Contacts of the helix formed by residues 826 - 840 (chain A) in PDB entry 5OQN
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 THR 826 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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763A GLN* 5.5 1.9 + - - -
824A LYS 3.5 14.4 - - - +
825A ASP* 1.3 78.1 + - - +
827A VAL* 1.3 62.5 + - - +
828A GLN 3.3 2.7 - - - -
829A LEU* 3.1 25.9 + - + -
830A THR* 3.1 34.0 + - - +
864A GLN* 4.7 1.1 - - + -
865A ASP* 4.2 29.6 - - + +
868A THR* 4.6 7.9 + - - +
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Residues in contact with VAL 827 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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762A GLN* 3.5 24.7 - - + +
763A GLN* 3.9 34.5 - - - +
766A SER* 2.8 50.1 + - - +
810A THR* 3.3 20.0 - - - +
812A PRO* 4.1 9.9 - - + -
825A ASP* 2.8 21.3 + - - +
826A THR* 1.3 77.0 - - - +
828A GLN* 1.3 65.3 + - - +
830A THR* 2.9 12.1 + - - -
831A PHE 3.1 1.2 + - - -
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Residues in contact with GLN 828 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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807A LEU* 2.7 41.5 - - + +
810A THR* 3.7 22.2 - - - +
811A ASP* 3.9 16.8 + - - +
812A PRO* 4.1 8.0 - - + +
826A THR 3.3 0.6 - - - -
827A VAL* 1.3 78.1 - - - +
829A LEU* 1.3 69.2 + - + +
831A PHE* 3.3 12.7 + - + +
832A LEU* 2.9 22.9 + - + +
857A ALA 4.4 2.6 - - - +
858A ILE* 3.8 16.6 - - + +
859A PHE* 3.1 41.2 + - - +
864A GLN* 6.3 0.9 - - - +
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Residues in contact with LEU 829 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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826A THR* 3.1 21.7 + - - +
828A GLN* 1.3 78.7 - - + +
830A THR* 1.3 58.8 + - - +
832A LEU* 2.9 8.0 + - - +
833A ILE* 2.7 33.6 + - + +
858A ILE* 5.5 3.8 - - + -
859A PHE 4.6 2.0 - - - +
860A LEU* 3.5 33.2 - - + -
864A GLN* 3.4 22.7 - - + +
868A THR* 4.2 16.4 - - + +
869A LEU* 3.3 33.7 - - + +
872A LEU* 3.8 22.2 - - + -
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Residues in contact with THR 830 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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763A GLN* 4.4 9.6 + - - +
766A SER* 3.2 7.4 + - - -
767A ARG* 6.1 0.7 - - - +
826A THR* 3.1 24.9 + - - +
827A VAL* 2.9 15.1 + - - -
829A LEU* 1.3 74.9 - - - +
831A PHE* 1.3 61.9 + - - +
833A ILE* 3.4 10.4 + - + +
834A ASP* 2.5 38.1 + - - +
868A THR* 4.4 13.5 - - + -
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Residues in contact with PHE 831 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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766A SER* 3.3 36.1 - - - +
769A ALA* 3.3 27.6 - - + -
770A ALA* 3.4 17.9 - - + -
773A LEU* 5.4 1.1 - - + -
803A PHE* 4.3 7.6 - + - -
806A LEU* 3.8 28.7 - - + -
807A LEU* 4.0 26.7 - - + -
810A THR* 4.2 14.1 - - + -
827A VAL 3.1 3.9 + - - +
828A GLN* 3.3 16.8 - - + +
829A LEU 3.1 0.4 - - - -
830A THR* 1.3 81.7 + - - +
832A LEU* 1.3 69.6 + - + +
834A ASP* 2.9 17.2 + - - +
835A VAL* 3.0 32.1 + - + +
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Residues in contact with LEU 832 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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803A PHE* 4.2 24.5 - - + -
807A LEU* 6.3 0.7 - - + -
828A GLN* 2.9 12.4 + - + +
829A LEU* 2.9 10.1 + - - +
831A PHE* 1.3 83.0 - - + +
833A ILE* 1.3 63.7 + - - +
835A VAL* 2.9 9.1 + - + -
836A LEU* 2.9 42.0 + - + +
851A ILE* 6.2 0.2 - - + -
855A ILE* 4.4 11.0 - - + +
858A ILE* 3.6 29.8 - - + -
872A LEU* 4.1 27.8 - - + -
896A LEU* 4.3 17.5 - - + -
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Residues in contact with ILE 833 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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829A LEU* 2.7 23.4 + - + +
830A THR* 3.6 8.7 - - + +
832A LEU* 1.3 71.2 - - - +
834A ASP* 1.3 64.4 + - - +
836A LEU* 3.3 6.8 + - - +
837A LYS* 3.2 30.5 + - + +
868A THR* 3.7 40.8 - - + +
871A GLU* 3.2 38.6 - - + +
872A LEU* 3.8 27.6 - - + +
875A TYR* 4.5 13.5 - - + -
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Residues in contact with ASP 834 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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766A SER* 4.7 4.0 + - - +
767A ARG* 5.0 11.3 - - - +
770A ALA* 3.4 20.4 - - + -
830A THR* 2.5 29.8 + - - +
831A PHE* 2.9 13.4 + - - +
833A ILE* 1.3 79.0 - - - +
835A VAL* 1.3 59.8 + - - +
837A LYS* 3.7 18.1 + - - +
838A ILE* 3.2 26.6 + - + +
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Residues in contact with VAL 835 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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770A ALA* 4.0 11.2 - - + +
773A LEU* 4.3 14.8 - - + -
803A PHE* 4.2 19.1 - - + -
831A PHE* 3.3 47.1 - - + +
832A LEU* 2.9 13.3 + - + +
834A ASP* 1.3 75.0 - - - +
836A LEU* 1.3 56.4 + - + +
838A ILE* 2.9 13.2 + - + -
839A TYR* 2.6 34.6 + - + +
842A ILE* 6.2 2.0 - - + -
851A ILE* 4.5 14.8 - - + -
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Residues in contact with LEU 836 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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832A LEU* 2.9 28.8 + - + +
833A ILE* 3.3 7.8 + - - +
835A VAL* 1.3 77.8 - - + +
837A LYS* 1.3 58.2 + - - +
839A TYR* 2.9 27.2 + - + +
840A ALA* 4.0 3.3 + - - +
851A ILE* 6.2 3.4 - - + -
852A ILE* 5.3 11.9 - - + -
855A ILE* 5.7 4.7 - - + -
872A LEU* 3.3 33.7 - - + -
875A TYR* 3.8 28.0 - - + -
876A SER* 4.2 13.9 - - - +
879A ILE* 3.9 25.7 - - + +
893A LEU* 6.4 2.0 - - + -
896A LEU* 6.3 2.7 - - + -
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Residues in contact with LYS 837 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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833A ILE* 3.2 20.0 + - + +
834A ASP* 3.9 20.1 + - - +
836A LEU* 1.3 77.2 - - - +
838A ILE* 1.3 61.5 + - + +
840A ALA* 4.1 10.3 + - - +
841A GLN* 3.6 12.1 + - - -
871A GLU* 5.3 2.2 + - - -
875A TYR* 3.4 42.4 + - + +
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Residues in contact with ILE 838 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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770A ALA* 3.6 36.3 - - + +
771A ASP* 3.8 9.2 - - + +
774A LEU* 3.6 41.1 - - + +
834A ASP* 3.2 16.1 + - + +
835A VAL* 2.9 15.3 + - + +
837A LYS* 1.3 78.1 - - + +
839A TYR* 1.3 63.2 + - - +
840A ALA 3.0 3.4 - - - -
841A GLN* 2.8 28.4 + - - +
842A ILE* 3.3 11.2 - - + +
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Residues in contact with TYR 839 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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835A VAL* 2.6 16.0 + - + +
836A LEU* 2.9 22.3 + - + +
838A ILE* 1.3 72.8 - - - +
840A ALA* 1.3 61.1 + - - +
841A GLN 3.4 0.5 + - - -
842A ILE* 3.7 15.3 - - + +
848A LYS* 3.3 74.3 - - + +
851A ILE* 4.7 11.4 - - + -
852A ILE* 3.9 25.1 - - + +
879A ILE* 3.4 41.1 - - + -
883A ASP* 4.9 12.0 + - - -
885A LEU* 4.6 10.6 - - + +
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Residues in contact with ALA 840 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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836A LEU 4.0 3.5 + - - +
837A LYS 4.4 9.9 - - - +
838A ILE 2.9 1.4 + - - -
839A TYR* 1.3 81.3 - - - +
841A GLN* 1.3 62.6 + - + +
842A ILE 3.5 6.7 - - - +
843A GLU* 5.6 1.0 - - - +
848A LYS* 4.9 4.2 + - - +
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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