Contacts of the helix formed by residues 911 - 929 (chain A) in PDB entry 5VBD
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 911 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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906A SER* 5.2 0.2 + - - -
909A ASN 5.2 2.2 - - - +
910A ASP* 1.3 76.0 - - - +
912A ILE* 1.3 63.8 + - - +
913A GLY* 3.5 4.7 + - - -
914A SER* 2.6 43.9 + - - -
915A VAL* 3.6 5.5 + - - +
917A ARG* 3.9 2.3 + - - -
1001A UNX 3.0 22.1 - - - -
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Residues in contact with ILE 912 (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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910A ASP 4.1 0.4 + - - -
911A THR* 1.3 72.8 - - - +
913A GLY* 1.3 64.5 + - - +
915A VAL* 3.0 19.1 + - + +
916A ARG* 3.1 29.2 + - + +
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Residues in contact with GLY 913 (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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911A THR* 3.2 5.8 + - - -
912A ILE* 1.3 80.8 - - - +
914A SER* 1.3 56.0 + - - +
916A ARG* 3.6 12.0 - - - +
917A ARG* 2.9 54.5 + - - +
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Residues in contact with SER 914 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
910A ASP* 3.6 22.9 + - - +
911A THR* 2.6 34.9 + - - -
913A GLY* 1.3 75.0 - - - +
915A VAL* 1.3 61.8 + - - +
917A ARG* 3.5 8.6 - - - +
918A CYS* 3.1 27.5 + - - +
1001A UNX 3.9 6.3 - - - -
1002A UNX 3.8 15.5 - - - -
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Residues in contact with VAL 915 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
904A VAL* 4.3 17.9 - - + -
906A SER* 3.5 31.9 - - - +
911A THR 4.2 7.6 - - - +
912A ILE* 3.0 11.0 + - + +
914A SER* 1.3 75.8 + - - +
916A ARG* 1.3 67.7 + - - +
918A CYS* 3.2 7.0 + - - +
919A ILE* 3.0 39.2 + - + +
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Residues in contact with ARG 916 (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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912A ILE* 3.1 28.0 + - + +
913A GLY* 3.2 14.2 + - - +
915A VAL* 1.3 79.3 - - - +
917A ARG* 1.3 59.7 + - + +
919A ILE* 3.3 10.5 + - + +
920A LEU* 3.0 27.6 + - + +
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Residues in contact with ARG 917 (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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911A THR* 3.9 1.8 + - - -
913A GLY* 2.9 31.5 + - - +
914A SER 3.5 11.6 - - - +
916A ARG* 1.3 77.0 - - + +
918A CYS* 1.3 60.0 + - - +
920A LEU* 3.8 8.5 - - + +
921A ASN* 2.9 43.2 + - - +
1001A UNX 3.1 25.7 - - - -
1002A UNX 3.1 26.2 - - - -
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Residues in contact with CYS 918 (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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902A LEU* 5.7 2.0 - - - -
904A VAL* 3.9 29.2 - - + -
905A TRP 5.6 1.6 - - - -
914A SER 3.1 19.0 + - - +
915A VAL* 3.5 8.7 - - - +
917A ARG* 1.3 75.2 - - - +
919A ILE* 1.3 62.8 + - - +
921A ASN* 3.9 6.3 - - - +
922A ARG* 3.1 22.7 + - - +
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Residues in contact with ILE 919 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
902A LEU* 4.3 16.4 - - + -
904A VAL* 4.1 20.4 - - + -
915A VAL* 3.0 37.5 + - + +
916A ARG* 3.7 9.0 - - + +
917A ARG 3.3 0.4 - - - -
918A CYS* 1.3 76.7 - - - +
920A LEU* 1.3 63.4 + - - +
922A ARG* 3.2 4.3 + - - +
923A ILE* 3.1 32.9 + - + +
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Residues in contact with LEU 920 (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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916A ARG* 3.0 17.4 + - + +
917A ARG* 3.9 9.2 - - + +
919A ILE* 1.3 76.4 - - - +
921A ASN* 1.3 60.0 + - - +
923A ILE* 3.2 13.9 + - + +
924A LYS* 2.9 63.3 + - + +
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Residues in contact with ASN 921 (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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917A ARG* 2.9 28.8 + - - +
918A CYS* 3.9 5.7 - - - +
920A LEU* 1.3 80.7 - - - +
922A ARG* 1.3 55.8 + - - +
924A LYS* 3.5 15.7 + - - +
925A ALA* 2.9 28.9 + - - +
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Residues in contact with ARG 922 (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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902A LEU* 3.5 42.6 - - + -
918A CYS* 3.1 14.9 + - - +
919A ILE 3.5 8.5 - - - +
921A ASN* 1.3 74.6 - - - +
923A ILE* 1.3 62.0 + - + +
925A ALA* 3.2 8.4 + - - +
926A ASN* 2.8 58.6 + - - +
967A GLN* 5.8 0.4 - - - +
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Residues in contact with ILE 923 (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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902A LEU* 6.0 2.7 - - + -
919A ILE* 3.1 26.6 + - + +
920A LEU* 3.2 16.4 + - + +
922A ARG* 1.3 79.1 - - + +
924A LYS* 1.3 65.1 + - + +
926A ASN* 3.2 17.6 + - + +
927A VAL* 3.1 31.9 + - + +
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Residues in contact with LYS 924 (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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920A LEU* 2.9 52.0 + - + +
921A ASN* 3.7 15.9 - - - +
923A ILE* 1.3 77.1 - - + +
925A ALA* 1.3 61.1 + - - +
927A VAL* 3.3 7.1 + - - +
928A ALA* 3.0 23.1 + - - +
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Residues in contact with ALA 925 (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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921A ASN 2.9 17.9 + - - +
922A ARG* 3.6 11.2 - - - +
924A LYS* 1.3 75.2 - - - +
926A ASN* 1.3 65.9 + - - +
928A ALA* 3.3 7.5 + - - +
929A HIS* 2.8 40.9 + - + +
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Residues in contact with ASN 926 (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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922A ARG* 2.8 46.6 + - - +
923A ILE* 3.2 19.7 + - + +
925A ALA* 1.3 78.1 - - - +
927A VAL* 1.3 55.7 + - + +
929A HIS* 3.3 12.6 + - - +
930A THR* 2.8 24.1 + - - -
967A GLN* 3.2 37.3 + - - +
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Residues in contact with VAL 927 (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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923A ILE* 3.1 23.9 + - + +
924A LYS* 3.9 6.1 - - - +
926A ASN* 1.3 74.0 - - + +
928A ALA* 1.3 65.1 + - - +
930A THR* 3.1 27.5 + - + +
965A LEU* 6.2 3.8 - - + -
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Residues in contact with ALA 928 (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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924A LYS 3.0 16.9 + - - +
925A ALA* 3.3 8.9 + - - +
927A VAL* 1.3 76.5 - - - +
929A HIS* 1.3 63.0 + - + +
930A THR 3.3 3.5 + - - +
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Residues in contact with HIS 929 (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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925A ALA* 2.8 32.4 + - + +
926A ASN* 3.3 6.0 + - - +
927A VAL 3.2 0.6 - - - -
928A ALA* 1.3 80.3 - - + +
930A THR* 1.3 60.0 + - - +
931A LYS* 3.9 0.7 + - - +
966A THR 3.7 0.2 - - - +
967A GLN* 3.5 25.0 + - + +
968A ILE* 2.8 42.1 + - + +
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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