Contacts of the helix formed by residues 620 - 644 (chain A) in PDB entry 3C7N
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 ILE 620 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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567A THR* 5.1 2.0 - - - -
619A SER* 1.3 92.7 + - - +
621A LYS* 1.3 56.5 + - - +
622A ALA* 2.6 30.0 + - + +
623A LYS* 2.7 46.7 + - + -
624A TYR* 3.3 12.6 + - - -
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Residues in contact with LYS 621 (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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563A LEU* 4.3 23.0 - - + +
566A GLU* 3.7 38.6 + - + +
567A THR* 3.2 31.4 + - - +
570A ARG* 3.4 41.7 - - + +
620A ILE* 1.3 70.6 - - - +
622A ALA* 1.3 55.7 + - - +
623A LYS 3.3 0.3 + - - -
624A TYR* 3.5 7.2 + - - +
625A ILE* 2.8 40.8 + - + +
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Residues in contact with ALA 622 (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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620A ILE* 2.6 21.0 + - + +
621A LYS* 1.3 77.6 - - - +
623A LYS* 1.3 71.3 + - - +
625A ILE* 3.6 8.4 - - - +
626A ALA* 3.0 24.1 + - - +
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Residues in contact with LYS 623 (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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611A TRP* 3.9 14.8 - - + -
619A SER* 3.2 20.2 - - - +
620A ILE* 2.7 34.8 + - + +
622A ALA* 1.3 86.1 + - - +
624A TYR* 1.3 57.0 + - - +
625A ILE 3.2 2.0 - - - -
626A ALA* 3.3 16.8 - - + +
627A LYS* 3.0 33.8 + - - +
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Residues in contact with TYR 624 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567A THR* 4.2 18.8 - - + +
570A ARG* 3.6 26.5 - - + +
571A LYS* 3.4 41.8 - - + +
574A LEU* 4.0 23.6 + - + +
611A TRP* 3.6 21.5 - + - -
612A LEU* 4.5 4.9 - - + -
616A GLY 2.8 22.2 + - - -
617A PHE 2.9 17.5 + - - -
618A ASP* 3.3 2.3 - - - -
619A SER* 3.1 32.5 + - - -
620A ILE 3.3 20.6 + - - -
621A LYS 3.5 4.7 + - - +
623A LYS* 1.3 77.3 - - - +
625A ILE* 1.3 58.2 + - - +
628A TYR* 3.5 16.5 + - - +
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Residues in contact with ILE 625 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570A ARG* 4.0 34.8 - - + +
573A THR* 6.5 0.7 - - - -
621A LYS* 2.8 43.3 - - + +
622A ALA* 3.6 10.8 - - - +
624A TYR* 1.3 76.9 - - - +
626A ALA* 1.3 60.7 + - - +
628A TYR* 3.6 12.6 - - + -
629A GLU* 2.8 50.3 + - - +
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Residues in contact with ALA 626 (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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622A ALA 3.0 20.7 + - - +
623A LYS* 3.3 29.6 - - + +
625A ILE* 1.3 77.4 - - - +
627A LYS* 1.3 67.5 + - + +
629A GLU* 3.0 25.4 + - - +
630A GLU* 3.6 12.5 + - - +
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Residues in contact with LYS 627 (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 LEU* 3.9 20.2 - - + -
607A LYS* 6.1 2.6 - - - +
608A ALA* 4.9 10.7 - - + +
611A TRP* 3.4 52.8 - - + +
623A LYS* 3.0 15.3 + - + +
626A ALA* 1.3 82.0 - - + +
628A TYR* 1.3 62.4 + - - +
630A GLU* 3.2 31.5 + - - +
631A LEU* 3.2 29.0 + - + +
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Residues in contact with TYR 628 (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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573A THR* 3.4 46.9 - - + +
574A LEU* 3.7 17.3 - - + +
577A TYR* 3.9 29.7 - + + -
624A TYR 3.5 16.1 + - - +
625A ILE* 3.3 18.0 + - + +
626A ALA 3.1 0.6 - - - -
627A LYS* 1.3 78.4 - - - +
629A GLU* 1.3 81.0 + - - +
631A LEU* 3.5 3.8 + - - +
632A ALA* 3.0 28.9 + - + +
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Residues in contact with GLU 629 (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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625A ILE* 2.8 49.0 + - - +
626A ALA* 3.0 11.6 + - - +
628A TYR* 1.3 86.7 - - - +
630A GLU* 1.3 59.7 + - + +
632A ALA* 2.8 24.4 + - - +
633A SER* 3.0 11.0 + - - -
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Residues in contact with GLU 630 (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 MET* 5.0 9.1 - - + +
626A ALA 3.6 14.0 + - - +
627A LYS* 3.2 39.0 + - - +
629A GLU* 1.3 79.9 - - + +
631A LEU* 1.3 62.1 + - + +
632A ALA 3.3 0.2 - - - -
633A SER* 3.4 13.1 - - - -
634A LEU* 3.0 29.5 - - + +
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Residues in contact with LEU 631 (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 LEU* 3.9 17.5 - - + -
577A TYR* 3.9 21.0 - - + -
578A ILE* 4.2 12.6 - - + -
581A LEU* 4.4 7.3 - - + +
601A LEU* 4.5 6.9 - - + +
604A MET* 4.2 23.3 - - + +
605A LEU* 3.8 29.6 - - + +
608A ALA* 3.6 26.0 - - + -
627A LYS 3.2 20.1 + - - +
628A TYR* 3.8 4.5 - - - +
629A GLU 3.1 0.6 - - - -
630A GLU* 1.3 80.7 - - + +
632A ALA* 1.3 60.7 + - - +
634A LEU* 3.6 6.9 + - - +
635A GLY* 3.4 14.4 + - - -
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Residues in contact with ALA 632 (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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577A TYR* 3.8 19.9 - - + +
628A TYR* 3.0 32.5 + - + +
629A GLU* 2.8 7.2 + - - +
631A LEU* 1.3 74.4 - - - +
633A SER* 1.3 64.2 + - - +
634A LEU 3.2 0.7 - - - -
635A GLY 3.2 3.7 + - - -
636A ASN* 2.7 42.6 + - - +
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Residues in contact with SER 633 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629A GLU 3.0 8.3 + - - -
630A GLU* 3.4 20.0 - - - -
632A ALA* 1.3 79.3 - - - +
634A LEU* 1.3 69.3 + - - +
635A GLY 4.3 0.2 - - - +
636A ASN* 4.2 5.9 - - - +
637A ILE* 3.1 28.4 - - - +
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Residues in contact with LEU 634 (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 LYS* 3.3 35.9 - - + -
601A LEU* 3.8 26.7 - - + -
604A MET* 3.5 27.4 - - + -
630A GLU* 3.0 29.4 - - + +
631A LEU 3.6 2.6 + - - +
632A ALA 3.2 0.2 - - - -
633A SER* 1.3 84.6 - - - +
635A GLY* 1.3 69.8 + - - +
637A ILE* 4.0 14.1 - - + +
638A ILE* 3.9 21.5 - - + +
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Residues in contact with GLY 635 (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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577A TYR* 3.6 17.9 - - - -
581A LEU* 4.6 13.2 - - - -
601A LEU* 5.0 0.6 - - - +
631A LEU 3.4 7.5 + - - -
632A ALA 3.2 5.3 + - - -
634A LEU* 1.3 87.1 - - - +
636A ASN* 1.3 69.9 + - - -
637A ILE 2.6 5.5 + - - -
638A ILE* 2.9 10.6 + - - -
639A ARG* 3.7 8.4 + - - -
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Residues in contact with ASN 636 (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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577A TYR* 4.1 8.3 + - - -
632A ALA* 2.7 33.0 + - - +
633A SER* 4.2 5.7 - - - +
635A GLY* 1.3 68.8 - - - -
637A ILE* 1.3 58.5 + - + +
639A ARG* 2.7 40.4 + - - +
640A GLY* 2.5 35.0 + - - -
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Residues in contact with ILE 637 (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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633A SER* 3.1 28.3 - - - +
634A LEU* 4.0 14.4 - - + +
635A GLY 2.6 5.3 + - - +
636A ASN* 1.3 75.3 - - + +
638A ILE* 1.3 75.3 + - + +
640A GLY* 3.3 0.7 + - - -
641A ARG* 3.1 33.4 + - - +
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Residues in contact with ILE 638 (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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585A LEU* 4.7 8.3 - - + -
589A TYR* 3.9 25.8 - - + -
592A PHE 4.7 1.3 - - - +
593A ALA* 3.8 34.5 - - + +
597A GLU* 4.8 11.0 - - + +
601A LEU* 4.4 20.0 - - + -
634A LEU* 3.9 15.3 - - + +
635A GLY* 2.9 8.6 + - - +
637A ILE* 1.3 81.0 - - + +
639A ARG* 1.3 65.2 + - - +
640A GLY 2.8 2.6 + - - -
641A ARG* 3.1 41.4 + - - +
642A TYR* 3.2 11.1 + - - +
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Residues in contact with ARG 639 (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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577A TYR* 5.5 5.1 + - - -
581A LEU* 6.3 1.6 - - + -
584A LYS* 5.4 5.4 - - - +
589A TYR* 3.2 36.8 - - + +
635A GLY* 3.7 3.0 + - - -
636A ASN* 2.7 51.6 + - - +
638A ILE* 1.3 76.9 - - - +
640A GLY* 1.3 56.4 + - - -
642A TYR* 3.3 7.4 - - + +
643A LEU* 3.2 41.7 + - + +
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Residues in contact with GLY 640 (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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636A ASN 2.5 18.8 + - - -
637A ILE 3.8 1.1 - - - -
638A ILE 2.8 3.4 + - - -
639A ARG* 1.3 73.2 - - - +
641A ARG* 1.3 55.3 + - - +
642A TYR 2.8 5.1 + - - -
643A LEU* 2.8 25.0 + - - -
644A ALA* 2.9 19.0 + - - +
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Residues in contact with ARG 641 (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 PHE* 3.1 21.5 + - + +
593A ALA* 3.1 8.7 - - - +
594A SER* 3.0 34.2 - - - +
597A GLU* 4.0 15.4 + - - +
637A ILE* 3.1 25.2 + - - +
638A ILE* 3.1 35.1 + - - +
640A GLY* 1.3 73.7 - - - +
642A TYR* 1.3 55.7 + - - +
644A ALA* 5.5 2.2 - - - -
645A LYS* 2.9 39.9 - - + +
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Residues in contact with TYR 642 (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 GLU* 3.2 56.5 + - + +
589A TYR* 3.7 14.4 - + + -
592A PHE* 3.0 49.3 - + + -
638A ILE 3.2 9.8 + - - +
639A ARG 3.3 14.4 - - - +
640A GLY 2.8 0.4 - - - -
641A ARG* 1.3 79.1 - - - +
643A LEU* 1.3 75.7 + - + +
645A LYS 3.3 0.7 + - - -
646A GLU* 3.2 49.3 + - + +
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Residues in contact with LEU 643 (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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639A ARG* 3.2 32.3 + - + +
640A GLY* 2.8 13.8 + - - +
642A TYR* 1.3 83.6 - - + +
644A ALA* 1.3 51.4 + - - +
645A LYS 3.1 4.7 - - - -
646A GLU* 5.4 0.4 - - - -
647A GLU* 2.8 77.2 + - + +
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Residues in contact with ALA 644 (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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640A GLY 2.9 12.1 + - - +
641A ARG* 5.5 1.1 - - - -
643A LEU* 1.3 75.3 - - + +
645A LYS* 1.3 60.7 + - + +
647A GLU* 4.0 5.6 - - - +
648A GLU* 2.6 44.3 - - - +
649A LYS* 4.1 2.1 - - - +
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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
------------------------------------------------------------
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