Contacts of the helix formed by residues 579 - 592 (chain A) in PDB entry 3O8C
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 579 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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577A SER* 3.2 18.3 + - - +
578A TRP* 1.3 82.8 - - - +
580A GLN* 1.3 66.7 + - - +
581A MET* 2.9 34.6 + - + +
582A TRP* 3.0 22.1 + - + +
583A LYS* 4.8 0.5 - - - -
586A ILE* 6.0 1.2 - - - +
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Residues in contact with GLN 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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555A ASP* 5.3 5.3 - - - +
578A TRP 3.9 2.1 + - - +
579A ASP* 1.3 77.7 + - - +
581A MET* 1.3 66.6 + - - +
582A TRP 3.0 0.4 - - - -
583A LYS* 3.0 56.9 + - + +
586A ILE* 4.1 13.2 - - - +
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Residues in contact with MET 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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550A THR* 5.4 1.2 - - - +
555A ASP* 5.2 8.0 + - - -
556A ASN 5.8 2.2 - - - +
561A VAL* 3.5 38.0 - - + +
579A ASP* 2.9 17.8 + - - +
580A GLN* 1.3 78.1 - - - +
582A TRP* 1.3 92.7 + - + +
583A LYS* 3.4 3.2 + - - +
584A CYS* 5.1 1.2 + - - -
602A LEU* 3.5 40.6 - - + +
603A GLY* 5.2 2.2 - - - -
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Residues in contact with TRP 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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561A VAL* 3.5 37.0 - - + -
564A GLN* 3.5 30.1 - - + -
565A ALA* 4.2 5.2 - - + -
575A PRO* 3.7 22.0 - - + -
576A PRO* 3.6 24.9 - - + +
577A SER* 3.1 46.8 + - - +
578A TRP* 4.2 5.6 - - + -
579A ASP* 3.0 11.3 + - + +
580A GLN 3.0 0.8 - - - -
581A MET* 1.3 105.0 - - + +
583A LYS* 1.3 63.4 + - - +
584A CYS* 3.1 6.1 - - - -
585A LEU* 3.1 26.2 + - + +
586A ILE* 4.0 2.5 + - - -
600A TYR* 5.6 0.7 - + - -
602A LEU* 4.3 22.4 - - + -
603A GLY* 6.0 0.4 - - - -
604A ALA 5.3 1.4 + - - -
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Residues in contact with LYS 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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553A ALA* 3.9 32.1 + - - +
555A ASP* 5.0 7.5 + - - -
579A ASP 4.8 0.9 - - - -
580A GLN* 3.0 45.2 + - - +
581A MET 3.4 2.9 + - - +
582A TRP* 1.3 78.4 - - - +
584A CYS* 1.3 64.6 + - + +
585A LEU 3.0 1.8 + - - -
586A ILE* 3.1 41.0 + - + +
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Residues in contact with CYS 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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546A PHE* 4.0 29.6 - - - -
549A GLN* 3.9 42.5 + - + +
550A THR* 4.5 16.8 - - + -
561A VAL* 5.5 2.2 - - - -
565A ALA* 3.8 29.4 - - - -
581A MET 5.1 1.1 + - - -
582A TRP* 3.1 7.0 + - - -
583A LYS* 1.3 82.3 - - + +
585A LEU* 1.3 61.0 + - - +
586A ILE 3.4 0.4 - - - -
587A ARG* 4.7 11.4 + - - +
588A LEU* 5.5 0.5 - - - +
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Residues in contact with LEU 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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546A PHE* 3.5 37.5 - - + -
565A ALA* 3.6 35.4 - - + +
568A CYS* 4.5 7.4 - - + -
569A ALA* 4.3 3.4 - - + -
575A PRO* 4.0 22.2 - - + -
578A TRP* 3.6 16.7 - - + -
582A TRP* 3.1 14.9 + - + +
583A LYS 3.0 1.0 - - - -
584A CYS* 1.3 78.8 - - - +
586A ILE* 1.3 66.4 + - - +
587A ARG 3.2 2.5 - - - -
588A LEU* 3.0 30.2 + - + +
589A LYS 3.3 8.0 + - - -
592A LEU* 4.1 14.4 - - + -
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Residues in contact with ILE 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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578A TRP* 3.8 25.1 - - + +
579A ASP 6.0 0.9 - - - +
580A GLN* 4.1 12.1 - - - +
583A LYS* 3.1 40.4 + - + +
584A CYS 3.4 0.2 - - - -
585A LEU* 1.3 77.9 - - - +
587A ARG* 1.3 63.4 + - - +
589A LYS* 3.2 26.1 + - + +
590A PRO* 4.4 1.4 - - - +
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Residues in contact with ARG 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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545A HIS* 3.2 36.4 + - - -
546A PHE* 4.6 11.1 - - - -
549A GLN* 5.3 3.8 - - - +
583A LYS 4.9 0.4 + - - -
584A CYS 4.7 11.0 + - - +
586A ILE* 1.3 80.9 - - + +
588A LEU* 1.3 82.0 + - + +
589A LYS 3.3 1.7 + - - -
590A PRO* 4.0 8.9 - - - +
591A THR* 5.7 0.7 - - - +
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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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546A PHE* 4.1 16.6 - - + -
569A ALA* 4.2 13.0 - - + -
584A CYS 5.6 0.2 - - - +
585A LEU* 3.0 34.3 + - + +
587A ARG* 1.3 102.6 - - + +
589A LYS* 1.3 65.5 + - - +
590A PRO* 3.3 4.0 - - - -
591A THR* 2.8 41.1 + - + +
592A LEU* 3.5 15.0 - - + +
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Residues in contact with LYS 589 (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 TRP* 3.5 66.6 - - + +
585A LEU 3.3 2.2 + - - -
586A ILE* 3.2 22.1 + - + +
588A LEU* 1.3 75.9 - - - +
590A PRO* 1.4 64.6 - - + +
591A THR 2.8 11.1 + - - -
592A LEU* 2.8 24.2 + - - +
593A HIS* 5.0 0.5 - - - -
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Residues in contact with PRO 590 (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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586A ILE 4.4 2.0 - - - +
587A ARG 4.0 9.4 - - - +
588A LEU 3.5 4.0 - - - -
589A LYS* 1.4 99.0 - - + +
591A THR* 1.3 60.9 + - + +
592A LEU 3.5 0.2 - - - -
593A HIS* 3.2 22.3 + - + -
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Residues in contact with THR 591 (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 GLN* 3.7 29.8 + - - +
587A ARG 5.7 0.4 - - - +
588A LEU* 2.8 33.2 + - + +
589A LYS 2.8 2.2 + - - -
590A PRO* 1.3 81.7 - - + +
592A LEU* 1.3 70.3 + - - +
593A HIS* 3.6 13.4 - - - -
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Residues in contact with LEU 592 (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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568A CYS 4.4 3.1 - - - +
569A ALA* 4.5 9.9 - - - +
572A GLN* 3.2 29.2 - - + -
573A ALA 3.5 23.6 - - - +
574A PRO* 3.7 15.9 - - + +
575A PRO* 4.2 0.2 - - + -
578A TRP* 4.1 20.4 - - + -
585A LEU* 4.1 26.5 - - + -
588A LEU* 3.5 24.0 - - + +
589A LYS* 2.8 13.4 + - - +
590A PRO 3.5 0.2 - - - -
591A THR* 1.3 85.5 - - - +
593A HIS* 1.3 74.4 + - - +
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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