Contacts of the helix formed by residues 607 - 620 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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517A GLU* 3.4 20.4 - - + +
601A ARG* 5.3 2.0 - - + -
602A ALA* 3.4 35.2 - - - +
605A GLY* 4.2 1.2 - - - -
606A LEU* 1.3 80.5 + - - +
608A ALA* 1.3 69.3 + - - +
609A ALA* 4.4 6.8 - - - +
610A GLY* 2.9 22.4 + - - -
611A MSE 2.8 23.2 + - - +
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Residues in contact with ALA 608 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517A GLU* 2.7 21.9 + - - +
520A LYS* 3.7 35.9 - - + +
521A VAL* 3.6 20.1 - - + +
607A ASP* 1.3 72.9 - - - +
609A ALA* 1.3 64.3 + - - +
611A MSE 3.3 0.3 + - - -
612A GLU* 3.1 21.6 + - - +
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Residues in contact with ALA 609 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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607A ASP* 3.3 7.5 + - - +
608A ALA* 1.3 79.3 - - - +
610A GLY* 1.3 64.0 + - - +
612A GLU* 3.2 6.2 + - - +
613A ALA* 3.1 23.3 + - - +
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Residues in contact with GLY 610 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602A ALA 5.7 0.2 - - - -
605A GLY* 3.6 21.9 - - - -
607A ASP* 2.9 19.2 + - - -
609A ALA* 1.3 76.1 - - - +
611A MSE 1.3 62.5 + - - +
613A ALA* 3.3 8.4 + - - +
614A LYS* 3.1 25.6 + - - +
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Residues in contact with MSE 611 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514A LEU* 3.9 22.0 - - + -
517A GLU* 3.9 13.9 - - + -
518A ALA* 4.2 21.8 - - - -
521A VAL* 3.8 12.6 - - + -
556A VAL* 4.2 23.3 - - + -
585A ILE* 4.1 23.0 - - + +
605A GLY 3.5 10.3 + - - +
606A LEU* 2.9 38.6 - - + +
607A ASP 2.8 18.8 + - - +
608A ALA 3.7 3.4 - - - +
610A GLY* 1.3 70.8 - - - +
612A GLU* 1.3 65.0 + - - +
614A LYS* 3.2 4.9 + - - +
615A ILE* 3.0 30.7 + - + +
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Residues in contact with GLU 612 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521A VAL* 4.4 9.4 - - + +
524A SER* 2.8 31.4 + - - -
525A LEU* 4.0 19.6 - - + +
608A ALA 3.1 16.7 + - - +
609A ALA* 3.7 6.5 - - - +
611A MSE 1.3 76.0 - - - +
613A ALA* 1.3 57.2 + - - +
615A ILE* 3.2 9.8 + - - +
616A LYS* 2.8 64.9 + - + +
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Residues in contact with ALA 613 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609A ALA 3.1 12.5 + - - +
610A GLY* 3.5 11.7 - - - +
611A MSE 3.2 0.2 - - - -
612A GLU* 1.3 76.7 - - - +
614A LYS* 1.3 57.2 + - + +
616A LYS* 3.0 9.5 + - - +
617A ALA* 2.8 31.5 + - - +
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Residues in contact with LYS 614 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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583A LEU* 4.1 13.4 - - + +
585A ILE* 4.2 24.3 - - + +
586A GLY 4.6 7.1 + - - +
604A LEU 2.8 28.5 + - - -
605A GLY* 3.1 26.0 + - - +
606A LEU* 4.2 11.3 - - - +
610A GLY 3.1 12.4 + - - +
611A MSE 3.5 7.0 - - - +
613A ALA* 1.3 75.8 - - + +
615A ILE* 1.3 58.7 + - - +
617A ALA* 3.2 6.2 + - - +
618A TRP* 2.8 31.7 + - - +
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Residues in contact with ILE 615 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506A LEU* 3.8 24.2 - - + -
508A ILE* 4.8 3.6 - - + -
521A VAL* 3.9 26.5 - - + -
525A LEU* 4.2 12.8 - - + -
554A VAL* 4.2 25.4 - - + -
583A LEU* 3.7 23.6 - - + -
585A ILE* 4.4 4.9 - - + -
611A MSE 3.0 16.2 + - + +
612A GLU* 3.5 7.0 - - - +
614A LYS* 1.3 74.8 - - - +
616A LYS* 1.3 60.4 + - + +
618A TRP* 3.7 3.7 - - + +
619A LEU* 3.0 43.8 + - + +
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Residues in contact with LYS 616 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525A LEU* 4.1 21.3 - - + +
612A GLU* 2.8 48.0 + - + +
613A ALA* 3.3 11.7 - - - +
615A ILE* 1.3 82.7 - - + +
617A ALA* 1.3 62.7 + - - +
619A LEU* 3.9 7.2 - - + +
620A ALA* 3.0 24.5 + - - +
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Residues in contact with ALA 617 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613A ALA 2.8 18.8 + - - +
614A LYS* 3.7 6.1 - - - +
616A LYS* 1.3 72.8 - - - +
618A TRP* 1.3 63.1 + - - +
620A ALA* 3.2 24.1 + - - +
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Residues in contact with TRP 618 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506A LEU* 5.3 1.1 - - + -
552A ALA* 3.8 17.5 - - + -
553A LEU 4.0 2.7 - - - -
554A VAL* 5.0 4.0 - - + -
581A PRO* 3.5 39.5 - - + -
582A VAL 3.5 21.3 - - - -
583A LEU* 3.5 47.9 - - + +
614A LYS 2.8 20.5 + - - +
615A ILE* 3.7 5.8 - - + +
617A ALA* 1.3 73.5 - - - +
619A LEU* 1.3 86.8 + - + +
620A ALA 3.4 6.2 - - - +
574B MSE 3.0 23.1 + - - -
575B ALA 3.3 19.3 + - - -
576B HIS 4.9 0.2 - - - -
577B ARG* 3.4 30.0 + - + +
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Residues in contact with LEU 619 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505A LYS* 3.5 28.0 - - - +
506A LEU* 4.8 6.1 - - + -
552A ALA* 4.8 9.6 - - + -
615A ILE* 3.0 37.4 + - + +
616A LYS* 4.0 7.9 - - + +
618A TRP* 1.3 104.3 - - + +
620A ALA* 1.3 62.5 + - - +
577B ARG* 3.6 26.5 + - - +
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Residues in contact with ALA 620 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616A LYS 3.0 18.3 + - - +
617A ALA* 3.4 16.0 - - - +
618A TRP 3.2 9.8 - - - +
619A LEU* 1.3 82.4 - - - +
577B ARG* 4.4 7.0 + - - -
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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