Contacts of the helix formed by residues 913 - 932 (chain A) in PDB entry 4QMH
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 ASN 913 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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874A TRP* 3.3 50.6 - - + +
877A ARG* 4.0 2.7 - - - +
911A ASP* 2.8 20.7 + - - +
912A SER* 1.3 79.9 + - - +
914A ALA* 1.3 64.0 + - - +
915A LYS* 2.9 36.1 + - - +
916A ILE* 3.1 13.6 + - + +
917A ALA* 3.1 18.2 + - - +
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Residues in contact with ALA 914 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
911A ASP 5.3 0.2 - - - -
912A SER 3.8 3.8 + - - -
913A ASN* 1.3 73.2 + - - +
915A LYS* 1.3 59.6 + - + +
917A ALA* 3.3 7.6 + - - +
918A GLN* 2.9 53.3 + - - +
952A ASP* 6.1 0.7 - - - +
954A LYS* 5.1 8.7 - - - +
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Residues in contact with LYS 915 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
874A TRP* 3.8 41.7 - - + -
878A ASN* 6.0 0.2 - - - -
913A ASN* 2.9 13.4 + - - +
914A ALA* 1.3 76.9 - - + +
916A ILE* 1.3 59.4 + - + +
918A GLN* 3.4 11.6 + - - +
919A THR* 2.9 34.9 + - - +
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Residues in contact with ILE 916 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
874A TRP* 3.5 32.3 - - + +
877A ARG* 4.0 6.1 - - + +
878A ASN* 3.5 33.0 - - + +
881A LEU* 3.9 15.0 - - + -
908A ARG* 4.0 11.7 - - - +
911A ASP* 3.4 33.2 - - + +
913A ASN* 3.1 24.6 + - + +
915A LYS* 1.3 75.9 - - - +
917A ALA* 1.3 57.9 + - - +
919A THR* 3.3 4.8 + - - -
920A THR* 2.8 38.7 + - - +
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Residues in contact with ALA 917 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
908A ARG 3.4 14.1 + - - +
909A LEU* 3.7 21.2 - - - +
911A ASP 4.3 10.8 - - - +
913A ASN 3.1 10.3 + - - +
914A ALA* 3.7 11.2 - - - +
916A ILE* 1.3 79.4 - - - +
918A GLN* 1.3 62.8 + - + +
920A THR* 3.4 3.1 + - - -
921A LEU* 3.2 27.9 + - + +
957A VAL* 6.3 2.0 - - + -
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Residues in contact with GLN 918 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
914A ALA* 2.9 32.8 + - - +
915A LYS* 3.8 11.0 - - - +
917A ALA* 1.3 75.7 - - + +
919A THR* 1.3 66.2 + - - +
921A LEU* 3.2 20.1 + - + +
922A ALA* 3.2 12.0 + - - +
952A ASP* 5.4 0.8 + - - -
954A LYS* 3.8 13.7 - - - +
956A PHE* 3.6 29.4 - - + -
957A VAL* 3.5 34.7 - - + +
960A ALA* 5.7 1.1 - - - +
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Residues in contact with THR 919 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
878A ASN* 4.2 15.5 + - - +
881A LEU* 3.9 23.6 - - + -
915A LYS* 2.9 22.6 + - - +
916A ILE* 3.7 4.5 - - - -
918A GLN* 1.3 76.4 - - - +
920A THR* 1.3 57.7 + - - +
922A ALA* 3.2 11.2 + - + +
923A ILE* 2.9 37.6 + - + +
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Residues in contact with THR 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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881A LEU* 3.5 10.7 - - - +
905A LEU* 3.6 40.4 - - + +
908A ARG* 3.2 25.1 - - + +
909A LEU* 3.6 16.8 - - + +
916A ILE 2.8 20.8 + - - -
917A ALA 3.7 5.4 - - - -
919A THR* 1.3 73.9 - - - +
921A LEU* 1.3 60.0 + - - +
923A ILE* 3.2 9.2 + - - +
924A CYS* 2.9 29.7 + - - -
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Residues in contact with LEU 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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909A LEU* 3.6 21.3 - - + +
917A ALA* 3.2 16.5 + - + +
918A GLN* 3.2 13.5 + - + +
920A THR* 1.3 75.8 - - - +
922A ALA* 1.3 63.3 - - - +
924A CYS* 3.2 1.6 + - - -
925A GLU* 3.0 19.5 + - - +
946A PHE* 3.9 18.8 - - + -
949A ALA* 4.3 13.5 - - + -
957A VAL* 4.1 26.5 - - + +
960A ALA* 3.9 29.6 - - + -
961A ALA* 4.1 17.9 - - + +
964A CYS* 3.2 17.5 - - - -
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Residues in contact with ALA 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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918A GLN 3.2 8.0 + - - +
919A THR* 3.2 14.0 + - + +
921A LEU* 1.3 76.7 - - - +
923A ILE* 1.3 63.7 + - + +
925A GLU* 3.3 9.8 + - - +
926A GLN* 3.0 22.2 + - - +
960A ALA* 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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881A LEU* 3.5 54.7 - - + +
884A LEU* 3.8 23.8 - - + -
885A GLN* 4.6 10.1 - - + -
888A ILE* 4.1 14.8 - - + -
905A LEU* 4.4 13.0 - - + -
919A THR* 2.9 25.1 + - + +
920A THR* 3.2 8.3 + - - +
922A ALA* 1.3 77.8 - - + +
924A CYS* 1.3 57.4 + - - +
926A GLN* 3.2 17.8 + - - +
927A LEU* 2.8 26.8 + - + +
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Residues in contact with CYS 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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905A LEU* 4.3 17.9 - - - -
909A LEU* 4.2 13.7 - - - -
920A THR* 2.9 24.3 + - - +
921A LEU 3.7 4.9 - - - +
923A ILE* 1.3 76.7 - - - +
925A GLU* 1.3 57.3 + - - +
927A LEU* 3.3 7.9 + - - +
928A ALA 3.0 22.9 + - - -
942A LEU* 4.2 17.5 - - - -
946A PHE* 3.8 34.1 - - + -
964A CYS* 4.0 0.9 - - - -
968A PHE* 3.4 14.8 - - + -
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Residues in contact with GLU 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 LEU 3.0 11.6 + - - +
922A ALA* 3.6 11.1 - - - +
923A ILE 3.2 0.2 - - - -
924A CYS* 1.3 76.2 - - - +
926A GLN* 1.3 63.0 + - - +
928A ALA* 3.2 7.9 + - - +
929A THR* 3.1 28.2 + - - +
960A ALA* 4.6 5.0 - - - +
963A ASN* 3.7 34.5 + - - +
964A CYS* 3.9 10.1 + - - +
967A SER* 4.4 18.3 - - - +
968A PHE* 5.1 0.7 - - - -
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Residues in contact with GLN 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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885A GLN* 3.0 52.6 + - - +
888A ILE* 3.4 19.5 - - + +
889A SER* 3.0 27.3 + - - +
922A ALA 3.0 11.2 + - - +
923A ILE* 3.2 17.5 + - - +
925A GLU* 1.3 77.2 - - - +
927A LEU* 1.3 60.7 + - - +
929A THR* 3.3 8.0 + - - -
930A ALA* 3.0 22.3 + - - +
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Residues in contact with LEU 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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857A ILE* 4.8 0.4 - - + -
888A ILE* 3.9 24.4 - - + +
894A ILE* 3.7 25.6 - - + -
898A ILE* 4.2 12.6 - - + -
901A LEU* 4.5 12.8 - - + -
905A LEU* 4.1 22.7 - - + -
923A ILE* 2.8 20.2 + - + +
924A CYS* 3.5 7.0 - - - +
925A GLU 3.2 0.4 - - - -
926A GLN* 1.3 73.3 - - - +
928A ALA* 1.3 63.0 + - - +
930A ALA* 3.2 4.5 + - - +
931A MET* 2.9 48.5 + - + +
938A HIS* 5.4 2.0 - - + -
942A LEU* 4.6 16.4 - - + -
968A PHE* 5.1 4.0 - - + -
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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 CYS 3.0 6.0 + - - +
925A GLU* 3.2 9.4 + - - +
927A LEU* 1.3 78.0 - - - +
929A THR* 1.3 63.4 + - - +
931A MET* 3.2 0.5 + - - +
932A GLY* 2.9 22.7 + - - +
935A CYS* 4.3 13.2 - - + -
967A SER* 3.5 20.4 - - - +
968A PHE* 3.6 32.0 - - + +
971A LYS* 3.3 14.6 - - + +
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Residues in contact with THR 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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854A ARG* 5.5 0.3 + - - -
892A ARG 5.9 0.4 - - - +
893A LEU* 4.3 10.5 - - + +
925A GLU* 3.1 14.2 + - - +
926A GLN* 3.7 9.0 - - - -
928A ALA* 1.3 79.6 - - - +
930A ALA* 1.3 63.0 + - - +
932A GLY* 3.7 6.6 + - - -
967A SER* 4.7 1.0 + - - -
971A LYS* 3.6 22.3 + - - +
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Residues in contact with ALA 930 (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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854A ARG* 3.0 10.9 + - - -
888A ILE* 3.8 21.1 - - + -
892A ARG 3.2 26.5 - - - +
893A LEU* 3.4 4.3 - - - +
894A ILE* 2.9 37.2 + - + -
926A GLN* 3.0 17.3 + - + +
927A LEU 3.2 4.5 + - - +
929A THR* 1.3 77.9 - - - +
931A MET* 1.3 57.2 + - - +
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Residues in contact with MET 931 (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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854A ARG* 3.5 14.6 + - - -
894A ILE* 3.7 21.1 - - + +
895A LYS 3.9 15.7 - - - +
896A PRO* 3.8 8.9 - - + +
898A ILE* 3.6 31.6 - - + -
927A LEU* 2.9 33.6 + - + +
928A ALA 4.0 1.8 - - - +
930A ALA* 1.3 77.4 - - - +
932A GLY* 1.3 64.4 + - - +
933A ALA 3.3 0.9 + - - -
934A GLY* 3.2 30.2 + - - +
935A CYS* 3.8 11.4 - - + +
938A HIS* 3.5 32.1 - - + +
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Residues in contact with GLY 932 (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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854A ARG* 4.3 9.8 - - - +
928A ALA 2.9 12.0 + - - -
929A THR 3.7 5.8 + - - -
930A ALA 3.6 1.8 - - - -
931A MET* 1.3 75.5 - - - +
933A ALA* 1.3 64.4 + - - -
935A CYS* 3.0 26.7 + - - -
971A LYS* 3.8 14.8 - - - +
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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
------------------------------------------------------------
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