN* 5.5 3.8 + - - -
644O PHE* 4.2 14.1 - - + -
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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