Contacts of the helix formed by residues 571 - 589 (chain A) in PDB entry 5OQN
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 SER 571 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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493A ASP* 2.7 23.3 + - - -
497A GLN* 5.2 6.8 - - - +
569A GLU 3.7 1.3 + - - -
570A ALA* 1.3 75.2 - - - +
572A SER* 1.3 71.3 + - - +
573A ALA* 3.9 11.2 + - - +
574A THR* 3.0 19.1 + - - -
575A ILE* 3.1 10.4 + - - +
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Residues in contact with SER 572 (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 ALA 3.6 1.2 + - - -
571A SER* 1.3 74.6 + - - +
573A ALA* 1.3 67.9 + - - +
575A ILE* 3.2 21.9 + - - +
576A VAL* 3.2 15.3 + - - +
613A ASN* 5.8 0.9 - - - -
618A ILE* 3.7 18.1 - - - +
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Residues in contact with ALA 573 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571A SER* 3.1 8.3 + - - +
572A SER* 1.3 81.6 + - - +
574A THR* 1.3 56.2 + - - +
576A VAL* 2.6 34.0 + - - +
577A LEU* 3.0 22.3 - - + +
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Residues in contact with THR 574 (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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489A ILE* 3.4 40.6 + - + +
490A ARG* 4.0 3.6 - - - -
493A ASP* 3.8 18.0 + - + +
570A ALA* 3.8 21.1 - - + -
571A SER* 3.0 13.2 + - - -
573A ALA* 1.3 76.9 - - - +
575A ILE* 1.3 61.8 + - - +
577A LEU* 3.1 11.0 + - - +
578A CYS* 3.0 26.7 + - - -
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Residues in contact with ILE 575 (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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569A GLU* 4.9 5.8 - - + +
570A ALA* 3.5 26.2 - - + +
571A SER 3.1 10.9 + - - +
572A SER* 3.3 15.5 - - - +
573A ALA 2.9 1.0 + - - -
574A THR* 1.3 75.3 - - - +
576A VAL* 1.3 63.2 + - - +
578A CYS* 3.7 5.3 + - - +
579A LEU* 3.2 42.9 + - + +
606A LEU* 3.9 35.7 - - + -
610A ALA* 5.0 2.2 - - + -
613A ASN* 4.8 12.3 - - - +
618A ILE* 4.0 15.9 - - + -
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Residues in contact with VAL 576 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572A SER 3.2 15.2 + - - +
573A ALA* 2.6 19.1 + - - +
575A ILE* 1.3 71.3 - - - +
577A LEU* 1.3 67.8 + - + +
579A LEU* 3.0 4.0 + - - +
580A THR* 2.9 35.4 + - + +
617A ASN* 4.8 13.0 - - - +
618A ILE* 3.9 20.2 - - + -
621A LEU* 3.8 24.9 - - + -
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Residues in contact with LEU 577 (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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454A THR* 3.0 42.4 - - - +
456A LEU 5.4 5.4 - - - +
461A ILE* 5.5 2.9 - - + -
489A ILE* 5.1 11.2 - - + -
573A ALA* 3.0 39.3 - - + +
574A THR* 3.1 10.5 + - - +
576A VAL* 1.3 82.4 - - + +
578A CYS* 1.3 63.8 + - - +
580A THR* 3.0 20.2 + - - -
581A ARG* 3.1 40.7 + - - +
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Residues in contact with CYS 578 (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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486A ILE* 3.6 44.6 - - + +
489A ILE* 4.6 7.4 - - - -
490A ARG* 4.2 11.4 - - - -
574A THR* 3.0 35.4 + - - +
575A ILE* 4.1 6.3 - - - +
577A LEU* 1.3 78.0 - - - +
579A LEU* 1.3 60.3 + - + +
581A ARG* 3.4 7.5 + - - +
582A SER* 3.0 28.9 + - - -
602A LEU* 5.7 2.5 - - + -
606A LEU* 6.0 7.4 - - + -
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Residues in contact with LEU 579 (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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575A ILE* 3.2 38.8 + - + +
576A VAL* 3.0 6.0 + - - +
578A CYS* 1.3 77.2 - - + +
580A THR* 1.3 64.8 + - - +
582A SER* 2.6 20.6 + - - +
583A SER* 3.0 3.3 + - - -
602A LEU* 6.3 1.6 - - + -
606A LEU* 4.6 6.3 - - + +
607A ILE* 4.2 24.0 - - + +
610A ALA* 3.7 26.5 - - + -
618A ILE* 4.3 6.1 - - + -
621A LEU* 4.1 20.9 - - + -
622A GLY* 4.7 1.3 - - - -
625A ASN* 2.8 38.1 - - - +
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Residues in contact with THR 580 (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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458A GLU* 4.9 16.4 - - - +
461A ILE* 4.3 16.2 - - - +
576A VAL* 2.9 22.0 + - + +
577A LEU* 3.0 14.4 + - - -
579A LEU* 1.3 74.9 - - - +
581A ARG* 1.3 62.9 + - - +
583A SER* 2.7 22.4 + - - -
584A TYR* 3.0 27.4 + - - -
621A LEU* 3.8 27.8 - - + -
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Residues in contact with ARG 581 (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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451A LEU* 2.9 26.3 + - - +
453A LEU 2.9 28.9 + - - -
456A LEU* 4.0 8.3 - - - +
461A ILE* 3.6 47.7 - - + +
465A ILE* 4.4 17.4 - - + +
485A ILE* 4.9 5.4 - - - -
486A ILE* 4.3 21.0 - - + +
489A ILE* 3.8 17.4 - - - +
577A LEU* 3.1 46.1 + - - +
578A CYS* 3.6 6.1 - - - +
580A THR* 1.3 82.3 + - - +
582A SER* 1.3 61.4 + - - +
584A TYR* 3.6 3.9 + - - +
585A MET* 3.2 21.8 + - - +
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Residues in contact with SER 582 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A ILE* 4.1 2.9 - - - +
578A CYS 3.0 13.2 + - - -
579A LEU* 2.6 16.2 + - - +
581A ARG* 1.3 75.9 - - - +
583A SER* 1.3 53.6 + - - +
585A MET* 3.1 12.4 + - - +
586A LEU* 2.6 45.6 + - - +
602A LEU* 4.0 27.6 - - - -
607A ILE* 5.0 1.9 - - - +
625A ASN* 2.3 33.9 + - - +
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Residues in contact with SER 583 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579A LEU 3.0 1.9 + - - -
580A THR* 2.7 28.4 + - - -
582A SER* 1.3 74.5 - - - +
584A TYR* 1.3 58.3 + - - -
586A LEU* 3.1 0.8 + - - -
587A GLU* 2.7 38.4 + - - +
621A LEU* 5.3 0.7 - - - +
624A LYS* 4.2 27.6 + - - +
625A ASN* 2.9 23.4 + - - -
628A LEU* 3.5 23.4 - - - +
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Residues in contact with TYR 584 (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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458A GLU* 3.2 37.5 + - + +
461A ILE* 4.7 6.7 - - + -
462A LYS* 3.3 58.5 - - + +
465A ILE* 4.0 19.3 - - + -
466A ARG* 5.0 6.6 + - + +
580A THR* 3.0 30.0 + - - +
581A ARG 4.0 3.6 - - - +
582A SER 3.4 0.4 - - - -
583A SER* 1.3 85.3 + - - +
585A MET* 1.3 62.5 + - - +
587A GLU* 3.6 23.7 + - - +
588A LEU* 3.3 22.4 - - + +
624A LYS* 5.1 11.4 + - - -
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Residues in contact with MET 585 (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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465A ILE* 4.0 10.6 - - + +
478A PHE* 3.9 22.8 - - + -
479A VAL* 4.2 15.7 - - + +
482A ALA* 3.4 28.3 - - + -
483A ILE* 3.7 29.4 - - + -
486A ILE* 4.2 3.4 - - + -
581A ARG 3.2 13.9 + - - +
582A SER* 3.1 25.4 + - - +
584A TYR* 1.3 74.1 - - - +
586A LEU* 1.3 69.1 + - + +
588A LEU* 2.7 26.5 + - - +
589A VAL* 3.1 19.1 + - + +
599A ILE* 5.5 2.2 - - + -
602A LEU* 4.1 9.2 - - + -
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Residues in contact with LEU 586 (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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582A SER* 2.6 30.6 + - - +
583A SER 3.8 2.0 - - - +
585A MET* 1.3 85.4 - - + +
587A GLU* 1.3 62.7 + - - +
588A LEU 3.2 0.7 + - - -
589A VAL* 3.3 24.2 - - + +
599A ILE* 3.9 35.9 - - + -
602A LEU* 5.8 1.6 - - + -
607A ILE* 4.5 5.2 - - + -
625A ASN* 3.9 22.9 - - + +
628A LEU* 3.7 24.4 - - + +
629A CYS* 3.7 25.8 - - - +
632A LEU* 4.9 10.1 - - + +
515B LYS* 4.2 5.0 + - - -
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Residues in contact with GLU 587 (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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466A ARG* 4.2 21.6 + - - -
583A SER 2.7 19.9 + - - +
584A TYR* 3.7 29.0 - - - +
585A MET 3.1 0.2 - - - -
586A LEU* 1.3 72.5 - - - +
588A LEU* 1.3 64.3 + - + +
590A ASN* 4.2 1.4 + - - +
628A LEU* 4.3 13.9 - - + +
514B ILE 4.6 3.4 - - - +
515B LYS* 3.3 36.7 - - + +
516B PRO* 3.4 27.4 - - - +
517B GLY* 4.2 9.6 + - - +
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Residues in contact with LEU 588 (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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465A ILE* 3.8 13.0 - - + +
466A ARG* 4.4 24.0 - - - +
469A LYS* 3.7 53.2 + - + -
475A GLU* 4.4 0.2 - - - +
478A PHE* 3.7 20.6 - - + -
584A TYR 3.3 18.4 - - - +
585A MET 2.7 7.2 + - - +
587A GLU* 1.3 86.0 - - + +
589A VAL* 1.3 62.1 + - - +
590A ASN* 3.5 13.1 + - - +
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Residues in contact with VAL 589 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475A GLU* 3.1 26.9 - - - +
478A PHE* 4.6 6.3 - - + -
479A VAL* 3.9 22.7 - - + -
585A MET* 3.1 26.4 + - + +
586A LEU* 3.3 15.5 + - + +
588A LEU* 1.3 76.4 - - - +
590A ASN* 1.3 68.8 + - - +
591A THR* 3.8 6.7 - - - +
596A ASN* 4.5 2.5 - - - +
599A ILE* 4.2 18.2 - - + -
632A LEU* 4.0 24.6 - - + +
515B LYS* 3.1 11.3 + - - -
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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
------------------------------------------------------------
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