Contacts of the helix formed by residues 904 - 915 (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 TYR 904 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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902I ARG 3.8 3.0 + - - -
903I SER* 1.3 73.8 + - - +
905I GLU* 1.3 68.1 + - + +
907I LEU* 3.1 22.9 + - + +
908I GLN* 3.1 45.5 + - + -
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Residues in contact with GLU 905 (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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903I SER* 3.0 12.3 + - - +
904I TYR* 1.3 81.7 - - + +
906I GLU* 1.3 63.3 + - + +
908I GLN* 3.0 18.8 + - - +
909I TRP* 3.0 51.8 + - + -
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Residues in contact with GLU 906 (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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871I PRO* 5.1 5.9 - - - +
875I LYS* 4.4 15.0 + - - -
897I TYR* 4.8 12.2 - - + -
898I THR* 4.6 16.0 - - + +
901I ASP* 3.5 33.2 - - + +
903I SER* 3.1 13.4 + - - +
905I GLU* 1.3 75.6 - - + +
907I LEU* 1.3 59.6 + - + +
909I TRP* 3.3 29.9 + - + +
910I LEU* 2.9 28.5 + - - +
913I MET* 5.8 0.2 - - - +
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Residues in contact with LEU 907 (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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898I THR* 4.4 14.8 - - - +
901I ASP 5.6 4.7 - - - +
902I ARG* 5.7 6.5 - - - -
903I SER 4.0 5.8 + - - +
904I TYR* 3.1 24.3 + - + +
906I GLU* 1.3 76.2 - - + +
908I GLN* 1.3 64.9 + - - +
910I LEU* 3.2 10.7 + - + -
911I LEU* 3.1 32.7 + - + +
930I LEU* 4.0 28.3 - - + -
935I PRO* 4.1 26.9 - - + +
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Residues in contact with GLN 908 (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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904I TYR* 3.1 41.3 + - + +
905I GLU* 3.0 13.1 + - - +
907I LEU* 1.3 79.4 - - - +
909I TRP* 1.3 64.3 + - + +
910I LEU 3.0 0.2 - - - -
911I LEU* 3.3 6.3 + - - +
912I ASN* 3.0 52.3 + - - +
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Residues in contact with TRP 909 (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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875I LYS* 4.6 17.0 - - - +
905I GLU* 3.0 60.9 + - + -
906I GLU* 3.5 33.2 - - - +
908I GLN* 1.3 80.8 - - + +
910I LEU* 1.3 56.3 + - - +
912I ASN* 3.6 18.8 + - + +
913I MET* 3.0 43.2 + - + +
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Residues in contact with LEU 910 (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* 4.5 13.7 - - + -
895I VAL* 4.0 23.6 - - + -
898I THR* 3.5 31.6 - - + +
906I GLU 2.9 16.5 + - - +
907I LEU* 3.5 10.3 - - + +
908I GLN 3.0 0.4 - - - -
909I TRP* 1.3 79.4 - - - +
911I LEU* 1.3 58.7 + - + +
913I MET* 3.8 15.0 - - + -
914I ILE* 3.0 28.2 + - - +
926I ILE* 4.1 11.0 - - + -
930I LEU* 3.3 39.9 - - + -
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Residues in contact with LEU 911 (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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907I LEU* 3.1 22.6 + - + +
908I GLN* 4.2 7.4 - - - +
910I LEU* 1.3 76.8 - - + +
912I ASN* 1.3 61.6 + - - +
913I MET 3.4 0.2 - - - -
914I ILE* 3.4 17.8 - - + +
915I GLN* 2.9 26.3 + - - +
927I LEU* 6.0 1.1 - - + -
930I LEU* 2.8 37.0 - - + -
949I LEU* 3.5 35.0 - - + -
952I GLN* 3.8 20.9 + - - +
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Residues in contact with ASN 912 (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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908I GLN* 3.0 44.0 + - - +
909I TRP* 3.6 21.4 - - + +
911I LEU* 1.3 78.5 - - - +
913I MET* 1.3 57.3 + - + +
915I GLN* 2.9 22.1 + - - +
916I ASN* 3.2 14.4 + - - +
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Residues in contact with MET 913 (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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875I LYS* 4.4 33.4 - - - -
891I LEU* 5.8 8.3 - - + -
894I VAL* 4.6 15.0 - - + -
909I TRP* 3.0 30.8 + - + +
910I LEU* 3.8 19.3 + - + +
912I ASN* 1.3 73.0 - - + +
914I ILE* 1.3 65.9 + - - +
915I GLN 3.5 0.2 + - - -
916I ASN 3.9 6.4 + - - +
917I ASP* 3.1 35.9 - - + +
926I ILE* 4.8 10.1 - - + -
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Residues in contact with ILE 914 (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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910I LEU 3.0 27.2 + - - +
911I LEU* 3.4 35.0 - - + +
913I MET* 1.3 78.3 - - - +
915I GLN* 1.3 67.2 + - - +
916I ASN 3.4 0.2 + - - -
917I ASP* 4.6 1.8 - - - +
923I ARG* 3.1 34.5 - - + +
926I ILE* 3.4 27.1 - - + +
927I LEU* 4.0 40.2 - - + +
930I LEU* 3.9 12.3 - - + -
952I GLN* 5.3 5.4 - - - +
956I LEU* 5.4 10.5 - - + -
967I LEU* 5.6 2.0 - - + -
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Residues in contact with GLN 915 (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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911I LEU 2.9 12.8 + - - +
912I ASN* 2.9 14.8 + - - +
914I ILE* 1.3 81.0 - - - +
916I ASN* 1.3 66.6 + - + +
917I ASP 4.3 0.2 - - - -
923I ARG* 4.3 16.0 + - - +
952I GLN* 3.2 28.0 + - - +
956I LEU* 4.2 18.8 - - - +
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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