Contacts of the helix formed by residues 607 - 621 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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517C GLU* 3.5 17.9 - - - +
601C ARG* 3.9 2.4 + - + -
602C ALA* 3.8 32.8 - - + +
605C GLY* 4.2 2.4 - - - -
606C LEU* 1.3 75.5 - - - +
608C ALA* 1.3 65.3 + - - +
609C ALA* 4.1 9.8 - - - +
610C GLY* 2.8 28.9 + - - -
611C MSE 2.8 25.0 + - - +
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Residues in contact with ALA 608 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517C GLU* 2.6 22.6 + - - +
520C LYS* 3.7 40.2 - - + +
521C VAL* 3.6 20.1 - - + +
607C ASP* 1.3 70.2 - - - +
609C ALA* 1.3 64.1 + - - +
611C MSE 3.2 0.2 + - - -
612C GLU* 2.9 28.9 + - - +
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Residues in contact with ALA 609 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607C ASP* 3.4 10.6 + - - +
608C ALA* 1.3 78.5 - - - +
610C GLY* 1.3 62.2 + - - +
612C GLU* 3.9 7.2 - - - +
613C ALA* 3.1 24.1 + - - +
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Residues in contact with GLY 610 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602C ALA 5.6 0.2 - - - -
605C GLY* 3.3 21.3 - - - -
607C ASP* 2.8 25.0 + - - -
609C ALA* 1.3 72.4 - - - +
611C MSE 1.3 63.5 + - - +
613C ALA* 3.4 6.9 + - - +
614C LYS* 3.1 26.3 + - - +
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Residues in contact with MSE 611 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514C LEU* 4.2 4.3 - - + -
517C GLU* 4.4 4.5 - - - -
518C ALA* 4.3 18.2 - - - -
521C VAL* 3.7 22.7 - - + -
556C VAL* 3.1 39.9 - - + -
585C ILE* 3.4 38.0 - - + +
605C GLY 3.7 9.6 - - - +
606C LEU* 4.1 23.1 - - + +
607C ASP 2.8 21.7 + - - +
608C ALA 3.7 2.9 - - - +
610C GLY* 1.3 72.3 - - - +
612C GLU* 1.3 66.2 + - - +
614C LYS* 2.9 6.2 + - - +
615C ILE* 2.9 27.2 + - + +
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Residues in contact with GLU 612 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521C VAL* 4.4 13.5 - - + +
524C SER* 2.8 33.6 + - - -
525C LEU* 3.9 20.0 - - + +
608C ALA* 2.9 18.2 + - - +
609C ALA* 3.9 6.3 - - - +
611C MSE 1.3 76.1 - - - +
613C ALA* 1.3 62.9 + - - +
615C ILE* 3.2 6.8 + - - +
616C LYS* 3.0 48.5 + - + +
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Residues in contact with ALA 613 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609C ALA 3.1 18.6 + - - +
610C GLY* 3.6 7.2 - - - +
611C MSE 3.1 0.4 - - - -
612C GLU* 1.3 76.0 - - - +
614C LYS* 1.3 65.2 + - + +
616C LYS* 3.4 6.9 + - - +
617C ALA* 3.0 25.3 + - - +
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Residues in contact with LYS 614 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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583C LEU* 4.1 15.8 - - + +
585C ILE* 4.3 18.5 - - + +
586C GLY 4.5 7.1 + - - +
588C PRO* 6.3 0.4 - - - +
604C LEU 2.9 26.6 + - - -
605C GLY* 3.1 25.6 + - - +
606C LEU* 3.8 14.6 - - - +
610C GLY 3.1 15.1 + - - +
611C MSE 2.9 12.2 + - - +
613C ALA* 1.3 76.4 - - + +
615C ILE* 1.3 59.1 + - - +
617C ALA* 3.4 5.5 + - - +
618C TRP* 2.8 31.0 + - - +
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Residues in contact with ILE 615 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506C LEU* 3.6 26.9 - - + -
508C ILE* 4.9 4.3 - - + -
521C VAL* 3.9 18.6 - - + -
525C LEU* 3.8 25.8 - - + -
554C VAL* 4.3 23.1 - - + -
583C LEU* 3.9 21.1 - - + -
585C ILE* 4.7 4.5 - - + -
611C MSE 2.9 17.0 + - - +
612C GLU* 3.2 6.9 + - - +
614C LYS* 1.3 76.8 - - - +
616C LYS* 1.3 60.3 + - + +
618C TRP* 3.6 6.5 - - + +
619C LEU* 2.9 40.1 + - + +
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Residues in contact with LYS 616 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505C LYS* 5.9 3.4 - - - +
525C LEU* 3.9 27.6 - - + +
612C GLU* 3.0 40.9 + - + +
613C ALA* 3.7 7.6 - - - +
615C ILE* 1.3 80.2 - - + +
617C ALA* 1.3 52.4 + - - +
619C LEU* 3.2 12.3 + - - +
620C ALA* 2.7 36.6 + - - +
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Residues in contact with ALA 617 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613C ALA 3.0 17.5 + - - +
614C LYS* 3.7 5.4 - - - +
616C LYS* 1.3 77.4 - - - +
618C TRP* 1.3 62.3 + - - +
620C ALA* 3.3 8.6 + - - +
621C LEU* 3.2 26.8 + - - +
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Residues in contact with TRP 618 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506C LEU* 5.8 1.3 - - + -
552C ALA* 3.7 18.6 - - + -
553C LEU 4.1 2.7 - - - -
554C VAL* 4.8 4.7 - - + -
581C PRO* 3.6 24.9 - - + -
582C VAL 3.4 23.6 - - - -
583C LEU* 3.5 52.0 - - + +
614C LYS 2.8 18.8 + - - +
615C ILE* 3.6 7.2 - - + +
617C ALA* 1.3 77.6 - - - +
619C LEU* 1.3 83.2 + - + +
621C LEU* 3.4 23.9 - - + +
574D MSE 3.0 22.3 + - - -
575D ALA 3.4 18.2 + - - -
577D ARG* 3.1 38.5 + - + +
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Residues in contact with LEU 619 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505C LYS* 4.3 24.7 - - - +
506C LEU* 4.4 11.2 - - + -
552C ALA* 5.1 4.3 - - + -
615C ILE* 2.9 35.2 + - + +
616C LYS* 3.8 10.8 - - - +
618C TRP* 1.3 95.4 - - + +
620C ALA* 1.3 65.9 + - - +
621C LEU 3.1 0.2 - - - -
577D ARG* 3.1 32.0 + - - +
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Residues in contact with ALA 620 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616C LYS 2.7 18.6 + - - +
617C ALA* 3.3 11.6 + - - +
619C LEU* 1.3 75.5 - - - +
621C LEU* 1.3 65.5 + - - +
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Residues in contact with LEU 621 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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617C ALA 3.2 11.9 + - - +
618C TRP* 3.4 28.7 - - + +
619C LEU 3.1 1.2 - - - -
620C ALA* 1.3 83.6 - - - +
575D ALA 3.8 21.3 - - - +
576D HIS* 4.3 21.5 - - + +
577D ARG* 3.5 21.3 - - - +
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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