Contacts of the helix formed by residues 915 - 926 (chain B) in PDB entry 4XUF
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 915 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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785B PHE* 3.9 22.4 - - + -
910B GLN* 3.3 12.5 + - - +
913B TYR 4.3 0.2 + - - -
914B ALA* 1.3 74.8 - - - +
916B GLU* 1.3 81.6 + - - +
917B GLU* 2.5 24.3 + - + +
918B ILE* 3.4 27.7 + - + +
919B TYR* 3.2 18.9 + - - +
946B GLN* 5.2 3.6 - - - +
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Residues in contact with GLU 916 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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932A LYS* 5.0 19.3 - - - +
910B GLN* 3.4 23.6 + - - +
914B ALA 4.7 0.2 - - - +
915B THR* 1.3 87.2 + - - +
917B GLU* 1.3 68.0 + - - +
919B TYR* 3.5 4.1 + - - +
920B ILE* 3.3 31.6 + - + +
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Residues in contact with GLU 917 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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915B THR* 2.5 34.3 + - + +
916B GLU* 1.3 80.3 + - - +
918B ILE* 1.3 59.0 + - - +
920B ILE* 3.1 30.1 - - + +
921B ILE* 3.6 14.9 - - - +
946B GLN* 3.4 26.2 - - + +
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Residues in contact with ILE 918 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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789B LEU* 3.6 32.3 - - + -
878B LEU* 5.1 6.5 - - + +
882B PHE* 4.1 19.3 - - + -
914B ALA* 3.9 13.2 - - + -
915B THR* 3.4 26.3 + - + +
916B GLU 3.3 0.4 - - - -
917B GLU* 1.3 77.9 - - - +
919B TYR* 1.3 65.9 + - - +
921B ILE* 3.2 16.3 + - + +
922B MET* 3.1 45.4 + - + +
943B LEU* 4.7 13.5 - - + -
946B GLN* 4.1 12.3 - - - +
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Residues in contact with TYR 919 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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904A ASN 4.8 3.6 + - - -
905A GLY* 5.5 4.0 + - - -
907B LYS* 4.8 7.6 - - - +
908B MET 2.7 30.4 + - - -
909B ASP* 3.5 9.9 + - - -
910B GLN* 3.4 49.8 - - + -
911B PRO* 4.1 7.6 - - + -
915B THR 3.2 13.9 + - - +
916B GLU* 3.5 4.7 + - - +
917B GLU 3.5 0.2 - - - -
918B ILE* 1.3 81.5 - - + +
920B ILE* 1.3 66.4 + - + +
922B MET* 3.1 21.2 + - + +
923B GLN* 3.1 39.8 + - + +
926B TRP* 4.6 8.3 - + - -
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Residues in contact with ILE 920 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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916B GLU* 3.3 16.6 - - + +
917B GLU* 3.1 30.3 - - + +
919B TYR* 1.3 82.0 - - + +
921B ILE* 1.3 60.0 - - + +
923B GLN* 3.2 27.3 + - - +
924B SER* 3.1 26.2 + - - -
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Residues in contact with ILE 921 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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878B LEU* 3.7 19.7 - - + -
917B GLU 3.6 14.6 - - - +
918B ILE* 3.2 17.4 + - + +
919B TYR 3.1 0.2 - - - -
920B ILE* 1.3 79.2 - - + +
922B MET* 1.3 60.2 + - - +
924B SER* 3.1 9.5 + - - -
925B CYS* 2.9 28.4 + - - -
934B PRO* 6.2 0.4 - - + -
939B LEU* 3.6 22.4 - - + -
942B PHE* 3.9 40.4 - - + -
943B LEU* 3.9 16.6 - - + -
946B GLN* 5.1 6.3 - - - +
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Residues in contact with MET 922 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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875B GLY* 4.1 3.4 - - - +
878B LEU* 3.2 52.9 - - + +
879B TRP* 4.3 10.8 - - - -
882B PHE* 4.1 2.9 - - + -
911B PRO* 3.6 36.6 - - + -
918B ILE* 3.1 32.1 + - + +
919B TYR* 3.1 17.4 + - + +
921B ILE* 1.3 78.4 - - - +
923B GLN* 1.3 57.9 + - - +
925B CYS* 3.1 6.2 + - - +
926B TRP* 3.0 52.2 + - + -
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Residues in contact with GLN 923 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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907A LYS* 5.4 7.9 + - - +
907B LYS* 2.9 46.0 + - + +
919B TYR* 3.1 33.5 + - + +
920B ILE* 3.2 40.5 + - - +
922B MET* 1.3 77.2 - - - +
924B SER* 1.3 62.7 + - - +
926B TRP* 3.2 15.0 + - + -
927B ALA* 3.3 6.2 + - - +
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Residues in contact with SER 924 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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920B ILE 3.1 19.7 + - - -
921B ILE* 3.3 11.2 - - - -
922B MET 3.1 0.2 - - - -
923B GLN* 1.3 78.1 - - - +
925B CYS* 1.3 58.9 + - - +
926B TRP 3.1 2.1 + - - -
927B ALA* 3.5 17.2 + - - +
932B LYS 4.5 3.3 + - - +
933B ARG* 3.7 2.6 - - - -
934B PRO* 3.3 31.9 - - - +
942B PHE* 5.9 1.6 - - - -
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Residues in contact with CYS 925 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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871B VAL* 3.2 42.6 - - + +
872B TRP* 3.3 13.2 - - - -
874B TYR* 4.5 11.7 - - - -
875B GLY* 4.0 11.4 - - - -
921B ILE* 2.9 30.5 + - - -
922B MET 3.4 8.1 - - - +
924B SER* 1.3 75.4 - - - +
926B TRP* 1.3 57.5 + - - +
927B ALA 3.4 2.0 - - - -
933B ARG* 3.3 21.7 + - - -
934B PRO* 4.2 9.4 - - - -
939B LEU* 4.4 9.0 - - - -
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Residues in contact with TRP 926 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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872B TRP* 3.2 46.4 + + + -
875B GLY* 3.2 40.4 - - - -
876B ILE* 3.3 24.8 - - + +
879B TRP* 4.3 16.8 - + + -
889B TYR* 5.8 0.9 - - - -
907B LYS* 3.6 37.0 + - + -
908B MET* 3.6 43.5 - - + -
919B TYR* 4.6 4.5 - + - -
922B MET* 3.0 35.8 + - + +
923B GLN* 3.2 13.4 + - + +
924B SER 3.1 0.8 - - - -
925B CYS* 1.3 85.7 - - - +
927B ALA* 1.3 63.8 + - - +
928B PHE 3.4 1.7 + - - -
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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