Contacts of the helix formed by residues 601 - 612 (chain A) in PDB entry 2DB3
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 ILE 601 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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566A MET* 4.0 26.7 - - + -
567A PRO* 3.6 26.9 - - + +
568A SER* 4.2 7.4 - - - +
569A LYS 3.6 7.9 - - - +
570A ILE* 3.5 50.5 - - + +
593A PHE* 4.2 5.8 - - + -
598A ASP* 3.4 21.9 + - + +
599A ARG 3.2 0.2 - - - -
600A ALA* 1.3 76.7 - - + +
602A ALA* 1.3 64.8 + - - +
603A ALA 3.3 2.7 - - - -
604A ASP* 4.1 8.3 - - + +
605A LEU* 3.0 18.1 + - + +
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Residues in contact with ALA 602 (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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593A PHE* 3.9 26.5 - - + -
598A ASP 3.6 0.6 + - - -
599A ARG* 3.1 17.7 + - + +
601A ILE* 1.3 80.0 - - - +
603A ALA* 1.3 63.0 + - - +
605A LEU* 3.4 4.5 + - - +
606A VAL* 3.0 30.5 + - - +
620A LEU* 3.8 24.6 - - + +
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Residues in contact with ALA 603 (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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599A ARG 4.5 1.8 + - - +
600A ALA 4.6 5.8 + - - +
601A ILE 3.3 0.4 - - - -
602A ALA* 1.3 78.2 - - - +
604A ASP* 1.3 67.6 + - - +
606A VAL* 3.3 9.3 + - - +
607A LYS* 3.3 30.0 + - - +
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Residues in contact with ASP 604 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570A ILE* 3.6 36.2 + - + +
600A ALA 4.9 7.2 - - - +
601A ILE* 3.6 10.1 + - + +
602A ALA 3.5 0.2 - - - -
603A ALA* 1.3 76.6 - - - +
605A LEU* 1.3 66.4 + - - +
607A LYS* 3.3 18.5 + - - +
608A ILE* 3.0 26.4 + - + +
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Residues in contact with LEU 605 (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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469A ILE* 4.1 19.3 - - + -
566A MET* 3.8 21.1 - - + -
570A ILE* 3.7 11.1 - - + +
573A TYR* 3.6 44.4 - - + +
593A PHE* 4.3 4.5 - - + -
601A ILE 3.0 20.5 + - - +
602A ALA 3.6 4.7 - - - +
603A ALA 3.3 0.2 - - - -
604A ASP* 1.3 77.8 - - - +
606A VAL* 1.3 57.0 + - - +
608A ILE* 3.3 1.8 + - + +
609A LEU* 2.9 49.4 + - + +
620A LEU* 3.8 26.5 - - + -
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Residues in contact with VAL 606 (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 3.0 19.2 + - - +
603A ALA* 3.5 10.8 - - - +
604A ASP 3.2 0.2 - - - -
605A LEU* 1.3 75.6 - - - +
607A LYS* 1.3 61.1 + - + +
609A LEU* 3.0 10.2 + - - +
610A GLU* 2.8 51.1 + - + +
616A VAL* 3.9 13.0 - - + -
620A LEU* 3.8 31.2 - - + +
621A ARG* 4.2 20.6 - - + +
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Residues in contact with LYS 607 (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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603A ALA* 3.3 16.8 + - - +
604A ASP* 3.3 19.5 + - - +
606A VAL* 1.3 81.6 - - + +
608A ILE* 1.3 56.5 + - + +
610A GLU* 3.9 12.4 - - - +
611A GLY* 2.7 34.1 + - - -
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Residues in contact with ILE 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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459A GLY 3.6 24.2 - - - +
460A GLY* 4.4 3.8 - - - -
461A ALA* 3.4 31.9 + - + +
467A GLN* 4.3 3.1 - - - +
570A ILE* 3.5 25.8 - - + -
573A TYR* 4.1 19.3 - - + -
574A VAL* 4.1 6.3 - - + -
604A ASP 3.0 20.2 + - - +
605A LEU* 3.7 6.3 - - - +
607A LYS* 1.3 77.8 - - + +
609A LEU* 1.3 55.4 + - - +
611A GLY* 3.7 2.0 - - - -
612A SER* 2.7 34.5 + - - -
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Residues in contact with LEU 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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467A GLN* 3.6 31.6 - - + +
469A ILE* 4.2 11.9 - - + -
573A TYR* 4.3 5.8 - - - +
605A LEU* 2.9 31.6 + - + +
606A VAL 3.3 6.3 - - - +
608A ILE* 1.3 74.2 - - - +
610A GLU* 1.3 66.7 + - - +
612A SER* 3.1 9.8 + - - -
613A GLY 3.2 0.2 + - - -
614A GLN* 3.0 43.1 + - + +
615A THR 4.1 14.8 - - - +
616A VAL* 3.9 16.6 - - + -
617A PRO* 4.3 1.6 - - + -
620A LEU* 3.6 29.8 - - + -
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Residues in contact with GLU 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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606A VAL* 2.8 32.0 + - - +
607A LYS* 3.9 10.3 - - - +
609A LEU* 1.3 70.7 - - - +
611A GLY* 1.3 59.4 + - - +
613A GLY* 2.9 21.4 + - - -
614A GLN 4.4 6.3 - - - -
616A VAL* 3.8 14.1 - - + -
621A ARG* 2.8 26.0 + - - +
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Residues in contact with GLY 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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457A ILE* 4.2 24.5 - - - +
461A ALA 5.4 1.8 - - - +
607A LYS 2.7 23.2 + - - -
608A ILE* 3.7 2.9 - - - -
610A GLU* 1.3 73.9 - - - +
612A SER* 1.3 57.1 + - - +
613A GLY 3.4 0.4 + - - -
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Residues in contact with SER 612 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461A ALA* 3.8 25.4 - - - +
463A SER* 3.7 25.7 - - - +
467A GLN* 3.2 26.5 + - - -
608A ILE 2.7 21.5 + - - -
609A LEU 3.3 4.7 + - - -
610A GLU 3.1 0.6 - - - -
611A GLY* 1.3 77.3 - - - +
613A GLY* 1.3 58.7 + - - +
614A GLN* 3.1 17.8 + - - +
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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