Contacts of the helix formed by residues 606 - 614 (chain A) in PDB entry 2IUK
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 ALA 606 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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603A THR 3.6 16.0 + - - +
605A GLN* 1.3 75.9 - - - +
607A LEU* 1.3 61.7 + - - +
608A PRO* 3.4 2.5 - - + -
609A ALA* 3.0 9.7 + - + +
610A ASP* 2.8 24.8 + - - +
644A TRP* 3.6 30.7 - - + -
703A GLN* 3.8 13.5 - - - +
707A ILE* 3.8 11.2 - - + +
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Residues in contact with LEU 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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605A GLN 3.5 4.1 + - - -
606A ALA* 1.3 69.5 - - - +
608A PRO* 1.4 57.5 - - + +
610A ASP* 3.7 14.4 - - - +
611A LEU* 2.7 53.6 + - + +
636A TYR* 3.6 35.2 - - + +
637A ALA* 4.3 2.2 - - - +
640A GLY* 3.9 4.7 - - - -
641A LEU* 3.4 48.5 - - + +
644A TRP* 4.0 11.5 - - + -
710A TRP* 3.6 30.0 - - + +
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Residues in contact with PRO 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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606A ALA* 3.4 4.5 - - + -
607A LEU* 1.4 92.0 - - + +
609A ALA* 1.3 56.8 + - - +
611A LEU* 3.8 1.6 - - + +
612A VAL* 2.8 35.8 + - - +
625A HIS* 5.2 5.4 - - + +
627A LEU* 3.9 29.6 - - + -
641A LEU* 4.4 6.7 - - + -
644A TRP* 3.3 41.7 - - + +
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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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603A THR 3.4 22.9 - - - +
604A HIS* 4.2 11.2 + - - +
606A ALA* 3.0 13.9 + - + +
608A PRO* 1.3 78.8 - - - +
610A ASP* 1.3 63.3 + - - +
612A VAL* 4.4 4.3 - - - -
613A LYS* 3.1 35.2 + - - +
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Residues in contact with ASP 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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381A ASN* 3.8 15.1 - - - +
604A HIS* 3.4 21.7 + - - +
605A GLN* 5.0 2.2 - - - +
606A ALA 2.8 10.1 + - - +
607A LEU* 3.4 24.1 - - - +
609A ALA* 1.3 75.9 - - - +
611A LEU* 1.3 65.0 + - - +
613A LYS* 3.2 11.7 + - - +
614A ARG* 2.9 54.5 + - - +
636A TYR* 4.4 1.9 + - - -
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Residues in contact with LEU 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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607A LEU* 2.7 52.3 + - + +
608A PRO* 3.8 3.6 - - + +
610A ASP* 1.3 75.6 - - - +
612A VAL* 1.3 62.6 + - - +
614A ARG* 3.1 35.7 + - - +
616A LEU* 3.1 31.8 + - + +
617A ALA* 3.7 17.5 - - + -
627A LEU* 4.7 0.7 - - + -
629A LEU* 4.2 11.0 - - + -
634A TYR* 4.1 15.5 - - + +
636A TYR* 4.9 0.7 - - + -
637A ALA* 3.7 21.3 - - + -
641A LEU* 4.3 8.5 - - + -
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Residues in contact with VAL 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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608A PRO 2.8 24.0 + - - +
609A ALA* 4.0 3.6 - - - +
611A LEU* 1.3 72.4 - - - +
613A LYS* 1.3 77.0 + - - +
615A GLY* 3.5 9.9 + - - -
617A ALA* 3.7 24.5 - - + +
619A GLU* 4.3 28.0 - - + +
627A LEU* 3.5 27.4 - - + -
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Residues in contact with LYS 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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604A HIS* 3.4 40.5 + - + +
609A ALA* 3.1 42.2 + - - +
610A ASP* 3.2 5.6 + - - +
612A VAL* 1.3 90.7 - - - +
614A ARG* 1.3 60.5 + - + +
615A GLY 3.4 0.9 + - - -
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Residues in contact with ARG 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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381A ASN* 2.9 28.4 + - - +
382A VAL* 4.8 0.4 - - - +
383A ILE* 2.7 47.2 + - - +
384A ARG* 3.2 13.6 - - + +
385A ARG 3.0 25.2 + - - -
610A ASP* 2.9 39.9 + - - +
611A LEU* 3.1 29.2 + - - +
613A LYS* 1.3 76.3 - - + +
615A GLY* 1.3 59.3 + - - +
616A LEU* 3.3 18.2 - - + +
634A TYR* 2.9 28.9 + - - -
636A TYR* 4.5 1.2 - - - -
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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