Contacts of the helix formed by residues 611 - 630 (chain D) in PDB entry 2BKU
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 611 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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605D LEU 3.7 11.4 - - - -
606D LEU* 4.1 9.2 + - - -
608D LYS* 3.6 21.1 + - - +
609D LYS* 4.3 0.8 - - - -
610D ASP* 1.3 75.0 - - - +
612D ALA* 1.3 65.0 + - - +
613D PHE* 2.9 6.0 + - - -
614D ILE* 2.9 24.3 + - - +
615D GLU* 2.8 49.0 + - - +
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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
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35C PHE* 3.1 40.0 - - + +
37C LYS* 3.7 23.8 - - + +
152C LYS* 5.5 0.5 - - - -
610D ASP* 3.6 2.0 - - - -
611D SER* 1.3 79.7 + - - +
613D PHE* 1.3 60.4 + - - +
614D ILE 3.5 0.5 + - - -
615D GLU* 3.6 22.3 + - - +
616D ASP* 4.7 2.4 + - - +
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Residues in contact with PHE 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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29C ARG* 3.3 30.5 - - - +
33C GLY 5.8 0.2 - - - -
35C PHE* 3.6 21.9 - - + +
152C LYS* 3.4 31.3 - - - +
570D GLN* 3.2 52.5 - - + -
573D GLN* 3.1 25.6 - - + -
574D SER* 3.6 15.1 + - - -
605D LEU* 5.4 0.2 - - + -
608D LYS* 5.6 4.0 - - - -
610D ASP 3.4 22.4 - - - -
611D SER* 2.9 1.9 + - - -
612D ALA* 1.3 79.4 - - - +
614D ILE* 1.3 90.3 + - + +
616D ASP 5.2 0.2 + - - -
617D ASP* 4.2 2.6 - - - +
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Residues in contact with ILE 614 (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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573D GLN* 4.5 3.1 - - + -
574D SER* 4.3 17.3 - - - +
577D LEU* 3.9 20.4 - - + -
605D LEU* 3.8 33.4 - - + +
606D LEU* 5.1 1.1 - - + +
608D LYS* 5.6 0.7 - - - -
611D SER* 2.9 39.2 + - - +
613D PHE* 1.3 114.9 - - + +
615D GLU* 1.3 73.0 + - + +
616D ASP 3.3 2.5 - - - -
617D ASP* 2.8 23.9 + - - +
618D VAL* 2.8 22.1 + - + -
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Residues in contact with GLU 615 (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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37C LYS* 2.8 36.0 + - - +
606D LEU* 3.9 27.4 - - + +
611D SER* 2.8 37.0 + - - +
612D ALA* 3.6 18.2 + - - +
613D PHE 3.7 1.2 - - - -
614D ILE* 1.3 76.1 - - - +
616D ASP* 1.3 57.8 + - - +
618D VAL* 3.3 2.8 + - - +
619D PHE* 2.9 29.7 + - - +
643D TYR* 6.3 0.9 - - + -
646D LYS* 3.5 14.9 + - - -
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Residues in contact with ASP 616 (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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37C LYS* 3.2 34.4 + - - +
152C LYS* 4.2 17.9 + - - +
612D ALA 4.7 2.7 + - - +
614D ILE 3.3 1.0 - - - -
615D GLU* 1.3 78.5 - - - +
617D ASP* 1.3 53.3 + - - +
619D PHE* 3.1 7.4 + - - +
620D TYR* 2.8 57.0 + - + -
650D GLN* 4.0 3.5 + - - +
653D SER* 4.1 13.5 + - - -
655D VAL* 3.9 19.8 - - - +
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Residues in contact with ASP 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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152C LYS* 3.1 28.1 + - - +
574D SER* 4.9 13.5 - - - +
577D LEU* 4.1 19.6 - - + +
581D ALA* 5.6 1.9 - - - +
613D PHE 4.2 9.0 - - - +
614D ILE* 2.8 24.6 + - + +
616D ASP* 1.3 71.5 - - - +
618D VAL* 1.3 57.0 + - - +
620D TYR* 3.3 13.6 + - - +
621D ALA* 2.9 28.8 + - - +
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Residues in contact with VAL 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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577D LEU* 3.5 33.9 - - + -
602D PHE* 3.6 27.4 - - + -
605D LEU* 3.8 19.3 - - + -
606D LEU* 3.6 33.2 - - + -
614D ILE* 2.8 20.3 + - + +
615D GLU 3.8 6.7 - - - +
617D ASP* 1.3 74.9 - - - +
619D PHE* 1.3 56.8 + - - +
621D ALA* 3.7 1.2 - - - +
622D ILE* 2.9 29.7 + - + +
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Residues in contact with PHE 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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606D LEU* 5.3 1.9 - - + +
615D GLU 2.9 14.6 + - - +
616D ASP* 3.4 11.2 - - - +
618D VAL* 1.3 74.3 - - - +
620D TYR* 1.3 65.7 + - - +
622D ILE* 3.3 6.9 + - - +
623D SER* 2.9 48.6 + - - -
640D PHE* 3.4 31.6 - + - -
643D TYR* 3.9 13.2 - - + -
644D LEU* 3.9 12.1 - - + -
647D ALA* 3.7 17.0 - - + -
655D VAL* 3.7 20.6 - - + -
658D THR* 3.5 19.5 - - - -
659D ALA* 3.6 33.0 - - + -
662D PHE* 4.7 1.8 - - + -
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Residues in contact with TYR 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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152C LYS* 5.2 4.0 - - - -
581D ALA* 6.2 2.2 - - + -
585D ARG* 3.3 27.5 + - - +
616D ASP* 2.8 43.7 + - + +
617D ASP* 3.6 14.6 - - - +
619D PHE* 1.3 75.9 - + - +
621D ALA* 1.3 62.1 + - - +
623D SER* 3.6 4.0 - - - -
624D ALA* 3.2 17.2 + - - +
653D SER* 4.9 0.3 + - - -
654D PRO* 3.8 12.9 - - - +
655D VAL* 3.4 33.6 + - + +
658D THR* 3.6 39.9 - - + -
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Residues in contact with ALA 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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577D LEU* 4.0 11.4 - - + -
581D ALA* 4.7 14.8 - - + +
584D ILE* 4.1 14.2 - - + +
585D ARG* 5.7 0.2 - - - +
602D PHE* 3.9 25.1 - - + -
617D ASP 2.9 16.6 + - - +
618D VAL 3.7 4.3 - - - +
619D PHE 3.2 0.2 - - - -
620D TYR* 1.3 74.5 - - - +
622D ILE* 1.3 59.9 + - - +
624D ALA* 3.3 7.4 + - - +
625D LEU* 3.0 28.9 + - - +
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Residues in contact with ILE 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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599D MET* 3.8 18.4 - - + -
602D PHE* 3.6 22.0 - - + -
603D PHE* 5.0 1.6 - - + -
606D LEU* 4.0 13.7 - - + -
618D VAL* 2.9 37.9 + - + +
619D PHE* 3.9 3.1 - - - +
621D ALA* 1.3 71.5 - - - +
623D SER* 1.3 56.0 + - - +
625D LEU* 3.2 8.0 + - - +
626D ALA* 2.7 34.0 + - + +
633D PHE* 3.4 32.9 - - + -
640D PHE* 3.5 33.9 - - + -
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Residues in contact with SER 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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585D ARG* 5.5 1.6 - - - -
619D PHE* 2.9 47.5 + - - -
620D TYR* 3.6 7.6 - - - -
622D ILE* 1.3 75.8 - - - +
624D ALA* 1.3 57.9 + - - +
626D ALA* 3.1 4.9 + - - +
627D ALA* 2.9 27.8 + - - +
640D PHE* 4.9 0.2 - - - -
658D THR* 4.5 9.8 + - - -
662D PHE* 4.2 26.4 - - - +
665D ASP* 5.0 3.0 - - - +
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Residues in contact with ALA 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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581D ALA* 6.5 0.2 - - - -
584D ILE* 3.7 16.0 - - + +
585D ARG* 3.8 35.4 - - + +
620D TYR 3.2 10.7 + - - +
621D ALA* 3.6 9.4 - - - +
623D SER* 1.3 77.7 - - - +
625D LEU* 1.3 65.2 + - - +
627D ALA* 3.2 21.3 + - - +
628D SER* 3.4 10.2 + - - -
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Residues in contact with LEU 625 (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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584D ILE* 3.3 19.4 - - + +
588D PRO* 5.0 4.0 - - + -
591D VAL* 4.2 14.6 - - + +
592D GLU* 4.9 14.8 - - + -
595D ALA* 4.7 4.9 - - + +
598D LEU* 3.9 36.6 - - + -
599D MET* 3.7 32.5 - - + -
602D PHE* 4.8 3.1 - - + -
621D ALA 3.0 16.8 + - - +
622D ILE* 3.6 5.8 - - - +
624D ALA* 1.3 75.2 - - - +
626D ALA* 1.3 62.0 + - - +
628D SER* 3.2 14.6 + - - -
629D LEU* 3.2 29.5 + - + +
633D PHE* 5.4 0.7 - - + -
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Residues in contact with ALA 626 (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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622D ILE 2.7 21.0 + - - +
623D SER 3.3 5.4 - - - +
625D LEU* 1.3 70.2 - - - +
627D ALA* 1.3 65.9 + - - +
628D SER 3.3 0.3 + - - -
629D LEU 4.6 0.2 - - - +
630D GLY* 3.3 22.2 + - - +
633D PHE* 3.6 30.2 - - + +
662D PHE* 3.5 31.4 - - + -
665D ASP* 5.4 3.5 - - + +
666D ILE* 5.2 5.8 - - + +
669D SER* 5.5 0.3 + - - -
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Residues in contact with ALA 627 (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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832B LYS* 4.5 7.3 + - - +
836B SER* 5.1 12.4 + - - +
623D SER 2.9 11.3 + - - +
624D ALA* 3.2 14.8 + - - +
626D ALA* 1.3 78.6 - - - +
628D SER* 1.3 58.9 + - - +
630D GLY* 4.2 4.9 + - - -
665D ASP* 3.9 27.1 + - - +
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Residues in contact with SER 628 (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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832B LYS* 3.1 23.1 + - - +
584D ILE 4.6 4.2 + - - -
588D PRO* 3.4 25.3 - - - +
592D GLU* 3.5 24.0 - - - +
624D ALA 3.4 7.8 + - - -
625D LEU* 3.2 11.0 + - - -
627D ALA* 1.3 75.6 - - - +
629D LEU* 1.3 64.5 + - - +
630D GLY 3.1 2.0 - - - -
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Residues in contact with LEU 629 (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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832B LYS* 5.0 1.3 + - - -
592D GLU* 3.6 37.9 - - + +
595D ALA* 4.3 14.4 - - + -
625D LEU* 3.2 25.8 + - + +
626D ALA 3.7 0.6 + - - +
628D SER* 1.3 78.6 - - - +
630D GLY* 1.3 53.6 - - - +
631D LYS 3.2 1.0 + - - -
632D GLY* 2.7 36.0 + - - +
633D PHE* 3.6 25.1 - - + +
635D LYS* 5.6 1.6 - - - +
636D TYR* 3.8 29.6 - - + -
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Residues in contact with GLY 630 (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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832B LYS* 4.8 6.3 - - - -
626D ALA 3.3 12.1 + - - +
627D ALA 4.7 4.0 - - - -
628D SER 3.1 7.4 - - - -
629D LEU* 1.3 74.0 - - - +
631D LYS* 1.3 62.7 + - - -
632D GLY 3.1 0.9 + - - -
633D PHE* 3.1 16.8 + - - +
634D GLU 4.5 0.9 + - - -
666D ILE* 4.6 3.6 - - - +
669D SER* 3.3 30.8 + - - -
670D LEU* 5.0 0.7 - - - +
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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