Contacts of the helix formed by residues 811 - 829 (chain A) in PDB entry 4UHX
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 VAL 811 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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775A THR* 4.4 3.4 - - - -
776A GLN* 3.6 22.4 - - + +
777A PHE* 4.2 20.6 - - + -
780A TYR* 3.4 12.3 - - + -
781A ILE* 4.5 1.7 - - - +
808A GLY* 3.7 12.3 + - - +
809A GLY 3.7 2.0 + - - -
810A LYS* 1.3 82.0 - - - +
812A LEU* 1.3 84.7 + - + +
813A LYS 3.6 1.5 - - - +
814A THR* 3.4 6.6 + - - +
815A GLY 3.1 17.8 + - - -
1085A ILE* 3.8 31.9 - - + -
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Residues in contact with LEU 812 (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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780A TYR* 3.3 35.3 + - + +
811A VAL* 1.3 90.1 - - + +
813A LYS* 1.3 62.5 + - + +
815A GLY 3.4 0.9 + - - -
816A ILE* 3.1 31.8 + - + +
880A LEU 5.8 3.8 - - - +
918A THR* 4.9 20.8 - - + +
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Residues in contact with LYS 813 (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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674A LEU* 5.8 6.1 - - + -
756A GLN* 5.5 3.1 - - + +
809A GLY 5.8 0.9 - - - +
811A VAL 4.9 0.4 - - - +
812A LEU* 1.3 77.2 - - + +
814A THR* 1.3 59.9 + - - +
816A ILE* 3.2 25.6 + - + +
817A ILE* 2.9 42.1 + - + +
844A ILE* 3.2 38.9 + - + +
845A THR* 4.4 19.1 - - - +
846A GLY 4.6 2.6 - - - +
916A SER* 3.9 36.2 + - - +
918A THR* 5.3 10.1 - - + +
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Residues in contact with THR 814 (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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756A GLN* 2.7 26.9 + - - +
758A MET* 3.4 9.5 - - + +
773A VAL* 3.4 32.1 - - + -
774A SER 3.6 11.0 - - - +
775A THR* 3.9 10.1 - - - -
781A ILE* 4.1 2.7 - - + -
809A GLY 4.3 0.2 + - - -
810A LYS* 3.2 25.8 - - - -
811A VAL 3.4 9.6 - - - +
813A LYS* 1.3 77.9 - - - +
815A GLY* 1.3 57.3 + - - +
817A ILE* 3.5 1.3 + - - -
818A ALA* 2.9 26.3 + - - +
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Residues in contact with GLY 815 (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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780A TYR* 3.8 14.4 - - - -
781A ILE* 3.4 20.6 - - - +
784A ILE* 3.4 15.5 - - - +
811A VAL 3.1 7.7 + - - -
812A LEU 3.4 0.2 + - - -
813A LYS 3.3 0.4 - - - -
814A THR* 1.3 78.4 - - - +
816A ILE* 1.3 54.6 + - - +
818A ALA* 3.6 1.3 - - - -
819A ALA* 2.7 36.2 + - - +
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Residues in contact with ILE 816 (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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661A LYS 5.3 5.6 - - - +
662A PHE* 4.0 39.0 - - + +
674A LEU* 3.9 25.4 - - + -
780A TYR* 4.6 2.2 - - - +
784A ILE* 3.9 9.6 - - + +
812A LEU* 3.1 24.5 + - + +
813A LYS* 3.2 32.1 + - + +
815A GLY* 1.3 74.1 - - - +
817A ILE* 1.3 59.0 + - - +
819A ALA* 3.3 3.5 + - - +
820A VAL* 3.0 29.7 + - + +
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Residues in contact with ILE 817 (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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614A PHE* 3.6 36.3 - - + -
674A LEU* 4.5 10.8 - - + -
756A GLN* 4.7 13.2 - - + -
758A MET* 3.8 15.0 - - + -
813A LYS* 2.9 26.4 + - + +
814A THR* 3.8 4.9 - - - +
816A ILE* 1.3 76.3 - - + +
818A ALA* 1.3 55.3 + - - +
820A VAL* 3.4 1.7 + - - +
821A THR* 2.6 37.9 + - - +
834A CYS* 3.6 18.8 - - - -
836A LEU* 3.9 27.6 - - + -
844A ILE* 4.4 13.7 - - + -
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Residues in contact with ALA 818 (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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758A MET* 3.3 19.9 - - + -
760A VAL* 4.6 2.4 - - - +
771A VAL* 4.6 8.3 - - + -
773A VAL* 5.2 1.3 - - + -
781A ILE* 4.1 26.5 - - + -
785A VAL* 3.7 6.7 - - + +
814A THR 2.9 18.9 + - - +
815A GLY* 3.7 5.4 - - - +
817A ILE* 1.3 73.5 - - - +
819A ALA* 1.3 59.2 + - - +
821A THR* 3.8 2.7 - - - -
822A ALA* 2.9 31.9 + - - +
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Residues in contact with ALA 819 (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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662A PHE* 3.8 15.3 - - + -
784A ILE* 3.9 14.1 - - + +
785A VAL* 4.1 10.3 - - - +
788A THR* 3.4 32.6 - - - +
815A GLY 2.7 21.4 + - - +
816A ILE 3.5 4.9 - - - +
818A ALA* 1.3 73.7 - - - +
820A VAL* 1.3 57.6 + - - +
822A ALA* 3.8 1.9 - - - +
823A PHE* 3.0 27.9 + - - +
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Residues in contact with VAL 820 (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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612A LEU* 4.2 3.8 - - + -
614A PHE* 3.8 28.7 - - + -
642A MET* 5.0 6.0 - - - +
647A LEU* 4.4 14.6 - - + -
662A PHE* 3.9 28.7 - - + -
663A LEU* 4.6 10.5 - - + -
674A LEU* 5.1 0.2 - - + -
677A ALA* 3.9 19.3 - - + -
788A THR* 5.7 0.2 - - - -
816A ILE* 3.0 25.0 + - + +
817A ILE 3.8 2.9 - - - +
819A ALA* 1.3 72.1 - - - +
821A THR* 1.3 67.1 + - - +
823A PHE* 3.3 9.1 + - - +
824A ALA* 3.3 19.8 + - - +
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Residues in contact with THR 821 (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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612A LEU* 3.4 20.6 - - + +
758A MET* 4.2 2.5 - - + -
760A VAL* 3.5 24.0 - - + -
817A ILE* 2.6 27.1 + - - +
818A ALA* 3.8 5.4 - - - -
820A VAL* 1.3 76.1 - - - +
822A ALA* 1.3 56.6 + - - +
824A ALA* 3.3 7.1 + - - +
825A ALA* 3.0 24.9 + - - +
832A VAL* 3.7 31.9 - - + +
834A CYS* 3.7 20.1 - - + +
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Residues in contact with ALA 822 (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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760A VAL* 3.7 24.2 - - + +
769A MET* 4.7 2.4 - - + +
785A VAL* 3.6 30.3 - - + -
789A LEU* 3.7 11.0 - - + +
818A ALA 2.9 19.5 + - - +
819A ALA 3.8 3.1 - - - +
821A THR* 1.3 73.6 - - - +
823A PHE* 1.3 60.5 + - - +
825A ALA* 3.8 0.8 - - - +
826A ASN* 3.0 31.7 + - - +
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Residues in contact with PHE 823 (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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642A MET* 4.0 11.7 - - + -
646A HIS 3.6 25.6 - - - -
647A LEU* 3.9 26.0 - - + -
648A SER* 6.0 0.4 - - - -
650A VAL* 3.8 21.8 - - + -
788A THR* 4.1 23.3 - - + -
789A LEU* 4.1 12.5 - - + +
819A ALA 3.0 13.8 + - - +
820A VAL* 3.3 12.8 + - - +
822A ALA* 1.3 77.5 - - - +
824A ALA* 1.3 57.2 + - - +
826A ASN* 3.9 4.9 + - - +
827A LYS* 2.9 49.3 + - + +
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Residues in contact with ALA 824 (chain A).
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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612A LEU* 4.2 9.0 - - + -
642A MET* 3.6 31.4 - - + +
679A LEU* 4.1 24.0 - - + -
820A VAL 3.3 9.4 + - - +
821A THR 3.3 8.5 + - - +
823A PHE* 1.3 77.0 - - - +
825A ALA* 1.3 65.8 + - - +
827A LYS* 3.1 1.7 + - - -
828A HIS* 2.9 30.3 + - - +
832A VAL* 4.3 2.7 - - + -
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Residues in contact with ALA 825 (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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760A VAL* 4.1 24.0 - - + +
762A PRO* 4.1 9.3 - - + +
769A MET* 4.2 1.8 - - + -
821A THR 3.0 16.3 + - - +
822A ALA 3.8 4.7 - - - +
823A PHE 3.4 0.2 - - - -
824A ALA* 1.3 74.1 - - - +
826A ASN* 1.3 58.4 + - - +
829A GLY* 2.9 26.5 + - - -
830A ARG* 3.1 30.8 + - - +
832A VAL* 3.6 12.3 - - + +
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Residues in contact with ASN 826 (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 PRO* 5.3 3.1 - - - -
767A GLN* 3.8 31.4 + - - +
769A MET* 4.7 10.6 - - - +
789A LEU* 3.6 28.3 - - + +
822A ALA 3.0 18.6 + - - +
823A PHE* 3.9 5.1 + - - +
825A ALA* 1.3 74.3 - - - +
827A LYS* 1.3 69.6 + - - +
828A HIS 3.4 0.2 + - - -
829A GLY* 3.5 8.8 + - - -
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Residues in contact with LYS 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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640A ASP* 2.7 27.1 + - - +
642A MET* 4.0 14.1 - - + +
646A HIS* 5.0 12.7 + - - +
823A PHE* 2.9 34.1 + - + +
824A ALA* 3.1 6.0 + - - +
826A ASN* 1.3 83.0 - - - +
828A HIS* 1.3 78.8 + - + +
829A GLY 3.8 0.2 + - - -
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Residues in contact with HIS 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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610A LEU* 4.5 16.4 - - + -
639A VAL* 3.7 19.3 - - + +
640A ASP* 2.8 43.8 + - + +
642A MET* 3.8 2.2 - - + +
679A LEU* 3.4 19.1 - - + -
824A ALA 2.9 24.8 + - - +
825A ALA* 4.6 0.9 - - - +
827A LYS* 1.3 96.4 + - + +
829A GLY* 1.3 65.6 + - - +
830A ARG* 3.3 10.8 + - + +
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Residues in contact with GLY 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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762A PRO* 4.3 10.5 - - - -
825A ALA 2.9 10.8 + - - -
826A ASN* 3.5 7.3 + - - -
827A LYS 3.5 2.4 + - - -
828A HIS* 1.3 78.1 - - - +
830A ARG* 1.3 64.3 + - - +
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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