Contacts of the helix formed by residues 595 - 609 (chain A) in PDB entry 1OAI
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 595 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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592A ASN 3.1 15.9 + - - +
593A ASN* 3.1 8.0 + - + +
594A TRP* 1.3 75.3 - - - +
596A TYR* 1.3 59.1 + - - +
597A THR* 3.4 9.0 + - - -
598A ARG* 3.1 35.4 + - - +
599A SER* 2.8 34.5 + - - -
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Residues in contact with TYR 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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570A MET* 3.8 45.3 - - + -
573A ALA* 3.2 31.4 + - + +
574A PHE* 3.3 28.0 - + + -
577A GLN* 2.7 31.1 + - - +
589A LEU* 4.4 3.6 - - + -
594A TRP 3.8 3.8 + - - -
595A ASP* 1.3 72.0 + - - +
597A THR* 1.3 59.6 + - - +
599A SER* 3.2 6.4 + - - -
600A ALA* 2.8 35.4 + - + +
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Residues in contact with THR 597 (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 ASP* 3.4 7.4 + - - -
596A TYR* 1.3 80.7 - - - +
598A ARG* 1.3 64.7 + - + +
600A ALA* 3.4 5.9 + - - +
601A GLN* 3.1 28.5 + - - +
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Residues in contact with ARG 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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591A ASP 4.3 0.6 + - - -
592A ASN* 3.0 33.7 + - + +
593A ASN* 3.1 24.3 - - - +
595A ASP* 3.1 30.8 + - - +
597A THR* 1.3 81.2 - - - +
599A SER* 1.3 57.7 + - - +
601A GLN* 3.3 8.5 + - - +
602A ALA* 2.9 28.5 + - + +
16B GLY* 6.0 0.2 - - - -
17B SER* 3.7 14.0 + - - +
18B LYS* 3.6 42.0 - - - +
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Residues in contact with SER 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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574A PHE* 3.6 18.5 - - - -
588A CYS* 3.7 7.6 - - - -
589A LEU* 3.5 25.1 + - - +
592A ASN* 3.2 25.2 - - - +
595A ASP 2.8 23.2 + - - -
596A TYR 3.5 5.2 - - - -
598A ARG* 1.3 78.1 - - - +
600A ALA* 1.3 56.8 + - - +
602A ALA* 3.7 1.4 - - - +
603A PHE* 2.9 31.0 + - - +
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Residues in contact with ALA 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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574A PHE* 3.6 15.2 - - + -
596A TYR* 2.8 27.3 + - + +
597A THR* 3.8 6.1 - - - +
599A SER* 1.3 74.3 - - - +
601A GLN* 1.3 65.2 + - - +
603A PHE* 3.4 3.8 + - - +
604A THR* 2.9 31.2 + - - +
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Residues in contact with GLN 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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597A THR* 3.1 22.7 + - + +
598A ARG* 3.6 6.8 - - - +
600A ALA* 1.3 75.4 - - - +
602A ALA* 1.3 64.2 + - - +
604A THR* 3.3 6.2 + - - -
605A HIS* 3.0 26.5 + - + +
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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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592A ASN* 3.7 11.2 - - - +
598A ARG* 2.9 18.1 + - + +
599A SER 3.7 3.6 - - - +
601A GLN* 1.3 77.8 + - - +
603A PHE* 1.3 63.8 + - - +
605A HIS* 3.4 7.4 + - - +
606A LEU* 3.2 29.5 + - - +
15B PHE* 4.4 1.8 - - + -
16B GLY* 3.4 37.5 - - - +
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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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574A PHE* 4.0 11.4 - + + -
578A SER* 3.4 36.1 - - - -
580A MET* 3.6 37.0 - - + -
588A CYS* 4.2 4.2 - - - -
599A SER 2.9 17.3 + - - +
600A ALA* 3.7 4.3 - - - +
602A ALA* 1.3 77.3 - - - +
604A THR* 1.3 68.5 + - - +
606A LEU* 3.3 1.7 + - - -
607A LYS* 2.8 50.7 + - + +
612A ILE* 3.5 25.4 - - + +
617A PHE* 3.9 9.6 - + - -
15B PHE* 4.4 10.1 - + - -
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Residues in contact with THR 604 (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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600A ALA* 2.9 20.3 + - - +
601A GLN* 3.3 6.3 + - - -
603A PHE* 1.3 86.8 - - - +
605A HIS* 1.3 63.1 + - - +
607A LYS* 3.8 4.1 - - - +
608A ALA* 3.1 25.5 + - + +
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Residues in contact with HIS 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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601A GLN* 3.0 18.1 + - + +
602A ALA* 3.5 8.3 + - - +
604A THR* 1.3 79.3 - - - +
606A LEU* 1.3 69.2 + - + +
608A ALA* 3.5 4.9 + - - +
609A LYS* 3.3 58.9 + - + +
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Residues in contact with LEU 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 3.2 16.6 + - - +
603A PHE 4.0 1.1 - - - +
605A HIS* 1.3 85.4 - - - +
607A LYS* 1.3 65.7 + - - +
609A LYS* 3.3 20.3 + - - +
611A GLU* 3.2 48.7 + - + +
612A ILE* 3.8 17.0 + - + +
13B PHE* 3.8 28.3 - - + -
14B SER 3.9 4.7 - - - +
15B PHE* 3.8 31.2 - - + -
16B GLY 4.2 4.5 - - - +
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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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578A SER 5.6 0.2 - - - -
603A PHE* 2.8 35.2 + - + +
604A THR* 3.8 4.9 - - - +
606A LEU* 1.3 77.6 - - - +
608A ALA* 1.3 63.9 + - - +
610A GLY* 2.9 15.5 + - - -
611A GLU 5.2 0.4 - - - +
612A ILE* 3.7 12.0 - - + +
617A PHE* 3.7 38.1 - - + -
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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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604A THR* 3.1 18.6 + - + +
605A HIS* 3.8 6.3 - - - +
606A LEU 3.3 0.2 - - - -
607A LYS* 1.3 77.8 - - - +
609A LYS* 1.3 62.2 + - + +
610A GLY* 3.1 1.4 + - - -
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Residues in contact with LYS 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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605A HIS* 3.3 52.7 + - + +
606A LEU* 3.3 16.7 + - - +
607A LYS 3.2 0.8 - - - -
608A ALA* 1.3 77.6 - - + +
610A GLY* 1.3 61.2 + - - +
611A GLU* 3.4 40.7 + - + +
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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