Contacts of the helix formed by residues 700 - 719 (chain D) in PDB entry 1K0Y
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 PRO 700 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A THR* 3.7 24.9 - - + -
41A THR* 4.9 0.2 - - + -
698D VAL 3.2 4.2 - - - +
699D ASP* 1.3 90.3 - - - +
701D GLU* 1.4 55.1 + - - +
702D ASN 3.1 0.4 - - - -
703D PHE* 2.9 41.0 + - + +
704D ARG* 3.7 8.3 + - - +
738D ALA* 5.4 0.5 - - - +
742D ALA* 3.7 24.5 - - + -
745D TYR* 3.5 36.8 - - + -
801D CNO 3.9 11.7 - - + +
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Residues in contact with GLU 701 (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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94A ASP* 3.3 32.2 - - - +
96A VAL* 3.9 14.5 - - + +
699D ASP* 3.0 21.9 + - - +
700D PRO* 1.4 77.3 - - - +
702D ASN* 1.4 59.9 + - - +
704D ARG* 3.0 54.9 + - - +
705D LEU* 3.2 22.5 + - + +
801D CNO 3.3 22.8 - - + +
802D CNO 5.2 10.9 + - - +
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Residues in contact with ASN 702 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A TYR* 5.1 1.6 + - - -
94A ASP* 5.0 5.1 + - - +
631D LEU* 4.6 1.4 - - - +
637D TRP* 5.1 2.8 - - - -
638D THR* 3.3 28.4 - - + +
641D PHE* 3.2 36.1 - - - -
698D VAL* 3.7 4.9 - - + +
699D ASP* 2.9 33.5 + - - +
701D GLU* 1.4 77.9 - - - +
703D PHE* 1.4 55.3 + - - +
705D LEU* 3.3 12.6 + - - +
706D LEU 3.0 23.9 + - - -
748D HEM 3.5 28.2 - - + +
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Residues in contact with PHE 703 (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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692D HIS* 3.9 23.3 - + + -
698D VAL* 4.2 9.2 - - + -
700D PRO* 2.9 37.6 + - + +
702D ASN* 1.4 75.4 - - - +
704D ARG* 1.4 56.2 + - - +
706D LEU* 3.6 3.8 + - - +
707D GLY* 3.0 24.3 + - - -
734D VAL 5.2 0.9 - - - +
738D ALA* 3.9 30.2 - - + +
741D LEU* 3.8 36.3 - - + -
745D TYR* 3.6 22.7 - + - -
748D HEM 3.7 52.5 - + + +
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Residues in contact with ARG 704 (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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700D PRO* 3.7 4.3 + - - +
701D GLU* 3.0 44.6 + - - +
703D PHE* 1.4 75.3 - - - +
705D LEU* 1.4 65.6 + - + +
707D GLY* 3.2 3.1 + - - -
708D ASN* 3.0 33.0 + - - +
738D ALA* 4.5 15.3 - - + -
739D ASN* 4.8 11.2 + - - -
801D CNO 3.1 52.1 + - - -
802D CNO 4.5 24.9 - - + +
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Residues in contact with LEU 705 (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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94A ASP* 3.6 22.7 - - - +
631D LEU* 3.7 12.8 - - + -
635D TYR* 4.2 22.3 - - + -
637D TRP* 4.0 15.5 - - + +
638D THR* 4.2 16.4 - - + -
701D GLU* 3.2 21.1 + - - +
702D ASN* 3.3 11.0 + - - +
704D ARG* 1.4 80.2 - - + +
706D LEU* 1.4 55.7 + - - +
708D ASN* 3.3 7.6 + - + +
709D VAL* 2.9 32.4 + - - +
802D CNO 4.1 41.7 - - + +
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Residues in contact with LEU 706 (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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627D ALA* 4.1 33.7 - - + +
628D LEU* 4.5 9.2 - - + +
631D LEU* 3.7 19.4 - - + +
667D VAL* 3.8 13.9 - - + -
668D LEU* 5.8 4.5 - - + -
702D ASN 3.0 17.1 + - - +
703D PHE 3.8 4.3 - - - +
705D LEU* 1.4 74.9 - - - +
707D GLY* 1.4 53.4 + - - +
709D VAL* 3.3 2.2 + - + -
710D LEU* 2.8 35.8 + - + +
748D HEM 3.6 59.0 - - + -
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Residues in contact with GLY 707 (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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671D PHE* 6.2 0.9 - - - -
703D PHE 3.0 15.3 + - - -
704D ARG* 3.2 4.4 + - - -
706D LEU* 1.4 76.8 - - - +
708D ASN* 1.4 61.6 + - - +
710D LEU* 3.3 7.6 + - - +
711D VAL* 3.1 26.9 + - - +
734D VAL* 3.8 31.1 - - - +
748D HEM 6.1 1.1 - - - +
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Residues in contact with ASN 708 (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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436C PHE* 5.3 0.3 - - - -
503C HIS* 3.5 27.0 + - + +
635D TYR* 6.0 3.4 - - + +
704D ARG* 3.0 24.5 + - - +
705D LEU* 3.8 6.7 - - + +
707D GLY* 1.4 71.9 - - - +
709D VAL* 1.4 66.3 + - + +
711D VAL* 3.2 3.4 + - - +
712D CYS* 3.1 20.4 + - - -
731D GLN* 3.4 22.9 + - - -
734D VAL* 5.0 2.3 - - - +
802D CNO 3.0 51.1 + - + +
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Residues in contact with VAL 709 (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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522C HIS* 4.8 11.2 - - + +
627D ALA* 3.4 31.6 - - + +
630D ARG* 3.8 21.5 - - + -
631D LEU* 3.9 12.6 - - + +
634D VAL* 5.3 0.2 - - + -
635D TYR* 3.8 29.4 - - + -
705D LEU 2.9 19.9 + - - +
706D LEU* 3.7 6.5 - - - +
708D ASN* 1.4 75.1 - - - +
710D LEU* 1.4 63.2 + - - +
712D CYS* 3.1 10.5 + - - +
713D VAL* 3.0 21.7 + - + +
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Residues in contact with LEU 710 (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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615D TRP* 4.7 5.8 - - + -
623D VAL* 3.9 27.6 - - + -
627D ALA* 4.2 14.8 - - + -
668D LEU* 4.2 22.4 - - + -
671D PHE* 3.8 39.9 - - + -
706D LEU* 2.8 23.8 + - + +
707D GLY* 3.5 6.1 - - - +
709D VAL* 1.4 73.8 - - - +
711D VAL* 1.4 57.7 + - + +
713D VAL* 3.2 4.2 + - + +
714D LEU* 2.9 43.1 + - + +
730D TYR* 5.8 1.3 - - + -
734D VAL* 4.3 9.6 - - + -
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Residues in contact with VAL 711 (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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503C HIS* 4.4 1.3 - - - +
507C VAL* 3.9 15.9 - - + -
707D GLY 3.1 14.9 + - - +
708D ASN 3.2 8.0 + - - +
710D LEU* 1.4 76.8 - - + +
712D CYS* 1.4 55.6 + - - +
714D LEU* 3.3 5.1 + - + +
715D ALA* 3.0 27.7 + - - +
722D PHE* 3.7 27.2 - - + -
727D GLN* 4.0 4.5 - - + -
730D TYR* 4.4 18.8 - - + -
731D GLN* 3.4 33.4 - - - +
734D VAL* 4.4 14.8 - - + -
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Residues in contact with CYS 712 (chain D).
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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503C HIS* 4.3 7.4 - - - -
506C LEU* 4.4 19.3 - - - -
507C VAL* 4.1 21.8 - - - -
510C ALA* 3.6 8.4 - - + +
517C PHE* 4.5 8.0 - - + -
522C HIS* 4.0 31.4 - - + -
630D ARG* 6.1 0.7 - - - -
708D ASN 3.1 16.9 + - - -
709D VAL* 3.1 10.4 + - - +
711D VAL* 1.4 75.6 - - - +
713D VAL* 1.4 56.3 + - + +
715D ALA* 3.5 5.0 + - - -
716D HIS* 2.9 28.6 + - - +
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Residues in contact with VAL 713 (chain D).
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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623D VAL* 4.1 27.6 - - + +
626D GLU* 3.9 22.9 - - + +
627D ALA* 3.9 22.0 - - + +
630D ARG* 3.8 31.0 - - - +
709D VAL* 3.0 17.3 + - + +
710D LEU* 3.2 9.2 + - - +
712D CYS* 1.4 72.0 - - + +
714D LEU* 1.4 61.9 + - - +
716D HIS* 3.3 9.2 + - + +
717D HIS* 2.8 31.8 + - + +
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Residues in contact with LEU 714 (chain D).
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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614D LEU* 4.3 4.3 - - + -
615D TRP* 4.5 7.4 - - + -
618D VAL* 4.0 27.4 - - + -
623D VAL* 4.4 20.0 - - + -
710D LEU* 2.9 32.4 + - + +
711D VAL* 3.3 6.9 + - + +
713D VAL* 1.4 75.3 - - - +
715D ALA* 1.4 53.9 + - - +
717D HIS* 4.5 0.7 - - - -
718D PHE* 2.8 53.3 + - + +
722D PHE* 3.8 25.3 - - + +
730D TYR* 3.9 34.5 - - + -
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Residues in contact with ALA 715 (chain D).
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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507C VAL* 3.6 30.5 - - + +
510C ALA* 4.1 2.5 - - + -
511C ALA* 3.5 12.3 - - + +
711D VAL 3.0 14.2 + - - +
712D CYS 3.7 4.9 - - - +
714D LEU* 1.4 75.1 - - - +
716D HIS* 1.4 56.8 + - - +
719D GLY* 2.9 30.5 + - - -
722D PHE* 3.6 30.4 - - + -
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Residues in contact with HIS 716 (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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510C ALA* 3.5 17.6 - - + +
514C PRO* 2.7 50.6 + - + +
517C PHE* 3.6 25.2 + + + -
518C THR* 5.8 0.2 - - - -
626D GLU* 4.5 7.6 + - - -
630D ARG* 3.5 27.1 + - - +
712D CYS 2.9 18.4 + - - +
713D VAL* 3.5 10.2 + - - +
715D ALA* 1.4 75.1 - - - +
717D HIS* 1.4 63.9 + - - +
719D GLY* 4.3 3.1 + - - -
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Residues in contact with HIS 717 (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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617D LYS 5.0 4.6 + - - -
618D VAL* 6.1 0.4 - - - -
619D ASN* 6.1 3.0 + - + -
622D GLU* 5.6 7.0 - - + -
623D VAL* 5.0 17.6 - - + +
713D VAL* 2.8 22.1 + - + +
714D LEU* 3.8 3.4 - - - +
716D HIS* 1.4 82.9 - - - +
718D PHE* 1.4 95.5 + + + +
719D GLY 3.9 0.2 + - - -
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Residues in contact with PHE 718 (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 LEU* 3.9 26.7 - - + -
617D LYS* 3.8 41.3 - - + -
618D VAL* 3.9 31.2 - - + -
623D VAL* 5.7 1.1 - - + -
714D LEU* 2.8 41.2 + - + +
717D HIS* 1.4 98.3 - + - +
719D GLY* 1.4 62.2 + - - +
720D LYS* 3.5 0.9 + - - +
721D GLU* 3.3 39.2 + - + +
722D PHE* 4.4 9.9 - - + +
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Residues in contact with GLY 719 (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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511C ALA* 3.5 29.3 - - - +
715D ALA 2.9 13.8 + - - -
716D HIS 4.3 2.5 + - - -
717D HIS 3.6 2.0 - - - -
718D PHE* 1.4 75.0 - - - +
720D LYS* 1.4 58.0 + - - -
721D GLU 2.9 6.9 + - - -
722D PHE* 2.9 21.7 + - - +
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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