Contacts of the helix formed by residues 579 - 596 (chain A) in PDB entry 3NC0
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 GLY 579 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577A HIS 3.4 1.2 + - - -
578A ASP* 1.3 69.0 - - - +
580A VAL* 1.3 64.6 + - - +
581A GLN 3.1 3.3 - - - +
582A ASP* 2.9 17.6 + - - +
583A MET* 2.9 22.8 + - - +
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Residues in contact with VAL 580 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538A ALA* 4.0 27.6 - - + -
542A SER* 5.3 3.1 - - - +
572A PHE* 3.7 20.0 - - + +
575A GLU* 3.4 35.9 - - + -
577A HIS* 3.3 18.8 + - + +
578A ASP 2.9 11.4 + - - +
579A GLY* 1.3 75.3 - - - +
581A GLN* 1.3 57.3 + - - +
583A MET* 3.3 18.3 + - + +
584A ALA* 2.8 26.9 + - - +
14B LEU* 4.0 9.9 - - + -
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Residues in contact with GLN 581 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572A PHE 3.7 15.0 - - - +
573A MET* 2.9 25.7 + - - +
574A HIS* 4.1 4.2 - - - +
575A GLU 3.0 23.9 + - - +
576A THR* 4.7 0.5 - - - -
577A HIS 4.5 2.8 + - - +
579A GLY 3.1 1.4 - - - +
580A VAL* 1.3 76.4 - - - +
582A ASP* 1.3 63.6 + - - +
584A ALA* 3.7 3.5 + - - +
585A CYS* 3.2 29.5 + - - -
624A ASP* 3.3 25.4 + - - +
625A LEU* 3.9 8.5 - - + +
626A GLN* 4.8 7.2 + - - +
629A GLN* 3.5 18.9 - - - +
145B SER* 2.9 25.4 + - - -
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Residues in contact with ASP 582 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A ARG* 3.4 46.2 + - - +
579A GLY* 2.9 16.8 + - - +
581A GLN* 1.3 74.4 - - - +
583A MET* 1.3 66.6 + - - +
585A CYS* 3.4 3.3 + - - +
586A ASP* 3.0 32.4 + - - +
626A GLN* 5.6 2.0 + - - +
629A GLN* 2.8 28.8 + - - +
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Residues in contact with MET 583 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538A ALA 5.2 0.4 - - - +
541A ALA* 5.0 1.6 - - + -
542A SER* 3.6 46.0 - - - +
545A MET* 3.6 27.1 - - + -
546A TYR 6.0 0.2 - - - +
572A PHE* 3.7 31.4 - - + -
579A GLY 2.9 11.7 + - - +
580A VAL* 3.4 23.8 - - + +
582A ASP* 1.3 78.9 - - - +
584A ALA* 1.3 66.8 + - - +
585A CYS 3.2 0.2 + - - -
586A ASP* 3.3 7.1 + - - +
587A THR* 3.1 30.4 + - - +
14B LEU* 6.2 0.2 - - + -
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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
----------------------------------------------------------
569A LEU* 2.9 43.9 - - + +
572A PHE* 3.8 27.1 - - + -
573A MET* 3.7 12.3 - - + +
580A VAL 2.8 17.7 + - - +
581A GLN* 4.0 4.5 - - - +
583A MET* 1.3 85.3 - - - +
585A CYS* 1.3 60.0 + - - +
588A PHE* 3.3 5.5 + - - +
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Residues in contact with CYS 585 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573A MET* 4.2 13.0 - - - -
581A GLN 3.2 19.6 + - - +
582A ASP* 4.0 4.7 - - - +
583A MET 3.2 0.6 - - - -
584A ALA* 1.3 77.2 - - - +
586A ASP* 1.3 68.6 + - - +
587A THR 3.2 0.2 - - - -
588A PHE* 3.0 6.3 + - - +
589A ILE* 3.0 25.8 + - - +
625A LEU* 4.1 21.5 - - - -
629A GLN* 4.1 32.3 - - + -
632A THR* 4.6 16.5 - - + +
633A PHE* 5.1 5.4 - - - +
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Residues in contact with ASP 586 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A GLU* 6.0 2.0 - - - +
442A ARG* 3.1 25.2 + - - -
444A PHE* 4.8 15.9 - - - -
582A ASP* 3.0 23.9 + - - +
583A MET* 3.7 7.7 - - - +
585A CYS* 1.3 77.6 - - - +
587A THR* 1.3 63.3 + - - +
589A ILE* 3.0 25.3 - - - +
590A LYS* 3.1 12.7 + - - +
632A THR* 5.0 6.1 - - - +
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Residues in contact with THR 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 MET* 3.5 41.8 + - + +
546A TYR* 5.2 1.6 - - - -
548A VAL* 5.7 0.4 - - + -
549A GLY* 4.6 5.2 - - - -
569A LEU* 3.4 22.7 - - + -
583A MET* 3.1 17.0 + - - +
586A ASP* 1.3 78.7 - - - +
588A PHE* 1.3 52.1 + - - +
590A LYS* 3.2 10.9 - - + +
591A ILE* 2.8 53.2 + - + +
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Residues in contact with PHE 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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566A VAL* 4.2 23.1 - - + -
569A LEU* 3.3 14.7 - - + +
570A PHE* 3.8 27.6 - + - -
573A MET* 4.0 10.1 - - + -
584A ALA 3.4 14.8 - - - +
585A CYS* 3.0 6.1 + - - +
587A THR* 1.3 77.1 - - - +
589A ILE* 1.3 59.6 + - - +
591A ILE* 3.6 5.2 + - + -
592A ALA* 2.9 32.5 + - + +
599A PHE* 4.9 5.8 - + - -
614A ILE* 4.7 4.7 - - + -
633A PHE* 3.4 39.0 - + - -
636A ALA* 3.6 29.6 - - + -
637A VAL* 4.4 12.1 - - + -
640A MET* 4.6 10.5 - - - -
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Residues in contact with ILE 589 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585A CYS 3.0 12.1 + - - +
586A ASP* 3.0 29.2 - - - +
588A PHE* 1.3 73.8 - - - +
590A LYS* 1.3 70.1 + - - +
592A ALA* 3.3 1.2 + - - +
593A GLN* 2.9 30.6 + - - +
632A THR* 4.0 26.0 - - + +
635A GLU* 3.7 36.6 - - + +
636A ALA* 3.6 19.9 - - + +
639A TYR* 4.0 17.0 - - + +
697A ARG* 5.2 0.4 - - - +
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Residues in contact with LYS 590 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A GLU* 4.1 10.4 + - - -
546A TYR* 4.0 23.4 + - - +
549A GLY* 3.9 20.5 + - - +
550A GLN* 3.1 33.9 + - - +
586A ASP 3.3 10.8 - - - +
587A THR* 3.2 13.7 - - - +
589A ILE* 1.3 83.7 - - + +
591A ILE* 1.3 65.4 + - + +
593A GLN* 3.3 14.4 + - - +
594A LYS* 3.2 41.2 + - - +
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Residues in contact with ILE 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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548A VAL* 4.7 4.5 - - + +
549A GLY* 4.5 10.1 - - - +
552A PRO* 6.3 1.1 - - + -
555A LEU* 3.7 24.2 - - + -
562A LEU* 4.7 4.3 - - + -
565A VAL* 3.7 30.7 - - + -
566A VAL* 4.6 8.5 - - + -
569A LEU* 4.5 4.5 - - + -
587A THR* 2.8 38.7 + - + +
588A PHE* 4.0 6.1 - - + +
590A LYS* 1.3 72.8 - - - +
592A ALA* 1.3 58.5 + - - +
594A LYS* 3.2 4.5 + - - +
595A CYS* 2.8 44.0 + - + +
599A PHE* 4.2 20.4 - - + -
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Residues in contact with ALA 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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588A PHE* 2.9 23.2 + - + +
589A ILE 3.6 4.0 - - - +
590A LYS 3.3 0.2 - - - -
591A ILE* 1.3 76.5 - - - +
593A GLN* 1.3 56.4 + - - +
596A ARG* 2.8 37.9 + - - +
599A PHE* 4.1 13.2 - - + -
636A ALA* 3.4 31.6 - - + +
639A TYR* 4.5 2.5 - - + -
640A MET* 4.5 14.1 - - + -
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Residues in contact with GLN 593 (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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589A ILE* 2.9 19.9 + - - +
590A LYS* 3.4 16.2 + - - +
592A ALA* 1.3 75.7 - - - +
594A LYS* 1.3 65.6 + - + +
595A CYS 3.7 0.3 + - - -
596A ARG* 3.1 35.1 + - - +
639A TYR* 3.4 52.5 + - + +
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Residues in contact with LYS 594 (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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549A GLY 3.0 26.4 + - - -
550A GLN* 4.3 6.7 + - - +
552A PRO* 3.3 34.1 - - + +
556A ARG* 2.6 34.5 + - - +
590A LYS* 3.2 39.8 + - - +
591A ILE* 4.2 2.9 - - - +
593A GLN* 1.3 83.3 - - + +
595A CYS* 1.3 59.5 + - - +
596A ARG* 3.6 1.3 - - - -
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Residues in contact with CYS 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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552A PRO* 4.2 11.2 - - - -
555A LEU* 4.2 12.3 - - - -
556A ARG* 3.9 21.1 - - + +
562A LEU* 3.7 33.7 - - + -
591A ILE* 2.8 26.6 + - - +
592A ALA 3.5 2.0 - - - -
594A LYS* 1.3 81.2 - - - +
596A ARG* 1.3 65.9 + - - +
597A ARG* 2.9 5.5 + - - -
598A HIS* 3.0 16.9 + - + +
599A PHE* 3.5 15.6 - - + -
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Residues in contact with ARG 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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592A ALA 2.8 15.4 + - - +
593A GLN* 3.1 24.6 + - - +
594A LYS 3.6 0.9 - - - -
595A CYS* 1.3 77.3 - - - +
597A ARG* 1.3 66.3 + - + +
598A HIS 3.4 0.3 + - - -
599A PHE* 3.5 19.6 + - - +
600A VAL* 4.0 4.5 + - - +
639A TYR* 3.6 61.5 + - - +
640A MET* 4.1 4.3 - - - -
642A GLY* 5.0 7.2 + - - -
643A ALA* 3.7 23.6 - - + +
701A ALA 4.9 5.5 + - - -
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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