Contacts of the helix formed by residues 620 - 641 (chain A) in PDB entry 4BI2
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 620 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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618A SER* 4.2 2.2 + - - -
619A ILE* 1.3 71.3 - - - +
621A PRO* 1.4 79.1 - - - +
622A TRP* 3.3 24.5 + - - +
623A GLU* 2.9 41.3 + - + +
624A ARG* 2.9 12.2 + - - +
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Residues in contact with PRO 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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619A ILE 3.5 6.5 - - - +
620A ASP* 1.4 88.5 - - - +
622A TRP* 1.4 55.2 + - - +
624A ARG* 3.4 24.7 + - - +
625A LYS* 2.9 30.3 + - - +
761A GLU* 3.4 28.4 - - + +
790A TYR* 4.2 0.2 + - - -
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Residues in contact with TRP 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 ASP* 3.1 19.9 + - - +
621A PRO* 1.4 74.6 - - - +
623A GLU* 1.4 65.0 + - + +
624A ARG 3.2 0.2 - - - -
625A LYS* 3.2 8.2 + - + +
626A SER* 2.8 42.0 + - - -
794A GLN* 6.5 0.7 - - + -
1798A EDO 3.5 39.8 + - - -
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Residues in contact with GLU 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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612A TRP* 2.9 43.2 + - - -
618A SER 5.3 1.4 - - - +
619A ILE* 3.6 17.5 - - + +
620A ASP* 2.9 30.1 + - + +
622A TRP* 1.4 85.1 - - + +
624A ARG* 1.3 57.1 + - - +
626A SER* 3.4 4.7 - - - -
627A TYR* 2.9 57.7 + - + +
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Residues in contact with ARG 624 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619A ILE* 4.0 24.8 + - + +
620A ASP 2.9 12.7 + - - +
621A PRO* 3.4 24.6 - - - +
623A GLU* 1.3 73.2 - - - +
625A LYS* 1.4 53.8 + - - +
627A TYR* 3.1 7.5 + - - +
628A TRP* 2.9 35.9 + - - +
724A LEU* 3.9 13.0 - - + -
727A MET* 2.7 52.2 + - + +
728A THR* 3.5 27.4 + - - +
761A GLU* 3.1 24.7 + - - +
764A LEU* 3.6 16.8 - - - +
790A TYR* 3.7 11.3 + - - +
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Residues in contact with LYS 625 (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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621A PRO 2.9 23.1 + - - +
622A TRP* 3.6 8.1 - - + +
624A ARG* 1.4 70.8 - - - +
626A SER* 1.4 60.5 + - - +
628A TRP* 3.5 3.6 - - - +
629A LYS* 3.1 22.7 + - - +
761A GLU* 3.9 13.5 + - - -
763A ASP* 5.6 1.8 + - - -
790A TYR* 2.8 63.6 + - + +
791A VAL* 5.0 7.9 - - - +
793A ILE 2.7 29.0 + - - +
794A GLN* 4.8 6.8 + - - +
1798A EDO 4.3 14.4 - - - +
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Residues in contact with SER 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 TRP* 2.8 23.8 + - - -
623A GLU* 3.4 7.9 - - - -
625A LYS* 1.4 76.2 - - - +
627A TYR* 1.4 65.2 + - - +
629A LYS* 3.1 16.7 + - - +
630A ASN* 3.1 24.4 + - - +
658A GLY 4.9 6.2 + - - -
1798A EDO 3.6 29.7 + - - -
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Residues in contact with TYR 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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609A LEU* 4.1 13.0 - - + -
612A TRP* 3.9 19.3 + + - -
619A ILE* 4.6 7.9 - - + -
623A GLU* 2.9 58.7 + - + +
624A ARG* 3.6 6.1 - - - +
626A SER* 1.4 76.6 - - - +
628A TRP* 1.3 56.0 + - - +
630A ASN* 3.3 8.7 + - - +
631A MET* 3.0 38.3 + - + +
655A ILE* 3.8 29.5 - - + +
658A GLY* 3.4 32.6 - - - -
660A LEU* 3.7 24.8 - - + +
727A MET* 4.8 5.4 - - - -
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Residues in contact with TRP 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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624A ARG 2.9 15.7 + - - +
625A LYS 3.5 6.3 - - - +
627A TYR* 1.3 72.5 - - - +
629A LYS* 1.3 64.7 + - - +
631A MET* 2.9 30.8 + - + +
632A LEU* 3.0 44.0 + - + +
720A LEU* 2.9 55.6 - - + -
721A GLY* 3.9 5.6 - - - -
724A LEU* 3.6 36.1 - - + -
767A VAL* 3.9 25.9 - - + +
771A CYS* 4.2 10.5 - - - -
785A LEU* 4.2 4.9 - - + +
790A TYR* 3.7 15.7 - + + -
791A VAL* 3.4 29.4 - - + +
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Residues in contact with LYS 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 LYS 3.1 9.7 + - - +
626A SER* 3.1 12.7 + - - +
628A TRP* 1.3 79.1 - - - +
630A ASN* 1.3 64.7 + - - +
632A LEU* 3.3 13.6 + - - +
633A GLU* 3.2 23.4 + - - +
786A LEU* 4.9 3.2 - - - +
791A VAL* 4.6 17.0 - - + +
1798A EDO 5.8 5.4 - - - -
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Residues in contact with ASN 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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584A LYS* 3.2 32.9 - - + +
626A SER* 3.1 20.9 + - - +
627A TYR* 3.4 10.5 - - - +
628A TRP 3.2 0.2 - - - -
629A LYS* 1.3 79.8 - - - +
631A MET* 1.3 57.0 + - - +
633A GLU* 3.7 1.0 + - - +
634A ALA* 3.2 26.9 + - - +
653A PHE* 5.1 0.6 - - - -
658A GLY 4.3 4.4 + - - -
659A MET* 3.5 17.8 - - - +
660A LEU* 3.1 43.1 - - + +
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Residues in contact with MET 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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609A LEU* 4.4 0.7 - - + -
627A TYR 3.0 26.9 + - - +
628A TRP* 2.9 21.0 + - + +
630A ASN* 1.3 72.8 - - - +
632A LEU* 1.3 63.2 + - - +
634A ALA* 4.1 1.0 - - - +
635A VAL* 3.2 29.8 + - - +
653A PHE* 3.6 31.9 - - + -
660A LEU* 3.8 18.6 - - + -
720A LEU* 3.6 24.8 - - + +
723A ILE* 3.7 21.5 - - + -
727A MET* 3.4 36.6 - - + -
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Residues in contact with LEU 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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628A TRP* 3.0 64.9 + - + +
629A LYS* 3.3 6.9 + - - +
631A MET* 1.3 75.5 - - - +
633A GLU* 1.4 56.0 + - - +
635A VAL* 3.4 0.9 + - - +
636A HIS* 2.7 39.4 + - - +
720A LEU* 4.5 8.5 - - + -
782A ILE* 4.0 14.0 - - + +
785A LEU* 3.9 32.5 - - + -
786A LEU* 3.7 26.0 - - + -
791A VAL* 3.8 15.3 - - + -
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Residues in contact with GLU 633 (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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581A HIS 5.0 1.4 - - - +
582A SER* 2.8 27.6 + - - +
583A ASP* 3.4 9.0 - - - +
584A LYS* 3.0 32.4 + - + +
629A LYS 3.2 14.4 + - - +
630A ASN* 3.9 5.2 - - - +
632A LEU* 1.4 78.0 - - - +
634A ALA* 1.3 61.1 + - - +
636A HIS* 3.7 6.5 + - - +
637A THR* 3.1 34.9 + - + +
786A LEU* 4.4 8.4 - - + +
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Residues in contact with ALA 634 (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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584A LYS* 3.7 27.1 - - + +
585A ILE* 4.2 3.4 - - + +
630A ASN 3.2 16.2 + - - +
631A MET 4.1 4.0 - - - +
632A LEU 3.3 0.2 - - - -
633A GLU* 1.3 75.6 - - - +
635A VAL* 1.4 63.7 + - - +
637A THR* 2.9 22.6 + - - -
638A ILE* 3.4 10.9 + - - +
653A PHE* 4.3 8.7 - - + -
661A LYS* 5.7 0.4 - - - -
662A LEU* 3.8 24.5 - - + +
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Residues in contact with VAL 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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631A MET 3.2 20.0 + - - +
632A LEU 4.2 0.9 - - - +
634A ALA* 1.4 73.3 - - + +
636A HIS* 1.3 61.8 + - - +
638A ILE* 3.2 16.2 - - + +
639A HIS* 3.0 51.5 + - + +
648A LEU* 4.1 22.4 - - + -
653A PHE* 4.3 6.5 - - + -
662A LEU* 5.0 4.0 - - + -
716A ASP* 3.7 18.6 - - + +
720A LEU* 3.7 20.2 - - + -
782A ILE* 3.8 7.6 - - + -
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Residues in contact with HIS 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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632A LEU 2.7 24.6 + - - +
633A GLU* 3.8 6.9 + - - +
635A VAL* 1.3 72.2 - - - +
637A THR* 1.3 59.1 + - - +
639A HIS* 3.4 9.2 + - + +
640A GLN* 3.0 59.2 + - + +
782A ILE* 3.5 28.1 - - + +
783A PRO* 4.2 20.6 - - + +
786A LEU* 3.7 18.2 - - + +
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Residues in contact with THR 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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578A LEU* 4.4 3.8 - - - -
581A HIS* 4.8 16.8 - - + +
582A SER* 3.6 21.5 - - - +
585A ILE* 3.4 18.7 - - - +
633A GLU* 3.1 19.2 + - + +
634A ALA 2.9 14.5 + - - -
636A HIS* 1.3 75.7 - - + +
638A ILE* 1.3 64.0 + - - +
640A GLN* 3.2 24.1 + - - +
641A HIS* 3.0 26.5 + - - -
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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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578A LEU* 3.6 19.7 - - + -
585A ILE* 4.1 3.6 - - + -
634A ALA 3.4 4.1 + - - +
635A VAL* 3.2 27.1 - - + +
637A THR* 1.3 75.3 - - - +
639A HIS* 1.4 56.6 + - + +
641A HIS 3.1 7.8 + - - -
642A GLY 3.3 0.2 + - - -
643A ILE* 2.8 51.1 + - + +
645A HIS* 3.6 41.7 - - + +
662A LEU* 3.7 19.3 - - + -
665A PHE* 3.6 33.0 - - + -
716A ASP* 4.5 3.6 - - - +
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Residues in contact with HIS 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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635A VAL* 3.0 22.3 + - + +
636A HIS* 3.5 15.4 - - + +
638A ILE* 1.4 77.0 - - + +
640A GLN* 1.3 56.6 + - - +
642A GLY* 3.0 19.9 + - - -
643A ILE 2.9 28.5 - - - -
644A VAL* 4.2 1.6 - - - -
713A PRO* 3.3 53.4 - - + +
716A ASP* 2.7 25.7 + - + -
782A ILE* 3.5 32.8 - - + +
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Residues in contact with GLN 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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581A HIS* 5.2 3.8 - - - -
636A HIS* 3.0 51.8 + - + +
637A THR* 3.2 25.4 + - - +
639A HIS* 1.3 77.2 - - - +
641A HIS* 1.3 68.9 + - + +
642A GLY 3.3 0.8 + - - -
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Residues in contact with HIS 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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574A TYR* 4.0 22.9 + + + -
577A LYS* 4.7 9.8 - - + +
578A LEU* 3.6 30.2 - - + +
581A HIS* 3.3 49.6 + + + -
637A THR 3.0 21.8 + - - +
638A ILE 3.1 8.7 + - - +
640A GLN* 1.3 84.9 - - + +
642A GLY* 1.3 58.8 + - - +
643A ILE* 3.4 8.5 + - + -
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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
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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