Contacts of the helix formed by residues 570 - 586 (chain A) in PDB entry 6O81
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 570 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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568A ASN 3.9 0.6 + - - -
569A ILE* 1.3 79.6 - - - +
571A CYS* 1.3 65.0 + - - +
572A ASP* 3.4 8.7 - - - -
573A ASN* 4.2 11.0 - - - +
574A LEU* 3.2 23.2 + - - +
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Residues in contact with CYS 571 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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570A SER* 1.3 74.9 - - - +
572A ASP* 1.3 59.6 + - - +
574A LEU* 3.8 4.7 - - - +
575A VAL* 2.9 30.1 + - - +
627A ALA 5.4 6.5 - - - +
628A TRP* 6.5 0.4 - - - -
630A PRO* 3.8 29.6 - - + -
631A VAL* 5.1 6.6 + - + +
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Residues in contact with ASP 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 SER* 3.4 5.8 - - - -
571A CYS* 1.3 77.2 - - - +
573A ASN* 1.3 60.7 + - - +
575A VAL* 3.3 6.0 + - - +
576A LEU* 2.9 29.0 + - - +
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Residues in contact with ASN 573 (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 ILE* 5.1 7.2 - - + -
570A SER* 3.8 18.5 + - - +
571A CYS 3.4 0.2 - - - -
572A ASP* 1.3 77.8 - - - +
574A LEU* 1.3 58.0 + - - +
576A LEU* 3.7 6.9 - - - +
577A GLU* 2.9 29.3 + - - +
456T TRP* 6.2 4.3 - - + -
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Residues in contact with LEU 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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569A ILE* 5.3 6.0 - - + +
570A SER 3.2 19.7 + - - +
571A CYS* 3.8 6.7 - - - +
572A ASP 3.3 0.2 - - - -
573A ASN* 1.3 74.3 - - - +
575A VAL* 1.3 59.0 + - - +
577A GLU* 3.4 6.7 + - - +
578A ILE* 2.9 28.8 + - - +
628A TRP* 3.6 35.0 - - + -
631A VAL* 5.2 5.8 - - + -
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Residues in contact with VAL 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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571A CYS 2.9 19.6 + - - +
572A ASP* 3.8 5.4 - - - +
574A LEU* 1.3 76.5 - - - +
576A LEU* 1.3 57.7 + - - +
578A ILE* 3.8 6.7 - - - +
579A ASN* 2.9 29.3 + - - +
630A PRO 6.2 0.2 - - - -
631A VAL* 5.1 11.4 - - + +
634A ASN* 5.1 16.2 - - + -
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Residues in contact with LEU 576 (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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572A ASP 2.9 17.7 + - - +
573A ASN* 3.7 8.3 - - - +
575A VAL* 1.3 76.6 - - - +
577A GLU* 1.3 56.3 + - - +
579A ASN* 3.4 5.9 + - - +
580A SER* 2.9 28.9 + - - -
177T ILE* 6.3 3.1 - - + -
456T TRP* 6.0 9.0 - - + -
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Residues in contact with GLU 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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560A THR* 5.1 16.1 - - - -
573A ASN 2.9 18.7 + - - +
574A LEU* 3.8 6.5 - - - +
575A VAL 3.3 0.2 - - - -
576A LEU* 1.3 72.5 - - - +
578A ILE* 1.3 61.1 + - - +
580A SER* 3.4 7.3 + - - -
581A LEU* 2.9 29.3 + - - +
378T LEU* 6.2 2.9 - - + -
379T ARG* 5.7 11.4 - - + +
380T ARG 6.1 1.3 - - - +
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Residues in contact with ILE 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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560A THR* 6.2 0.9 - - - -
574A LEU 2.9 17.8 + - - +
575A VAL* 3.8 7.2 - - - +
576A LEU 3.3 0.2 - - - -
577A GLU* 1.3 76.1 - - - +
579A ASN* 1.3 58.1 + - - +
581A LEU* 3.4 6.2 + - - +
582A LYS* 2.9 29.3 + - - +
631A VAL* 6.1 3.8 - - + -
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Residues in contact with ASN 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 VAL 2.9 18.9 + - - +
576A LEU* 3.7 7.0 - - - +
578A ILE* 1.3 77.5 - - - +
580A SER* 1.3 56.6 + - - +
582A LYS* 3.4 7.0 + - - +
583A TYR* 2.9 29.1 + - - +
173T HIS* 6.1 0.4 - - - -
176T ALA* 5.8 9.0 - - + -
216T ALA* 5.9 6.7 - - + -
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Residues in contact with SER 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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576A LEU 2.9 17.4 + - - -
577A GLU* 3.7 8.3 - - - -
578A ILE 3.3 0.2 - - - -
579A ASN* 1.3 77.5 - - - +
581A LEU* 1.3 56.6 + - - +
583A TYR* 3.4 5.7 + - - +
584A ALA* 2.9 29.8 + - - +
173T HIS* 4.9 6.3 - - - -
380T ARG* 6.5 0.4 - - - -
381T LEU 4.2 5.4 - - - -
382T LEU* 4.1 12.6 - - - -
383T GLY* 3.9 24.2 - - - +
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Residues in contact with LEU 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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553A PHE* 5.6 4.1 - - + +
556A GLU* 5.4 12.3 - - + -
557A VAL* 5.7 9.4 - - + +
560A THR* 6.4 1.8 - - - -
577A GLU 2.9 17.9 + - - +
578A ILE* 3.8 6.7 - - - +
580A SER* 1.3 75.9 - - - +
582A LYS* 1.3 56.8 + - - +
584A ALA* 3.9 5.5 - - - +
585A TYR* 2.9 32.7 + - - +
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Residues in contact with LYS 582 (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 ILE 2.9 17.6 + - - +
579A ASN* 3.8 7.2 - - - +
581A LEU* 1.3 75.9 - - - +
583A TYR* 1.3 58.7 + - - +
585A TYR* 4.9 2.7 - - - -
586A ASN* 3.1 24.4 + - - -
587A ILE* 3.7 13.3 + - - +
592A VAL* 4.6 20.4 - - + -
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Residues in contact with TYR 583 (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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579A ASN 2.9 17.2 + - - +
580A SER* 3.8 6.1 - - - +
582A LYS* 1.3 76.7 - - - +
584A ALA* 1.3 63.1 + - - +
586A ASN* 3.7 11.1 + - - +
169T GLN* 3.3 41.8 - - + +
172T GLU* 5.5 4.0 - - + -
173T HIS* 4.9 8.3 - - + +
383T GLY* 5.0 1.6 - - - -
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Residues in contact with ALA 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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580A SER 2.9 17.9 + - - +
581A LEU* 3.9 6.3 - - - +
582A LYS 3.4 0.2 - - - -
583A TYR* 1.3 79.4 - - - +
585A TYR* 1.3 62.0 + - - +
586A ASN* 3.5 2.4 + - - +
169T GLN* 5.0 1.3 - - - -
381T LEU 6.1 0.2 - - - +
383T GLY* 4.7 15.6 - - - -
385T ARG* 3.7 34.2 - - + +
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Residues in contact with TYR 585 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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549A ASP 5.4 2.0 - - - +
553A PHE* 3.8 29.6 - - + -
581A LEU 2.9 17.2 + - - +
582A LYS* 4.6 2.2 - - - +
584A ALA* 1.3 76.0 - - - +
586A ASN* 1.3 68.7 + - - +
587A ILE* 3.3 12.7 + - + +
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Residues in contact with ASN 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 LYS 3.1 12.6 + - - -
583A TYR* 3.7 8.9 + - - +
584A ALA 3.3 4.4 - - - +
585A TYR* 1.3 79.0 - - - +
587A ILE* 1.3 63.1 + - - +
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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