Contacts of the helix formed by residues 621 - 643 (chain A) in PDB entry 3RC3
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 ASN 621 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619A PRO* 4.1 1.7 - - - +
620A LYS* 1.3 81.3 - - - +
622A ILE* 1.3 65.0 + - - +
623A LYS* 3.3 12.7 + - - +
624A ASP* 2.8 45.7 + - - +
625A LEU* 3.2 17.7 + - - +
676A LEU* 3.6 18.3 - - - +
679A MSE 4.2 11.0 - - + +
680A SER* 3.4 15.3 - - - +
684A LYS* 3.9 31.6 - - + +
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Residues in contact with ILE 622 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A TYR* 3.5 48.7 - - + +
621A ASN* 1.3 71.6 - - - +
623A LYS* 1.3 65.4 + - - +
625A LEU* 3.0 13.7 + - + +
626A MSE 2.9 33.0 + - + +
673A ILE* 5.6 2.0 - - + -
676A LEU* 3.8 4.6 + - + +
677A ILE* 3.9 36.6 - - + +
680A SER* 3.0 29.7 + - - +
686A LEU* 4.1 14.6 - - + -
688A LEU* 4.3 4.5 - - + -
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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
----------------------------------------------------------
583A GLN* 5.8 1.4 + - - -
621A ASN* 3.3 11.9 + - - +
622A ILE* 1.3 78.7 - - - +
624A ASP* 1.3 60.8 + - - +
626A MSE 3.2 32.2 + - + +
627A ASP* 2.9 51.5 + - - +
680A SER* 4.4 1.2 + - - -
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Residues in contact with ASP 624 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618A PRO 4.9 0.3 - - - +
619A PRO* 3.4 18.7 - - + +
620A LYS* 2.7 31.2 + - - +
621A ASN* 2.8 35.6 + - - +
623A LYS* 1.3 76.7 - - - +
625A LEU* 1.3 62.8 + - - +
627A ASP* 3.4 11.3 + - - +
628A LEU* 3.1 25.6 + - - +
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Residues in contact with LEU 625 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A TYR* 5.8 1.6 - - + +
396A TYR* 3.2 25.1 - - - +
619A PRO* 3.7 8.2 - - + +
621A ASN 3.2 7.8 + - - +
622A ILE* 3.0 16.2 + - + +
624A ASP* 1.3 78.6 - - - +
626A MSE 1.3 58.7 + - - +
628A LEU* 3.2 7.9 + - + +
629A GLU* 3.0 36.6 + - + +
666A ILE* 3.8 33.0 - - + +
670A VAL* 3.9 18.8 - - + +
673A ILE* 4.1 17.3 - - + -
676A LEU* 4.0 20.6 - - + -
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Residues in contact with MSE 626 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A LYS* 6.4 0.4 - - - +
379A TYR* 5.4 3.4 - - - +
583A GLN* 3.5 32.5 - - - +
622A ILE* 2.9 21.3 + - + +
623A LYS* 3.5 42.4 - - + +
625A LEU* 1.3 72.7 - - - +
627A ASP* 1.3 66.1 + - - +
629A GLU* 3.3 15.2 + - + +
630A ALA* 2.9 22.2 + - - +
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Residues in contact with ASP 627 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583A GLN* 4.9 5.7 - - - +
623A LYS* 2.9 45.1 + - - +
624A ASP* 3.6 13.6 - - - +
625A LEU 3.3 0.4 - - - -
626A MSE 1.3 77.5 - - - +
628A LEU* 1.3 58.3 + - + +
630A ALA* 3.1 7.9 + - - +
631A VAL* 2.9 34.1 + - + +
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Residues in contact with LEU 628 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616A LEU* 3.9 33.9 - - + -
617A LEU 4.1 8.5 - - - +
619A PRO* 3.7 37.0 - - + -
624A ASP* 3.1 17.4 + - + +
625A LEU* 3.2 8.5 + - + +
627A ASP* 1.3 78.9 - - + +
629A GLU* 1.3 53.0 + - - +
631A VAL* 3.3 7.7 + - - +
632A HIS* 2.8 32.4 + - - +
662A LEU* 3.9 14.8 - - + +
665A ILE* 3.9 14.4 - - + -
666A ILE* 3.6 24.4 - - + +
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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
----------------------------------------------------------
375A LYS* 4.1 3.8 + - - -
396A TYR* 2.5 37.3 + - - -
398A SER* 2.9 40.1 + - - +
399A LEU* 3.6 7.3 - - - +
400A PRO* 4.6 5.6 - - + -
625A LEU* 3.0 30.6 + - + +
626A MSE 3.5 15.9 - - + +
627A ASP 3.2 0.2 - - - -
628A LEU* 1.3 75.7 - - - +
630A ALA* 1.3 57.6 + - - +
632A HIS* 3.3 5.9 + - - +
633A ASP* 3.0 33.6 + - - +
666A ILE* 4.1 13.0 - - + -
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Residues in contact with ALA 630 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583A GLN* 3.7 32.5 - - + +
585A PHE* 4.6 12.8 - - + -
586A VAL* 3.9 6.0 - - + +
626A MSE 2.9 14.0 + - - +
627A ASP* 3.1 12.5 + - - +
629A GLU* 1.3 74.9 - - - +
631A VAL* 1.3 63.7 + - - +
633A ASP* 3.2 11.3 + - - +
634A VAL* 3.0 26.5 + - - +
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Residues in contact with VAL 631 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585A PHE* 4.2 18.8 - - + -
612A ILE* 3.8 33.4 - - + +
616A LEU* 3.8 29.4 - - + -
627A ASP* 2.9 22.6 + - + +
628A LEU* 3.5 8.1 - - + +
630A ALA* 1.3 71.2 - - - +
632A HIS* 1.3 66.6 + - - +
634A VAL* 3.0 16.6 + - - +
635A LEU* 3.0 14.7 + - + +
662A LEU* 3.7 16.6 - - + -
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Residues in contact with HIS 632 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A SER 5.8 0.8 + - - -
400A PRO* 3.4 38.1 - - + +
401A PRO* 4.1 14.8 - - + +
628A LEU 2.8 17.9 + - - +
629A GLU* 3.4 11.2 + - - +
631A VAL* 1.3 72.1 - - - +
633A ASP* 1.4 64.3 + - - +
635A LEU* 3.2 3.7 + - - +
636A ASP* 3.0 38.7 + - - +
659A GLN* 3.2 58.4 + - + +
662A LEU* 3.4 15.1 - - + +
663A ASP* 4.5 6.7 + - + -
666A ILE* 4.1 8.5 - - + -
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Residues in contact with ASP 633 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A SER* 5.2 11.2 - - - +
580A ASN* 4.4 23.0 + - - +
583A GLN* 5.3 1.4 - - - +
586A VAL* 4.0 18.5 - - + +
629A GLU* 3.0 20.9 + - - +
630A ALA* 3.5 11.0 - - - +
631A VAL 3.2 0.2 - - - -
632A HIS* 1.4 81.3 + - - +
634A VAL* 1.3 62.0 + - - +
636A ASP* 3.4 12.4 + - - +
637A LEU* 2.9 26.2 + - - +
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Residues in contact with VAL 634 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585A PHE* 3.6 24.0 - - + -
586A VAL* 3.9 15.9 - - + -
589A SER* 3.4 40.2 - - - +
593A PHE* 3.8 15.2 - - + -
608A LEU* 4.6 8.5 - - + -
611A TYR* 4.6 5.4 - - + -
612A ILE* 4.8 4.5 - - + -
630A ALA 3.0 17.2 + - - +
631A VAL* 3.0 9.6 + - - +
633A ASP* 1.3 77.9 - - - +
635A LEU* 1.3 56.9 + - + +
637A LEU* 3.2 7.8 + - + +
638A TYR* 3.0 25.5 + - - +
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Residues in contact with LEU 635 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608A LEU* 3.6 34.3 - - + -
612A ILE* 4.2 19.7 - - + -
631A VAL* 3.0 17.0 + - + +
632A HIS 3.2 7.2 + - - +
634A VAL* 1.3 76.6 - - + +
636A ASP* 1.3 57.7 + - - +
638A TYR* 3.2 5.9 + - - +
639A LEU* 3.0 32.2 + - - +
655A ILE* 4.1 10.4 - - + +
658A LEU* 4.2 15.9 - - + -
659A GLN* 3.6 48.0 - - + +
662A LEU* 4.1 14.8 - - + -
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Residues in contact with ASP 636 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A LYS* 4.0 15.8 + - - -
257A GLU* 3.7 23.2 - - + +
632A HIS* 3.0 25.9 + - - +
633A ASP* 3.5 14.6 - - - +
635A LEU* 1.3 75.7 - - - +
637A LEU* 1.3 56.7 + - - +
639A LEU* 3.2 8.5 + - - +
640A TRP* 2.8 30.7 + - - +
659A GLN* 2.9 25.4 + - - +
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Residues in contact with LEU 637 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577A ALA* 3.5 32.5 - - + -
578A PRO 5.1 4.3 - - - +
579A ILE* 4.0 21.1 - - + -
586A VAL* 4.4 9.0 - - + +
589A SER* 4.4 3.8 - - - -
590A LEU* 3.9 33.0 - - + +
593A PHE* 3.8 26.9 - - + -
633A ASP 2.9 14.1 + - - +
634A VAL* 3.2 9.8 + - - +
636A ASP* 1.3 74.7 - - - +
638A TYR* 1.3 64.2 + - - +
640A TRP* 3.6 5.7 - - + +
641A LEU* 3.0 36.3 + - + +
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Residues in contact with TYR 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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593A PHE* 3.9 15.0 - + + -
603A LEU* 2.7 44.6 + - + -
604A THR 4.8 0.4 - - - -
608A LEU* 3.5 33.9 - - + -
634A VAL 3.0 13.3 + - - +
635A LEU 3.5 8.3 - - - +
637A LEU* 1.3 77.5 - - - +
639A LEU* 1.3 62.9 + - + +
641A LEU* 3.3 2.4 + - - +
642A SER* 3.0 24.6 + - - -
649A PHE* 3.3 34.0 - + + -
651A ASP* 3.0 36.5 + - - +
652A ALA* 4.1 3.4 - - - -
655A ILE* 3.7 27.6 - - + -
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Residues in contact with LEU 639 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A GLU* 3.8 18.8 - - + +
258A GLU* 5.9 0.9 - - + -
635A LEU 3.0 18.4 + - - +
636A ASP* 3.5 12.6 - - - +
638A TYR* 1.3 77.3 - - + +
640A TRP* 1.3 62.6 + - - +
642A SER* 2.6 22.9 + - - +
643A TYR* 3.2 13.9 - - + -
652A ALA* 3.4 42.6 - - + +
655A ILE* 4.1 11.4 - - + -
656A ARG* 4.1 31.2 - - + +
659A GLN* 3.5 27.1 - - - +
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Residues in contact with TRP 640 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A GLY* 3.6 22.5 - - - -
257A GLU* 3.3 26.5 - - - +
573A VAL* 3.6 21.5 - - + -
576A THR* 3.3 29.8 - - - -
577A ALA* 3.5 31.4 - - + -
578A PRO* 3.6 22.7 - - + +
636A ASP 2.8 20.0 + - - +
637A LEU* 3.6 8.7 - - + +
639A LEU* 1.3 72.9 - - - +
641A LEU* 1.3 74.5 + - + +
643A TYR 3.4 2.9 + - - -
644A ARG* 2.7 69.1 + - - +
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Residues in contact with LEU 641 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574A PHE* 3.8 34.8 - - + -
577A ALA* 4.4 4.5 - - + -
590A LEU* 5.1 0.4 - - + -
593A PHE* 3.7 27.8 - - + -
637A LEU* 3.0 32.4 + - + +
638A TYR 3.8 3.1 - - - +
640A TRP* 1.3 101.7 - - + +
642A SER* 1.3 56.9 + - - +
644A ARG* 2.9 5.0 + - - +
645A PHE* 2.8 45.1 + - + +
649A PHE* 3.8 26.5 - - + -
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Residues in contact with SER 642 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638A TYR* 3.0 15.8 + - - -
639A LEU* 2.6 21.3 + - - -
641A LEU* 1.3 76.3 - - - +
643A TYR* 1.3 66.2 + - - +
644A ARG 3.3 0.2 - - - -
645A PHE 3.9 1.3 - - - -
646A MSE 3.4 27.4 - - - +
649A PHE* 3.3 34.0 - - - +
652A ALA* 3.5 26.0 - - - +
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Residues in contact with TYR 643 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A GLY 4.0 6.3 - - - -
257A GLU 3.3 24.2 - - - -
258A GLU* 3.7 1.0 - - - -
259A ARG* 3.3 81.8 + - + +
639A LEU* 3.2 21.8 - - - -
640A TRP 3.4 1.2 + - - -
641A LEU 3.1 0.8 - - - -
642A SER* 1.3 83.8 + - - +
644A ARG* 1.4 70.8 + - - +
646A MSE 5.0 6.8 - - + +
652A ALA* 5.4 2.0 - - + -
656A ARG* 3.1 26.1 + - - -
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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) + - + + + + + -
------------------------------------------------------------
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