Contacts of the helix formed by residues 602 - 625 (chain D) in PDB entry 3A8P
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 SER 602 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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584D HIS* 3.4 20.6 - - - -
600D ALA* 3.4 2.6 + - - +
601D THR* 1.3 83.2 + - - +
603D GLN* 1.3 60.1 + - - +
604D THR* 3.4 9.2 + - - -
605D ASP* 3.1 20.3 + - - +
606D LEU* 3.0 27.4 + - - +
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Residues in contact with GLN 603 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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712C ALA* 3.8 32.0 - - + +
584D HIS* 3.3 21.8 + - + +
602D SER* 1.3 75.7 - - - +
604D THR* 1.3 58.3 + - - +
606D LEU* 3.4 19.7 + - - +
607D GLU* 3.0 69.1 + - - +
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Residues in contact with THR 604 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602D SER* 3.2 7.7 + - - -
603D GLN* 1.3 78.7 - - - +
605D ASP* 1.3 59.6 + - - +
607D GLU* 3.2 14.8 + - - +
608D ASN* 2.9 45.0 + - - +
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Residues in contact with ASP 605 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507D LYS* 4.0 10.6 + - - -
510D TRP 4.4 1.2 - - - +
511D LEU* 4.3 1.7 - - - +
600D ALA* 3.1 9.5 - - - +
601D THR* 2.8 45.7 + - - +
602D SER* 3.1 17.3 + - - +
604D THR* 1.3 75.3 - - - +
606D LEU* 1.3 65.8 + - - +
608D ASN* 3.2 8.1 + - - +
609D TRP* 3.0 48.1 + - - -
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Residues in contact with LEU 606 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575D SER* 4.1 21.1 - - - -
584D HIS* 3.6 23.1 - - - +
585D VAL 3.5 26.9 - - - +
586D PHE* 4.0 15.7 - - + -
600D ALA* 3.5 12.7 - - + +
602D SER 3.0 16.3 + - - +
603D GLN* 3.6 24.5 - - - +
605D ASP* 1.3 76.3 - - - +
607D GLU* 1.3 69.8 + - + +
609D TRP* 3.0 4.8 + - - +
610D VAL* 2.9 42.0 + - + +
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Residues in contact with GLU 607 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603D GLN* 3.0 45.2 + - - +
604D THR* 3.6 14.8 + - - +
606D LEU* 1.3 82.1 - - + +
608D ASN* 1.3 59.9 + - - +
610D VAL* 3.5 5.1 + - - +
611D THR* 3.0 34.0 + - - +
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Residues in contact with ASN 608 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507D LYS* 3.4 27.9 - - - +
604D THR* 2.9 35.1 + - - +
605D ASP* 3.6 8.8 - - - +
606D LEU 3.1 0.2 - - - -
607D GLU* 1.3 75.7 - - - +
609D TRP* 1.3 59.7 + - - +
611D THR* 3.6 5.6 + - - +
612D ALA* 3.0 30.5 + - - +
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Residues in contact with TRP 609 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507D LYS* 3.5 33.6 - - + +
508D ALA 4.1 0.7 - - - -
509D GLY* 3.8 23.1 - - - -
510D TRP 4.9 1.4 + - - -
511D LEU* 3.6 43.8 - - + +
538D VAL* 3.4 24.9 - - + -
539D THR 4.7 0.2 - - - -
540D LEU* 4.4 11.7 - - + -
545D LEU* 4.0 22.7 - - + -
586D PHE* 3.8 20.0 - + + -
600D ALA* 4.5 2.2 - - + -
605D ASP* 3.0 46.7 + - - -
606D LEU 3.5 6.5 - - - +
608D ASN* 1.3 75.9 - - - +
610D VAL* 1.3 64.8 + - - +
612D ALA* 3.9 1.5 - - + -
613D ILE* 3.0 49.4 + - + +
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Residues in contact with VAL 610 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573D VAL* 3.6 30.5 - - + +
574D GLN* 5.7 0.2 - - - -
575D SER 5.4 3.8 - - - +
586D PHE* 4.7 5.8 - - + -
606D LEU* 2.9 38.5 + - + +
607D GLU* 3.9 6.1 - - - +
609D TRP* 1.3 75.1 - - - +
611D THR* 1.3 59.2 + - - +
613D ILE* 4.0 0.7 - - - +
614D HIS* 3.0 56.8 + - + +
698D SER* 4.3 2.9 - - - +
704D LEU* 3.9 20.2 - - + -
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Residues in contact with THR 611 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607D GLU* 3.0 17.1 + - - +
608D ASN* 3.7 6.7 - - - +
610D VAL* 1.3 80.8 - - - +
612D ALA* 1.3 56.7 + - - +
614D HIS* 3.9 0.9 - - - +
615D SER* 2.7 43.3 + - - +
698D SER* 3.8 35.0 + - - +
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Residues in contact with ALA 612 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506D ARG* 3.9 11.7 - - + +
507D LYS* 4.2 22.2 - - + -
540D LEU* 3.5 17.6 - - + +
608D ASN 3.0 19.0 + - - +
609D TRP* 3.9 3.8 - - + +
610D VAL 3.4 0.2 - - - -
611D THR* 1.3 78.3 - - - +
613D ILE* 1.3 57.7 + - + +
615D SER* 3.4 5.8 + - - -
616D ALA* 2.9 30.1 + - - +
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Residues in contact with ILE 613 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540D LEU* 4.0 18.8 - - + -
545D LEU* 4.5 14.8 - - + -
568D ALA* 4.6 8.1 - - + -
571D SER* 4.9 1.6 - - - -
573D VAL* 3.6 27.8 - - + -
586D PHE* 4.3 20.9 - - + -
588D LEU* 4.0 26.5 - - + -
598D PHE* 5.9 0.2 - - + -
609D TRP* 3.0 36.3 + - + +
610D VAL 4.0 0.2 - - - +
612D ALA* 1.3 74.8 - - - +
614D HIS* 1.3 64.0 + - + +
616D ALA* 3.2 3.9 + - - +
617D CYS* 2.9 34.3 + - - -
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Residues in contact with HIS 614 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571D SER 4.2 3.8 - - - -
572D ILE* 3.9 3.4 - - - -
573D VAL* 2.9 51.8 + - + +
610D VAL* 3.0 24.9 + - + +
613D ILE* 1.3 77.3 - - + +
615D SER* 1.3 58.1 + - - +
617D CYS* 3.2 4.1 + - + +
618D ALA* 2.8 31.5 + - - +
694D CYS* 3.5 25.3 + - + +
695D TYR* 3.9 30.2 - + + -
698D SER* 2.9 34.7 + - - +
699D LEU* 5.5 0.2 - - - -
704D LEU* 3.9 7.2 - - + +
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Residues in contact with SER 615 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506D ARG* 3.6 21.9 + - - -
611D THR* 2.7 34.1 + - - +
612D ALA* 3.6 5.2 - - - -
614D HIS* 1.3 75.2 - - - +
616D ALA* 1.3 63.4 + - - +
618D ALA* 3.4 1.8 + - - +
619D SER* 3.0 24.4 + - - -
698D SER* 4.3 4.7 + - - -
699D LEU* 3.4 31.7 - - - +
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Residues in contact with ALA 616 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506D ARG* 3.7 21.9 - - - +
540D LEU* 4.1 9.4 - - + -
542D GLY 3.4 27.7 - - - +
543D CYS* 3.5 14.2 + - - +
612D ALA 2.9 17.9 + - - +
613D ILE 3.5 4.3 - - - +
615D SER* 1.3 77.1 - - - +
617D CYS* 1.3 62.7 + - - +
619D SER* 3.5 2.6 + - - -
620D LEU* 3.2 18.0 + - - +
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Residues in contact with CYS 617 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543D CYS* 3.7 13.5 - - - -
568D ALA* 3.0 28.5 - - - -
570D ASP* 3.9 6.9 + - - +
571D SER* 3.6 20.0 - - - -
613D ILE* 2.9 23.9 + - - +
614D HIS* 3.6 4.9 - - - +
616D ALA* 1.3 75.8 - - - +
618D ALA* 1.3 59.0 + - - +
620D LEU* 3.3 2.6 + - - +
621D PHE* 2.8 30.7 + - - +
695D TYR* 3.3 27.5 - - + +
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Residues in contact with ALA 618 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614D HIS 2.8 16.4 + - - +
615D SER 3.7 4.7 - - - +
617D CYS* 1.3 77.0 - - - +
619D SER* 1.3 57.7 + - - +
621D PHE* 3.3 4.6 + - - +
622D ALA* 2.9 30.1 + - - +
630D THR* 3.5 10.6 - - + +
634D LEU* 4.3 2.0 - - + -
695D TYR* 3.7 27.8 - - + -
699D LEU* 3.9 28.7 - - + -
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Residues in contact with SER 619 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506D ARG* 3.7 18.4 + - - -
615D SER 3.0 17.0 + - - -
616D ALA 3.7 4.9 - - - -
618D ALA* 1.3 76.9 - - - +
620D LEU* 1.3 57.8 + - - +
622D ALA* 3.2 7.3 + - - +
623D LYS* 3.0 44.4 + - - +
630D THR* 4.6 7.4 - - - -
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Residues in contact with LEU 620 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543D CYS* 3.8 22.0 - - + -
569D GLU* 3.6 45.3 - - + +
570D ASP* 5.2 0.4 - - - +
616D ALA 3.2 13.8 + - - +
617D CYS* 3.7 4.0 - - - +
619D SER* 1.3 75.7 - - - +
621D PHE* 1.3 66.9 + - - +
623D LYS* 3.2 25.0 + - + +
624D LYS* 2.9 35.2 + - + +
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Residues in contact with PHE 621 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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570D ASP* 3.9 19.5 + - - +
617D CYS 2.8 17.9 + - - +
618D ALA* 3.5 7.4 - - - +
620D LEU* 1.3 76.0 - - - +
622D ALA* 1.3 64.7 + - - +
624D LYS* 3.3 14.0 + - - +
625D HIS* 3.0 59.8 + + - -
633D LEU* 4.0 15.7 - - + -
634D LEU* 4.1 15.0 - - + -
637D GLN* 3.8 23.1 - - + -
691D ARG* 4.1 14.1 - - - -
692D MET* 3.7 34.8 - - + -
695D TYR* 4.6 3.1 - - + -
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Residues in contact with ALA 622 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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618D ALA 2.9 16.9 + - - +
619D SER* 3.5 5.6 - - - +
620D LEU 3.2 0.2 - - - -
621D PHE* 1.3 78.4 - - + +
623D LYS* 1.3 61.2 + - + +
625D HIS* 3.1 8.0 + - - +
627D LYS 3.0 38.6 + - - +
630D THR* 3.6 30.1 - - + +
633D LEU* 3.4 18.8 - - + -
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Residues in contact with LYS 623 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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619D SER* 3.0 25.5 + - - +
620D LEU* 3.2 36.0 + - + +
622D ALA* 1.3 78.3 - - + +
624D LYS* 1.3 57.6 + - - +
625D HIS 3.0 0.2 - - - -
626D GLY* 2.9 20.5 + - - +
627D LYS 4.6 5.4 - - - +
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Residues in contact with LYS 624 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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569D GLU* 2.5 30.8 + - - +
570D ASP* 2.8 29.5 + - - -
620D LEU* 2.9 32.7 + - + +
621D PHE* 3.3 20.3 + - - +
623D LYS* 1.3 76.4 - - - +
625D HIS* 1.3 65.0 + - + +
626D GLY 3.3 0.9 - - - -
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Residues in contact with HIS 625 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621D PHE* 3.0 51.7 + + - +
622D ALA 3.1 1.4 + - - +
623D LYS 3.0 1.0 - - - -
624D LYS* 1.3 85.0 - - + +
626D GLY* 1.3 63.2 + - - +
627D LYS* 3.2 18.5 + - + +
633D LEU* 3.5 40.8 - - + -
637D GLN* 4.4 12.1 + - - -
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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