Contacts of the helix formed by residues 607 - 621 (chain D) in PDB entry 2O1S
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 ASP 607 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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517D GLU* 3.6 18.4 - - - +
601D ARG* 5.2 2.0 - - + -
602D ALA* 3.3 35.7 - - - +
605D GLY* 4.3 1.2 - - - -
606D LEU* 1.3 79.7 - - - +
608D ALA* 1.3 55.9 + - - +
609D ALA* 3.6 7.9 + - - +
610D GLY* 2.6 36.2 + - - -
611D MSE 2.7 35.8 + - - +
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Residues in contact with ALA 608 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517D GLU* 2.7 24.4 + - - +
520D LYS* 3.9 31.6 - - + -
521D VAL* 3.6 18.7 - - + +
607D ASP* 1.3 71.5 - - - +
609D ALA* 1.3 66.0 + - - +
611D MSE 3.2 0.2 + - - -
612D GLU* 2.9 26.7 + - - +
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Residues in contact with ALA 609 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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607D ASP* 3.3 8.3 + - - +
608D ALA* 1.3 79.4 - - - +
610D GLY* 1.3 62.6 + - - +
612D GLU* 3.4 5.3 + - - +
613D ALA* 3.0 24.6 + - - +
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Residues in contact with GLY 610 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602D ALA 5.8 0.2 - - - -
605D GLY* 3.3 21.8 - - - -
607D ASP* 2.6 23.9 + - - -
609D ALA* 1.3 74.4 - - - +
611D MSE 1.3 60.9 + - - +
613D ALA* 3.4 7.8 + - - +
614D LYS* 3.1 27.0 + - - +
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Residues in contact with MSE 611 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514D LEU* 4.2 15.3 - - + +
517D GLU* 3.9 15.0 - - + -
518D ALA* 4.2 24.2 - - - -
521D VAL* 3.9 11.2 - - + -
556D VAL* 4.0 32.5 - - + -
585D ILE* 4.1 20.9 - - + +
605D GLY 3.3 9.8 + - - +
606D LEU* 2.9 34.1 - - + +
607D ASP 2.7 19.4 + - - +
608D ALA 3.7 3.1 - - - +
610D GLY* 1.3 70.0 - - - +
612D GLU* 1.3 66.0 + - - +
614D LYS* 3.2 5.6 + - - +
615D ILE* 3.0 28.8 + - + +
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Residues in contact with GLU 612 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521D VAL* 4.5 8.0 - - + +
524D SER* 2.6 29.9 + - - -
525D LEU* 3.2 24.2 - - + +
608D ALA 2.9 17.3 + - - +
609D ALA* 3.8 6.5 - - - +
611D MSE 1.3 75.7 - - - +
613D ALA* 1.3 64.0 + - - +
615D ILE* 3.0 10.8 + - - +
616D LYS* 2.9 51.3 + - + +
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Residues in contact with ALA 613 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609D ALA 3.0 14.3 + - - +
610D GLY* 3.5 11.4 - - - +
612D GLU* 1.3 76.3 - - - +
614D LYS* 1.3 56.8 + - + +
616D LYS* 3.1 8.7 + - - +
617D ALA* 2.8 31.5 + - - +
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Residues in contact with LYS 614 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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583D LEU* 3.9 13.1 - - + +
585D ILE* 4.4 18.6 - - + +
586D GLY 4.6 6.3 + - - +
588D PRO* 6.3 0.2 - - - +
604D LEU 2.7 29.1 + - - -
605D GLY* 3.2 22.5 + - - +
606D LEU* 4.2 12.3 - - - +
610D GLY 3.1 12.6 + - - +
611D MSE 3.5 10.1 - - - +
613D ALA* 1.3 78.4 - - + +
615D ILE* 1.3 57.7 + - - +
617D ALA* 3.8 5.6 - - - +
618D TRP* 2.9 32.1 + - - +
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Residues in contact with ILE 615 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506D LEU* 3.6 24.7 - - + -
508D ILE* 4.8 3.4 - - + -
521D VAL* 3.9 26.9 - - + -
525D LEU* 3.9 13.2 - - + -
554D VAL* 4.2 24.7 - - + -
583D LEU* 3.8 20.9 - - + -
585D ILE* 4.6 4.5 - - + -
611D MSE 3.0 21.4 + - + +
612D GLU* 3.0 6.5 + - - +
614D LYS* 1.3 76.4 - - - +
616D LYS* 1.3 61.0 + - + +
618D TRP* 3.5 3.3 - - + +
619D LEU* 2.9 51.7 + - + +
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Residues in contact with LYS 616 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525D LEU* 4.5 11.9 - - - +
612D GLU* 2.9 52.3 + - + +
613D ALA* 3.4 11.2 - - - +
615D ILE* 1.3 79.8 - - + +
617D ALA* 1.3 67.5 + - - +
619D LEU* 3.1 12.0 + - + +
620D ALA* 2.9 24.5 + - - +
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Residues in contact with ALA 617 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613D ALA 2.8 20.5 + - - +
614D LYS* 3.8 6.5 - - - +
616D LYS* 1.3 69.9 - - - +
618D TRP* 1.3 65.0 + - - +
620D ALA* 3.0 18.1 + - - +
621D LEU* 3.3 16.5 + - - +
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Residues in contact with TRP 618 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574C MSE 3.2 27.4 + - - -
575C ALA 3.5 19.1 + - - -
577C ARG* 2.6 50.4 + - + +
506D LEU* 5.0 4.3 - - + -
552D ALA* 3.9 17.9 - - + -
553D LEU 4.4 2.7 - - - -
554D VAL* 5.1 1.8 - - + -
581D PRO* 3.7 24.2 - - + -
582D VAL 3.6 8.7 - - - -
583D LEU* 3.5 60.1 - - + +
614D LYS 2.9 19.7 + - - +
615D ILE* 3.5 5.2 - - + +
617D ALA* 1.3 77.5 - - - +
619D LEU* 1.3 73.8 + - + +
620D ALA 3.2 0.7 + - - -
621D LEU* 3.2 20.4 + - + +
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Residues in contact with LEU 619 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577C ARG* 3.2 25.5 + - - +
506D LEU* 4.8 15.7 - - + -
552D ALA* 5.1 3.8 - - + -
615D ILE* 2.9 42.8 + - + +
616D LYS* 3.8 9.4 - - + +
618D TRP* 1.3 93.7 - - + +
620D ALA* 1.3 58.3 + - - +
621D LEU 3.3 0.6 - - - +
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Residues in contact with ALA 620 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616D LYS 2.9 11.7 + - - +
617D ALA* 3.0 14.3 + - - +
619D LEU* 1.3 75.2 - - - +
621D LEU* 1.3 65.8 + - - +
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Residues in contact with LEU 621 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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575C ALA 3.7 23.6 - - - +
576C HIS* 4.4 16.4 - - - +
577C ARG* 2.8 37.9 + - + +
578C LYS* 5.2 7.5 + - - +
617D ALA 3.3 10.2 + - - +
618D TRP* 3.2 26.3 + - + +
619D LEU 4.1 0.5 - - - +
620D ALA* 1.3 82.8 - - - +
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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