Contacts of the helix formed by residues 841 - 860 (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 841 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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756B ASP* 3.2 19.3 - - - -
797B ALA* 5.2 0.7 - - - +
796D ASP* 2.7 31.7 + - - -
800D ARG* 3.7 6.8 + - - -
838D GLN* 4.5 1.8 - - - -
839D LEU 3.7 3.4 + - - -
840D PHE* 1.3 77.3 - - - +
842D GLN* 1.3 66.2 + - - +
843D ALA* 3.9 5.1 + - - +
844D THR* 3.1 8.7 + - - -
845D LYS* 3.1 19.4 + - - +
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Residues in contact with GLN 842 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668B ASN* 5.0 2.4 + - - -
704B SER 4.4 1.7 - - - +
707B GLY* 3.4 9.5 - - - -
708B ASP* 3.1 35.1 + - - +
711B SER* 3.1 28.5 + - - -
756B ASP* 2.9 44.6 + - + +
759B VAL* 3.9 7.2 - - + -
760B GLY* 3.6 15.7 - - - +
835D ARG* 6.1 0.4 - - - +
841D SER* 1.3 68.5 - - - +
843D ALA* 1.3 67.3 + - - +
845D LYS* 3.2 13.9 + - - +
846D ASP* 2.9 41.4 + - - +
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Residues in contact with ALA 843 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
756B ASP* 4.8 0.4 + - - -
759B VAL* 3.7 16.8 - - + +
801B ALA* 4.3 18.2 - - + -
800D ARG* 3.4 33.2 - - - +
841D SER* 3.3 4.6 + - - +
842D GLN* 1.3 78.0 - - - +
844D THR* 1.3 62.2 + - - +
846D ASP* 3.3 4.6 + - - +
847D THR* 3.1 26.5 + - - -
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Residues in contact with THR 844 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
796D ASP* 2.4 39.5 + - - +
799D SER* 4.5 0.4 - - - -
800D ARG* 3.1 36.6 + - + +
803D VAL* 4.6 0.3 - - - +
834D THR* 3.3 25.5 - - + +
840D PHE* 3.9 14.4 - - + -
841D SER* 3.1 8.7 + - - -
843D ALA* 1.3 74.5 - - - +
845D LYS* 1.3 61.8 + - - +
847D THR* 3.3 2.9 + - - -
848D ALA* 2.9 26.9 + - - +
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Residues in contact with LYS 845 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664B ALA* 4.3 1.8 - - - +
668B ASN* 3.8 15.9 - - - +
708B ASP* 2.6 40.0 + - - +
834D THR 3.6 19.7 - - - +
835D ARG* 2.9 43.5 + - - +
836D SER 4.4 2.2 - - - -
837D GLY 2.9 29.5 + - - -
838D GLN* 4.6 4.4 - - - +
840D PHE* 3.7 14.5 + - + +
841D SER 3.1 14.1 + - - +
842D GLN* 3.7 20.5 + - - +
844D THR* 1.3 75.3 - - - +
846D ASP* 1.3 58.8 + - - +
848D ALA* 3.4 4.8 + - - +
849D ARG 3.0 13.9 + - - -
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Residues in contact with ASP 846 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711B SER* 4.1 9.4 + - - -
759B VAL* 3.9 14.7 - - - +
763B ALA* 3.3 27.2 - - - +
835D ARG* 5.3 2.4 + - - -
842D GLN* 2.9 36.9 + - - +
843D ALA* 3.7 6.1 - - - +
844D THR 3.2 0.2 - - - -
845D LYS* 1.3 74.3 - - - +
847D THR* 1.3 65.0 + - - +
849D ARG* 3.2 9.9 + - - +
850D TRP* 3.1 20.4 + - - +
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Residues in contact with THR 847 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
800D ARG* 3.4 40.3 - - + +
803D VAL* 4.0 2.2 - - + -
804D GLY* 3.7 20.2 - - - +
843D ALA 3.1 16.3 + - - -
844D THR 3.8 4.3 - - - -
846D ASP* 1.3 77.0 - - - +
848D ALA* 1.3 57.1 + - - +
850D TRP* 3.1 14.9 + - + +
851D ALA* 2.9 27.0 + - - +
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Residues in contact with ALA 848 (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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803D VAL* 3.8 14.9 - - + +
831D ILE* 3.3 9.3 - - - +
834D THR* 3.7 24.7 - - + -
835D ARG* 3.5 19.5 - - + -
844D THR 2.9 16.8 + - - +
845D LYS 3.5 6.5 - - - +
847D THR* 1.3 74.4 - - - +
849D ARG* 1.3 59.3 + - - +
851D ALA* 3.7 0.2 - - - +
852D ARG* 2.8 30.5 + - - +
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Residues in contact with ARG 849 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631B LYS* 5.6 6.7 - - - +
668B ASN 4.8 2.2 + - - -
669B SER 5.5 1.8 + - - -
671B GLU* 3.0 52.0 + - - +
672B GLU* 4.9 7.1 + - - -
835D ARG* 3.6 28.8 - - - +
845D LYS 3.0 8.3 + - - +
846D ASP* 3.2 13.7 + - - +
848D ALA* 1.3 74.8 - - - +
850D TRP* 1.3 63.0 + - - +
852D ARG* 3.3 18.7 + - - +
853D GLU* 2.9 53.1 + - - +
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Residues in contact with TRP 850 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
804D GLY* 4.9 3.1 - - - -
807D GLY* 3.8 14.3 - - - -
808D ASP* 3.3 23.7 + - - -
811D ALA* 4.3 15.5 - - + -
846D ASP 3.1 11.9 + - - +
847D THR* 3.2 22.2 - - + +
849D ARG* 1.3 77.9 - - - +
851D ALA* 1.3 64.5 + - + +
853D GLU* 3.4 4.9 + - + +
854D GLN* 3.0 66.3 + - + +
857D ARG* 5.8 0.9 - - - -
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Residues in contact with ALA 851 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
803D VAL* 3.2 46.2 - - + +
806D ILE* 4.4 8.3 - - + +
807D GLY* 3.9 19.0 - - - +
831D ILE* 4.4 3.4 - - + -
847D THR 2.9 8.8 + - - +
848D ALA 3.7 2.9 - - - +
850D TRP* 1.3 73.4 - - - +
852D ARG* 1.3 61.1 + - - +
854D GLN* 3.8 1.0 - - - +
855D GLN* 2.8 34.2 + - - +
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Residues in contact with ARG 852 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
828D ILE* 3.8 22.2 - - - +
831D ILE* 3.6 19.9 - - + +
832D LYS* 5.6 13.3 - - - +
835D ARG* 5.0 6.1 - - - -
848D ALA 2.8 19.0 + - - +
849D ARG* 3.5 25.8 - - - +
851D ALA* 1.3 78.0 - - - +
853D GLU* 1.3 59.2 + - + +
855D GLN* 2.9 39.6 + - - +
856D LYS* 3.1 52.6 + - + +
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Residues in contact with GLU 853 (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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849D ARG* 2.9 57.7 + - - +
850D TRP* 4.0 6.1 - - + +
852D ARG* 1.3 76.2 - - + +
854D GLN* 1.3 67.2 + - - +
855D GLN 3.1 2.0 - - - -
856D LYS* 3.1 17.9 + - + +
857D ARG* 3.2 33.8 + - - +
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Residues in contact with GLN 854 (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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807D GLY* 3.8 8.7 - - - +
810D ALA* 3.8 19.4 - - + +
811D ALA* 3.6 23.6 + - - +
850D TRP* 3.0 67.8 + - + +
851D ALA 3.9 3.1 - - - +
853D GLU* 1.3 77.1 - - - +
855D GLN* 1.3 59.3 + - - +
857D ARG* 3.5 40.5 + - - +
858D GLN* 3.3 25.1 + - - +
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Residues in contact with GLN 855 (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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806D ILE* 5.3 0.2 - - + -
810D ALA* 4.8 0.4 - - - +
822D TYR* 3.6 44.8 - - + +
827D VAL* 5.0 1.6 - - + -
828D ILE* 3.3 26.6 - - - +
831D ILE* 4.2 14.6 - - + +
851D ALA 2.8 19.2 + - - +
852D ARG* 2.9 26.2 + - - +
853D GLU 3.1 0.2 - - - -
854D GLN* 1.3 77.3 - - - +
856D LYS* 1.3 93.3 + - - +
858D GLN* 3.4 11.7 + - - +
859D LEU* 3.4 16.1 + - - +
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Residues in contact with LYS 856 (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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828D ILE* 5.8 1.5 - - - +
852D ARG* 3.1 47.0 + - + +
853D GLU* 3.1 13.2 + - + +
855D GLN* 1.3 102.9 - - - +
857D ARG* 1.3 53.2 + - + +
859D LEU* 3.6 25.9 + - - +
860D SER* 2.5 31.9 + - - -
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Residues in contact with ARG 857 (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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850D TRP* 5.8 1.0 - - - -
853D GLU* 3.2 27.9 + - - +
854D GLN* 3.6 39.4 + - - +
855D GLN 3.3 0.4 - - - -
856D LYS* 1.3 75.3 - - + +
858D GLN* 1.3 63.8 + - - +
860D SER* 3.1 16.4 + - - +
861D LEU* 3.2 26.2 + - + +
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Residues in contact with GLN 858 (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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810D ALA* 2.9 36.5 + - + +
813D PHE 2.9 23.7 + - - +
814D PRO* 4.4 3.2 - - - +
816D GLY* 4.1 5.0 - - - -
818D ILE* 4.0 4.7 - - - +
819D LYS* 3.4 45.5 + - + +
822D TYR* 3.7 35.2 - - + -
854D GLN 3.3 14.4 + - - +
855D GLN 3.6 7.9 - - - +
856D LYS 3.4 0.6 - - - -
857D ARG* 1.3 74.6 - - - +
859D LEU* 1.3 65.8 + - - +
861D LEU* 3.1 19.7 + - - +
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Residues in contact with LEU 859 (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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819D LYS* 4.2 16.5 - - + +
822D TYR 3.5 22.2 - - - +
823D GLY* 3.6 19.1 - - - +
828D ILE* 4.8 10.1 - - + -
855D GLN* 3.4 18.3 + - - +
856D LYS* 3.6 38.8 - - - +
857D ARG 3.4 0.2 - - - -
858D GLN* 1.3 76.6 - - - +
860D SER* 1.3 58.1 + - - +
861D LEU 3.3 10.6 + - - +
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Residues in contact with SER 860 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
856D LYS 2.5 24.1 + - - -
857D ARG* 3.1 19.7 + - - +
858D GLN 3.1 0.6 - - - -
859D LEU* 1.3 75.8 - - - +
861D LEU* 1.3 59.4 + - - +
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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