Contacts of the helix formed by residues 884 - 898 (chain I) in PDB entry 5FUR
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 884 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313I TYR* 2.8 65.5 - - + +
881I GLY 6.0 0.7 - - - +
883I PHE* 1.3 70.4 - - - +
885I ASP* 1.4 67.8 + - - +
887I ARG* 3.0 23.1 + - + +
888I ILE* 3.2 27.3 + - + +
922I VAL* 6.1 2.0 - - + -
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Residues in contact with ASP 885 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336I ILE* 5.9 3.3 - - - +
845I SER 4.5 2.2 - - - +
846I TYR* 4.3 7.3 - - - +
847I ARG 4.0 16.2 + - - +
848I HIS* 5.9 3.1 - - - -
851I THR* 4.8 0.8 + - - +
883I PHE* 2.7 30.9 - - + -
884I VAL* 1.4 83.2 - - - +
886I ILE* 1.4 49.9 + - - +
888I ILE* 3.1 11.2 + - - +
889I ALA* 2.8 35.2 + - - +
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Residues in contact with ILE 886 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
841I LYS* 4.1 33.0 - - + +
847I ARG* 3.9 26.5 - - + +
850I ILE* 6.2 1.6 - - + -
877I TYR* 4.2 26.5 - - + +
882I HIS 4.2 3.8 - - - +
883I PHE* 1.5 132.4 - - + -
885I ASP* 1.4 66.5 - - - +
887I ARG* 1.3 59.1 + - + +
889I ALA* 3.2 7.6 + - + +
890I ALA* 2.8 29.2 + - + +
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Residues in contact with ARG 887 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313I TYR* 6.0 4.6 - - - -
877I TYR 4.2 17.3 - - - +
878I ALA* 2.5 37.4 + - + +
879I GLU 4.1 4.4 + - - -
881I GLY* 3.6 39.4 - - - +
882I HIS 5.0 1.1 - - - +
883I PHE 3.1 12.6 + - - +
884I VAL* 3.0 15.7 + - + +
886I ILE* 1.3 79.1 - - - +
888I ILE* 1.4 59.6 + - + +
890I ALA* 3.3 2.5 + - - +
891I LEU* 2.9 40.9 + - + +
917I ASP* 3.6 22.8 + - - +
919I VAL* 4.3 18.7 - - - +
922I VAL* 4.9 12.2 - - + +
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Residues in contact with ILE 888 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313I TYR* 6.4 0.9 - - + -
884I VAL* 3.2 25.3 + - + +
885I ASP* 3.1 11.7 + - - +
887I ARG* 1.4 70.8 - - + +
889I ALA* 1.4 69.0 + - - +
891I LEU* 2.8 9.3 + - + +
892I GLU* 2.7 52.3 + - + +
922I VAL* 4.3 24.5 - - + -
925I LYS* 4.9 15.5 - - + -
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Residues in contact with ALA 889 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
851I THR* 3.4 48.5 - - + +
854I CYS* 4.7 7.2 - - - -
885I ASP 2.8 15.6 + - - +
886I ILE* 3.4 11.0 - - + +
888I ILE* 1.4 76.6 - - - +
890I ALA* 1.3 62.0 + - - +
892I GLU* 3.1 15.6 + - - +
893I ALA* 3.1 14.0 + - - +
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Residues in contact with ALA 890 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
874I PHE* 3.4 48.3 - - + +
877I TYR* 3.7 25.1 - - + -
878I ALA* 4.2 1.3 - - + +
886I ILE 2.8 19.6 + - - +
887I ARG 3.6 4.5 - - - +
889I ALA* 1.3 73.5 - - - +
891I LEU* 1.3 57.5 + - - +
893I ALA 3.0 2.9 + - - -
894I VAL* 2.8 23.9 + - - +
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Residues in contact with LEU 891 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
874I PHE 5.2 1.1 - - - +
878I ALA* 3.4 26.2 - - + -
887I ARG* 2.9 31.0 + - + +
888I ILE* 2.8 11.5 + - - +
890I ALA* 1.3 72.5 - - - +
892I GLU* 1.3 59.7 + - + +
894I VAL* 3.0 29.9 - - + +
895I VAL* 3.5 12.6 + - - +
913I MET* 5.8 8.7 - - + -
917I ASP* 5.0 2.7 - - + +
922I VAL* 3.9 30.1 - - + -
925I LYS* 6.2 3.8 - - + -
926I ILE* 3.9 35.3 - - + +
929I MET* 4.8 1.8 - - - +
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Residues in contact with GLU 892 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
855I LEU* 6.3 0.2 - - - -
888I ILE* 2.7 45.2 + - + +
889I ALA* 3.7 8.2 - - - +
891I LEU* 1.3 71.7 - - - +
893I ALA* 1.3 59.6 + - - +
895I VAL 3.5 0.7 + - - -
896I ASP* 2.9 36.1 + - - +
925I LYS* 3.4 21.7 + - + -
929I MET* 3.7 29.9 - - + +
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Residues in contact with ALA 893 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
854I CYS* 4.1 7.9 - - - -
855I LEU* 5.0 9.4 - - + -
858I ILE* 4.8 5.6 - - + +
874I PHE* 3.0 45.2 - - + -
889I ALA 3.1 7.9 + - - +
890I ALA 3.0 2.3 + - - +
892I GLU* 1.3 78.1 - - - +
894I VAL* 1.3 60.8 + - - +
895I VAL 3.1 1.6 - - - -
896I ASP* 3.8 9.0 - - + +
897I TYR* 3.0 27.9 + - - +
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Residues in contact with VAL 894 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
871I PRO* 4.7 15.5 - - + -
874I PHE* 4.1 18.3 - - + -
875I LYS* 4.8 11.0 - - + +
890I ALA 2.8 11.9 + - - +
891I LEU* 3.0 40.8 - - + +
893I ALA* 1.3 76.6 - - - +
895I VAL* 1.4 65.4 + - + +
897I TYR* 3.6 4.8 + - + +
898I THR* 3.1 34.0 + - + +
910I LEU* 4.5 10.3 - - + -
913I MET* 4.6 20.9 - - + -
926I ILE* 5.4 2.2 - - + -
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Residues in contact with VAL 895 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
891I LEU 3.5 16.1 + - - +
892I GLU 3.5 5.0 + - - +
893I ALA 3.1 0.2 - - - -
894I VAL* 1.4 85.9 - - + +
896I ASP* 1.4 58.7 + - - +
897I TYR 3.2 0.7 - - - -
898I THR* 2.6 24.7 + - - +
899I LYS* 2.8 17.1 + - + +
910I LEU* 4.0 17.7 - - + -
926I ILE* 4.1 18.2 - - + +
929I MET* 3.9 44.0 - - + +
930I LEU* 4.3 8.7 - - + +
933I ASN* 4.9 8.5 - - + +
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Residues in contact with ASP 896 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
855I LEU* 4.3 18.4 - - + +
858I ILE* 3.9 19.5 - - + +
859I ARG* 5.0 7.1 + - - -
892I GLU* 2.9 25.8 + - - +
893I ALA* 3.5 6.9 + - - +
895I VAL* 1.4 78.2 - - - +
897I TYR* 1.3 59.1 + - - +
899I LYS* 3.8 34.2 + - - +
900I VAL* 4.1 10.6 - - - +
929I MET* 4.4 9.9 - - - +
933I ASN* 4.9 6.1 + - - -
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Residues in contact with TYR 897 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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858I ILE* 4.3 8.0 - - + +
866I HIS 4.3 1.6 - - - -
867I VAL* 1.9 77.1 - - + +
868I PRO* 3.7 0.9 - - - +
870I ASP* 3.9 16.2 - - + -
871I PRO* 3.3 36.3 - - + -
893I ALA 3.0 17.4 + - - +
894I VAL* 3.9 6.7 - - + +
896I ASP* 1.3 75.2 - - - +
898I THR* 1.4 71.1 + - + +
899I LYS 3.1 0.7 - - - -
900I VAL* 3.0 13.9 + - + +
901I ASP* 2.9 42.3 + - + -
906I GLU* 4.8 10.3 - - - -
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Residues in contact with THR 898 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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894I VAL* 3.1 15.7 + - + +
895I VAL* 2.6 30.2 + - - +
897I TYR* 1.4 77.0 - - + +
899I LYS* 1.3 59.0 + - - +
900I VAL 2.9 0.7 + - - -
901I ASP* 2.7 33.8 + - - +
906I GLU* 4.6 24.0 - - + +
907I LEU* 4.4 11.6 - - - +
910I LEU* 3.5 37.8 - - + +
930I LEU* 4.5 2.9 - - - +
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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