Contacts of the helix formed by residues 594 - 603 (chain A) in PDB entry 1OAK
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 THR 594 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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558A TYR* 3.7 24.7 - - + +
592A ALA 3.4 5.1 + - - +
593A SER* 1.3 69.2 - - - +
595A SER* 1.3 68.3 + - - +
597A VAL* 3.1 9.9 + - - +
598A LEU* 3.0 29.5 + - - +
620A LEU* 4.1 22.2 - - + -
622A MET* 4.4 13.9 - - + -
624A SER* 5.6 4.7 - - - +
626A GLU* 3.0 10.2 + - - +
634A PHE* 4.2 3.8 - - - -
658A ASN* 5.8 0.4 - - + -
661A GLN* 2.4 35.7 + - - +
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Residues in contact with SER 595 (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 SER* 3.3 1.1 - - - -
594A THR* 1.3 79.5 + - - +
596A GLU* 1.3 57.5 + - - +
598A LEU* 3.8 3.2 - - - +
599A LYS* 2.9 31.9 + - - +
626A GLU* 2.5 26.4 + - - -
630A MET 3.0 22.5 + - - -
631A SER* 3.5 6.6 - - - -
634A PHE* 3.6 20.0 - - - +
637A TYR* 3.7 23.1 - - - -
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Residues in contact with GLU 596 (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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559A HIS 5.3 0.4 - - - +
560A ASP 3.8 20.8 - - - +
561A GLY* 5.4 5.1 - - - -
562A SER* 4.4 4.2 + - - +
593A SER* 3.1 28.3 + - - +
595A SER* 1.3 81.3 - - - +
597A VAL* 1.3 57.4 + - - +
599A LYS* 3.5 27.2 + - - +
600A TYR* 2.8 30.4 + - - +
630A MET* 4.4 7.2 - - + -
637A TYR* 6.0 0.3 - - - -
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Residues in contact with VAL 597 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518A LEU* 3.9 27.8 - - + -
556A VAL* 4.5 5.2 - - + -
558A TYR* 3.3 51.1 - - + -
562A SER* 3.9 10.5 + - - +
593A SER 2.6 28.4 + - - +
594A THR* 3.2 13.9 - - - +
596A GLU* 1.3 71.8 - - - +
598A LEU* 1.3 54.4 + - - +
600A TYR* 3.2 5.7 + - + +
601A THR* 2.6 41.2 + - - +
620A LEU* 4.5 2.7 - - + -
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Residues in contact with LEU 598 (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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518A LEU* 4.5 14.4 - - + -
594A THR 3.0 19.1 + - - +
595A SER* 3.8 3.6 - - - +
597A VAL* 1.3 74.5 - - - +
599A LYS* 1.3 54.8 + - - +
601A THR* 3.1 6.3 + - - +
602A LEU* 2.7 36.7 + - - +
618A ALA* 5.0 3.4 - - + -
620A LEU* 4.3 24.0 - - + -
634A PHE* 3.5 33.9 - - + -
637A TYR* 4.2 11.9 - - + -
638A VAL* 3.9 16.2 - - + -
641A LEU* 3.6 26.8 - - + +
648A VAL* 4.5 11.0 - - + -
665A ILE* 4.7 2.7 - - + -
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Residues in contact with LYS 599 (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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595A SER 2.9 18.6 + - - +
596A GLU* 3.6 29.2 + - - +
598A LEU* 1.3 78.2 - - - +
600A TYR* 1.3 57.9 + - - +
602A LEU* 4.3 1.3 - - - -
603A PHE* 2.8 60.4 + - + +
637A TYR* 3.4 44.3 - - + +
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Residues in contact with TYR 600 (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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518A LEU* 5.8 0.2 - - + -
556A VAL* 4.2 15.0 - - + -
562A SER* 3.6 35.9 - - - +
564A ALA* 3.4 23.2 - - + +
596A GLU* 2.8 20.7 + - - +
597A VAL* 3.5 6.7 - - + +
599A LYS* 1.3 75.8 - - - +
601A THR* 1.3 63.9 + - - +
603A PHE* 5.3 0.2 - - - -
604A GLN* 2.8 68.6 + - + +
605A ILE* 3.2 29.3 + - + +
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Residues in contact with THR 601 (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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516A VAL* 4.9 2.2 - - + -
518A LEU* 3.6 24.3 - - - +
597A VAL 2.6 26.0 + - - -
598A LEU* 3.3 8.7 - - - -
600A TYR* 1.3 73.4 - - - +
602A LEU* 1.3 55.2 - - - +
605A ILE* 3.3 19.0 - - + +
606A PHE* 2.8 61.4 + - + -
618A ALA* 4.5 15.5 - - + -
641A LEU* 4.1 10.5 - - + -
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Residues in contact with LEU 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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598A LEU 2.7 20.7 + - - +
599A LYS 3.6 3.6 - - - +
601A THR* 1.3 74.2 - - - +
603A PHE* 1.3 91.1 + - + +
606A PHE* 3.4 13.1 - - + -
636A ARG 5.1 0.9 - - - +
637A TYR* 4.1 18.8 - - + +
640A GLY* 3.5 43.1 - - - +
641A LEU* 3.6 15.3 - - + -
644A LYS* 3.2 43.0 + - + +
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Residues in contact with PHE 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 LYS* 2.8 49.4 + - + +
600A TYR* 5.3 0.2 - - - -
602A LEU* 1.3 101.3 - - + +
604A GLN* 1.3 73.2 + - + +
607A SER* 3.2 19.7 - - - +
637A TYR* 3.9 23.8 - + - -
644A LYS* 5.1 3.4 - - - +
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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