Contacts of the helix formed by residues 824 - 835 (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 GLN 824 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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780D PHE* 4.8 0.6 - - - +
820D GLN 3.4 13.9 - - - +
821D PHE* 3.3 45.5 + - - +
822D TYR 3.4 1.8 - - - -
823D GLY* 1.3 81.2 - - - +
825D ASP* 1.3 64.8 + - - +
826D TRP* 3.4 40.7 + - + +
827D VAL* 3.6 5.3 + - + +
828D ILE* 3.4 22.4 + - - +
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Residues in contact with ASP 825 (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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823D GLY 4.6 4.3 - - - +
824D GLN* 1.3 70.8 - - - +
826D TRP* 1.3 61.9 + - - +
827D VAL 3.1 2.0 + - - -
828D ILE* 3.2 12.4 + - - +
829D ASP* 2.8 44.9 + - - +
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Residues in contact with TRP 826 (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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780D PHE* 3.1 40.8 - + + -
783D ILE* 3.8 22.0 - - + -
784D ALA* 3.4 32.5 - - + -
787D ALA* 4.2 14.0 - - + +
788D GLU* 5.7 5.4 - - - +
806D ILE* 5.8 0.4 - - + -
824D GLN* 3.4 40.4 + - + +
825D ASP* 1.3 79.3 - - - +
827D VAL* 1.3 75.0 + - + +
829D ASP* 3.7 6.1 - - - +
830D TYR* 2.7 38.4 + + + +
833D ARG* 4.9 1.6 + - - -
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Residues in contact with VAL 827 (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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780D PHE* 4.1 9.9 - - + -
806D ILE* 4.1 22.9 - - + -
821D PHE 3.5 23.1 - - - +
822D TYR* 4.9 9.9 - - + -
824D GLN* 3.7 9.0 - - + +
825D ASP 3.1 0.6 - - - -
826D TRP* 1.3 114.4 - - + +
828D ILE* 1.3 65.8 + - + +
830D TYR* 3.2 4.2 + - - +
831D ILE* 3.0 46.0 + - + +
855D GLN* 5.0 2.7 - - + -
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Residues in contact with ILE 828 (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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822D TYR 4.5 7.6 - - - +
823D GLY 4.9 6.7 - - - +
824D GLN 3.4 15.0 + - - +
825D ASP* 3.2 13.3 + - - +
827D VAL* 1.3 76.1 - - - +
829D ASP* 1.3 64.4 + - - +
831D ILE* 3.5 5.5 + - - +
832D LYS* 3.2 37.8 + - + +
852D ARG* 3.8 24.6 - - - +
855D GLN* 3.3 24.9 - - - +
856D LYS* 5.8 1.1 - - - +
859D LEU* 4.8 10.5 - - + -
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Residues in contact with ASP 829 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
825D ASP* 2.8 33.9 + - - +
826D TRP* 3.9 6.1 - - - +
828D ILE* 1.3 79.4 - - - +
830D TYR* 1.3 57.7 + - - +
832D LYS* 3.4 14.8 + - - +
833D ARG* 3.0 40.2 + - + +
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Residues in contact with TYR 830 (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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783D ILE* 4.7 8.7 - - + -
786D VAL* 3.6 15.3 - - + +
787D ALA* 3.8 22.4 - - + -
793D TYR* 4.0 9.2 - - + -
799D SER* 2.9 35.2 + - - -
802D ALA* 3.7 16.0 - - + +
803D VAL* 4.2 13.2 - - + -
806D ILE* 3.8 22.0 - - + -
826D TRP* 2.7 25.7 + + + +
827D VAL* 3.2 5.8 + - - +
829D ASP* 1.3 70.8 - - - +
831D ILE* 1.3 63.5 - - - +
833D ARG* 3.3 37.3 + - + +
834D THR* 2.9 41.8 + - - -
840D PHE* 6.2 1.3 - + - -
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Residues in contact with ILE 831 (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* 4.2 17.7 - - + -
806D ILE* 4.2 17.3 - - + -
827D VAL* 3.0 34.1 + - + +
828D ILE* 3.9 4.3 - - - +
829D ASP 3.4 0.2 - - - -
830D TYR* 1.3 74.8 - - - +
832D LYS* 1.3 62.5 + - + +
834D THR* 3.4 14.7 + - - -
835D ARG* 3.5 16.5 + - - +
848D ALA* 3.3 30.5 - - + +
851D ALA* 4.3 6.1 - - + +
852D ARG* 3.6 22.9 - - + +
855D GLN* 4.2 29.2 - - + +
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Residues in contact with LYS 832 (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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627B ALA 5.5 2.0 + - - -
628B SER 4.9 10.5 + - - -
629B LEU 5.7 0.4 + - - -
630B GLY* 4.9 12.1 - - - -
669B SER* 6.0 1.4 - - - -
828D ILE* 3.2 32.8 + - + +
829D ASP* 3.6 15.9 - - - +
830D TYR 3.1 0.2 - - - -
831D ILE* 1.3 74.4 - - + +
833D ARG* 1.3 63.0 + - + +
834D THR 3.1 2.5 + - - -
835D ARG* 3.2 13.9 + - - +
836D SER* 2.8 19.9 + - - -
852D ARG* 5.6 13.0 - - - +
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Residues in contact with ARG 833 (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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787D ALA* 3.1 30.8 + - - +
793D TYR* 4.0 21.8 - - - -
826D TRP 4.9 1.2 + - - -
829D ASP* 3.0 29.7 + - + +
830D TYR* 3.3 47.3 + - + +
832D LYS* 1.3 76.3 - - + +
834D THR* 1.3 60.9 + - - +
836D SER* 3.6 18.1 + - - +
840D PHE* 3.4 17.7 - - + -
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Residues in contact with THR 834 (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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799D SER* 4.7 5.7 - - - -
803D VAL* 4.4 11.1 - - + +
830D TYR* 2.9 33.7 + - - -
831D ILE* 3.6 11.5 - - - -
832D LYS 3.1 0.8 - - - -
833D ARG* 1.3 76.9 - - - +
835D ARG* 1.3 57.7 + - - +
836D SER 3.2 5.5 + - - -
840D PHE* 3.6 22.2 - - + +
844D THR* 3.3 30.5 - - + +
845D LYS* 3.6 14.0 - - - +
848D ALA* 3.7 16.8 - - + -
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Residues in contact with ARG 835 (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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665B ASP* 4.7 1.9 - - - +
668B ASN* 3.0 75.8 + - + +
671B GLU* 2.7 28.8 + - - -
712B ASN* 3.7 3.0 - - - +
831D ILE* 3.5 8.2 + - - +
832D LYS* 3.2 11.8 + - - +
834D THR* 1.3 73.9 - - - +
836D SER* 1.3 58.3 + - - +
842D GLN* 6.1 0.4 - - - +
845D LYS* 2.9 40.5 + - - +
846D ASP* 4.9 2.4 + - - +
848D ALA* 3.5 21.8 - - + -
849D ARG* 3.6 34.1 - - - +
852D ARG* 5.0 8.1 - - - -
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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
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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