Contacts of the helix formed by residues 903 - 921 (chain G) 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 PRO 903 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612G HIS* 3.9 18.2 - - + -
616G ALA 3.6 25.4 - - - +
617G VAL* 4.2 12.1 - - + +
619G LEU* 3.8 5.4 - - + -
624G PHE* 3.6 27.5 - - + -
717G MET* 3.9 19.3 - - + -
901G VAL 4.6 0.9 - - - +
902G SER* 1.3 87.9 - - - +
904G GLU* 1.3 66.1 + - - +
906G CYS* 3.2 4.3 + - - +
907G CYS* 3.0 26.0 + - - -
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Residues in contact with GLU 904 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612G HIS* 2.7 32.3 + - - -
717G MET* 4.5 2.5 - - + -
767G ASN* 3.1 41.3 + - + +
768G LEU* 3.8 26.9 - - + +
810G PHE* 3.7 24.1 - - + -
902G SER* 3.2 17.8 + - - +
903G PRO* 1.3 80.7 - - - +
905G GLN* 1.3 58.0 + - - +
907G CYS* 3.1 4.4 + - - +
908G ALA* 2.9 28.9 + - - +
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Residues in contact with GLN 905 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
810G PHE* 3.9 16.1 - - + -
819G ARG* 3.7 29.1 + - - +
823G HIS* 3.5 21.3 + - + -
900G MET 4.1 5.6 + - - +
901G VAL* 3.2 12.0 - - - +
902G SER* 2.8 40.8 + - - +
904G GLU* 1.3 76.8 - - - +
906G CYS* 1.3 62.3 + - - +
908G ALA* 3.5 2.6 + - - +
909G TYR* 3.1 19.1 + - - +
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Residues in contact with CYS 906 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619G LEU* 3.9 12.8 - - - -
624G PHE* 3.6 19.1 - - + -
823G HIS* 3.5 20.2 - - + -
827G PHE* 3.7 31.9 - - - -
901G VAL* 3.8 6.3 - - - -
902G SER 3.3 12.5 + - - -
903G PRO 3.2 8.1 + - - +
905G GLN* 1.3 76.2 - - - +
907G CYS* 1.3 57.3 + - - +
909G TYR* 3.2 2.6 + - - +
910G TYR* 2.8 44.7 + - + -
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Residues in contact with CYS 907 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624G PHE* 4.6 0.2 - - - -
636G PHE* 5.8 0.2 - - - -
711G LEU* 4.5 4.8 - - + +
712G MET 3.4 28.6 + - - +
714G GLN* 4.0 17.0 - - - -
717G MET* 3.4 37.5 - - - -
768G LEU* 3.9 13.7 - - + -
903G PRO 3.0 12.6 + - - -
904G GLU 3.1 7.8 + - - +
906G CYS* 1.3 73.8 - - - +
908G ALA* 1.3 66.1 + - - +
910G TYR* 3.4 8.2 + - - +
911G SER* 3.0 24.4 + - - -
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Residues in contact with ALA 908 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711G LEU* 4.0 12.6 - - + +
810G PHE* 3.6 36.3 - - + -
811G GLU 3.9 2.2 - - - +
812G VAL* 3.5 13.4 - - - +
813G PRO* 3.6 19.2 - - + +
819G ARG* 4.1 2.9 - - - +
904G GLU 2.9 6.6 + - - +
905G GLN 3.7 7.2 - - - +
907G CYS* 1.3 74.3 - - - +
909G TYR* 1.3 62.9 + - - +
911G SER* 3.3 5.2 + - - -
912G MET 3.2 15.9 + - - -
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Residues in contact with TYR 909 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626G THR 6.1 0.9 - - - -
813G PRO* 4.4 9.1 - - + +
819G ARG* 5.2 0.7 - - - +
820G ALA* 4.1 13.0 - - + -
823G HIS* 3.4 42.2 - + + +
824G ILE* 3.4 47.3 - - + +
905G GLN 3.1 9.8 + - - +
906G CYS 3.6 1.3 - - - +
908G ALA* 1.3 74.1 - - - +
910G TYR* 1.3 80.6 + + - +
912G MET* 3.1 38.7 + - + +
913G ILE* 3.1 43.1 + - + +
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Residues in contact with TYR 910 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624G PHE* 3.2 21.5 - + - +
625G PRO* 2.6 34.3 + - + -
626G THR 6.0 0.7 - - - -
628G MET* 3.6 20.8 - - + +
633G LEU* 5.1 0.5 - - - +
636G PHE* 3.5 23.2 - + + -
714G GLN* 3.8 38.4 - - + -
823G HIS* 6.0 0.9 - + - -
827G PHE* 4.2 7.2 - + - -
906G CYS* 2.8 42.5 + - + +
907G CYS* 3.7 8.3 - - - +
909G TYR* 1.3 87.0 - + - +
911G SER* 1.3 64.2 + - - +
913G ILE* 3.4 9.9 - - + +
914G ALA* 3.0 26.9 + - - +
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Residues in contact with SER 911 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636G PHE* 4.6 5.6 - - - -
709G GLY 4.8 1.2 + - - -
710G PRO* 2.6 29.1 + - - +
711G LEU* 5.0 2.9 - - - -
712G MET 5.8 0.7 - - - -
812G VAL* 4.0 6.7 - - - -
907G CYS 3.0 13.4 + - - -
908G ALA* 3.4 10.5 - - - -
909G TYR 3.1 0.2 - - - -
910G TYR* 1.3 79.0 - - - +
912G MET* 1.3 61.2 + - - +
914G ALA* 3.9 3.9 - - - +
915G ALA* 3.0 25.1 + - - +
918G ARG* 5.1 1.0 + - - -
952G PRO* 3.4 16.2 - - - +
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Residues in contact with MET 912 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
812G VAL* 3.9 4.7 - - + +
813G PRO* 3.1 30.5 - - + +
815G PRO* 3.7 25.1 - - + -
816G ASN 4.9 1.1 - - - +
820G ALA* 3.8 19.5 - - + -
908G ALA 3.2 7.6 + - - +
909G TYR* 3.1 39.6 + - + +
911G SER* 1.3 76.2 - - - +
913G ILE* 1.3 74.5 + - + +
915G ALA 3.2 1.7 + - - -
916G GLU* 2.8 39.3 + - - +
953G TRP* 3.5 21.1 - - + -
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Residues in contact with ILE 913 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628G MET* 4.0 22.7 - - + +
633G LEU* 3.6 29.9 - - + +
909G TYR* 3.1 41.0 + - + +
910G TYR* 3.4 13.2 - - + +
912G MET* 1.3 102.1 - - + +
914G ALA* 1.3 60.4 + - - +
916G GLU* 3.3 13.8 + - - +
917G GLN* 2.9 28.6 + - - +
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Residues in contact with ALA 914 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633G LEU* 3.9 27.1 - - + +
636G PHE* 3.9 22.9 - - + -
910G TYR 3.0 18.3 + - - +
911G SER* 3.9 3.8 - - - +
913G ILE* 1.3 78.1 - - - +
915G ALA* 1.3 62.3 + - - +
917G GLN* 3.2 4.0 + - - +
918G ARG* 3.0 41.5 + - - +
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Residues in contact with ALA 915 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
911G SER 3.0 17.9 + - - +
912G MET 3.6 2.9 - - - +
914G ALA* 1.3 77.3 - - - +
916G GLU* 1.3 62.7 + - - +
918G ARG* 3.2 23.6 + - - +
919G LEU* 3.0 30.5 + - + +
951G ALA* 5.1 1.8 - - + -
952G PRO* 3.4 32.1 - - + -
953G TRP* 3.9 6.5 - - + -
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Residues in contact with GLU 916 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
815G PRO* 3.7 21.3 - - + +
912G MET* 2.8 32.5 + - - +
913G ILE* 3.6 14.7 - - - +
914G ALA 3.2 0.2 - - - -
915G ALA* 1.3 72.9 - - - +
917G GLN* 1.3 64.3 + - - +
919G LEU* 3.3 6.6 + - - +
920G LYS* 3.0 50.7 + - - +
926G GLU* 5.0 5.5 - - - +
929G PHE* 4.1 17.2 - - + -
953G TRP* 4.2 16.1 - - + -
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Residues in contact with GLN 917 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
630G PRO* 3.7 34.9 - - - +
633G LEU* 3.8 30.3 - - + +
634G ARG* 3.6 13.0 + - + +
913G ILE 2.9 14.4 + - - +
914G ALA 3.2 8.0 + - - +
916G GLU* 1.3 78.1 - - - +
918G ARG* 1.3 62.1 + - - +
920G LYS* 3.2 21.5 + - - +
921G ASP* 3.0 55.6 + - - +
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Residues in contact with ARG 918 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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633G LEU 5.1 7.1 + - - +
634G ARG* 5.6 8.7 - - + +
636G PHE* 5.8 2.6 - - - +
708G ASN* 3.8 50.0 + - - +
911G SER 5.1 1.0 + - - -
914G ALA* 3.0 35.7 + - - +
915G ALA* 3.2 31.1 + - - +
917G GLN* 1.3 76.7 - - + +
919G LEU* 1.3 62.4 + - + +
921G ASP* 3.6 11.6 + - - +
922G ALA* 3.2 22.2 + - - +
952G PRO* 4.9 5.3 - - - +
151H THR* 5.6 1.2 - - - +
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Residues in contact with LEU 919 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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915G ALA* 3.0 20.4 + - + +
916G GLU 3.6 4.5 - - - +
917G GLN 3.2 0.2 - - - -
918G ARG* 1.3 76.1 - - + +
920G LYS* 1.3 65.6 + - - +
922G ALA* 3.0 11.3 + - - +
923G GLY 3.3 0.2 + - - -
924G TYR* 3.0 39.9 + - + +
929G PHE* 3.8 23.1 - - + -
947G GLU* 4.0 39.3 - - + +
948G VAL* 4.4 6.3 - - + +
950G THR* 5.7 0.2 - - - +
951G ALA* 4.2 12.1 - - + -
953G TRP* 3.7 31.4 - - + -
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Residues in contact with LYS 920 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
916G GLU* 3.0 45.7 + - + +
917G GLN* 3.6 26.7 - - - +
919G LEU* 1.3 72.8 - - - +
921G ASP* 1.3 56.0 + - - +
923G GLY* 2.8 26.7 + - - -
924G TYR 3.6 15.2 + - - +
925G GLY* 5.7 1.1 - - - -
926G GLU* 4.3 28.0 + - + -
929G PHE* 4.9 3.8 - - + -
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Residues in contact with ASP 921 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634G ARG* 2.8 44.5 + - - +
917G GLN* 3.0 35.9 + - - +
918G ARG* 3.6 10.8 - - - +
919G LEU 3.3 0.2 - - - -
920G LYS* 1.3 75.9 - - - +
922G ALA* 1.3 58.3 + - - +
923G GLY 3.2 1.1 + - - -
153H LYS* 4.0 12.9 + - - -
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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) + - + + + + + -
------------------------------------------------------------
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