Contacts of the helix formed by residues 909 - 930 (chain A) in PDB entry 4G34
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 GLU 909 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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898A TRP* 6.0 0.2 - - - -
905A ILE 4.9 0.4 - - - -
906A GLU 3.8 16.8 + - - +
907A GLU 3.6 4.5 + - - +
908A ARG* 1.3 70.7 - - - +
910A ARG* 1.3 66.4 + - - +
911A SER* 4.6 2.9 - - - +
912A VAL* 3.2 30.0 + - + +
913A CYS* 3.1 23.0 + - - -
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Residues in contact with ARG 910 (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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908A ARG 3.5 4.7 + - - -
909A GLU* 1.3 70.7 - - - +
911A SER* 1.3 65.7 + - - +
913A CYS* 3.3 4.9 + - - +
914A LEU* 3.0 51.0 + - + +
1017A LEU* 4.6 4.0 - - + -
1046A TYR* 3.5 38.5 + - + +
1049A GLU* 3.4 24.6 + - - +
1075A VAL* 4.3 14.3 + - - +
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Residues in contact with SER 911 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
909A GLU* 3.3 2.6 - - - +
910A ARG* 1.3 78.3 - - - +
912A VAL* 1.3 61.6 + - - +
914A LEU* 3.5 6.8 + - - +
915A HIS* 2.9 31.5 + - - +
1078A ASP 6.0 2.4 - - - -
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Residues in contact with VAL 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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898A TRP* 3.9 28.3 - - + -
909A GLU* 3.2 35.0 + - + +
911A SER* 1.3 77.5 - - - +
913A CYS* 1.3 58.8 + - - +
915A HIS* 3.4 11.1 + - + +
916A ILE* 3.0 34.1 + - + +
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Residues in contact with CYS 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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898A TRP* 4.2 16.4 - - - -
908A ARG* 3.9 23.1 - - - -
909A GLU 3.1 17.6 + - - -
910A ARG* 3.6 7.4 - - - +
912A VAL* 1.3 76.1 - - - +
914A LEU* 1.3 57.3 + - - +
916A ILE* 3.2 11.9 + - - +
917A PHE* 2.9 27.9 + - - +
1013A LEU* 6.0 0.4 - - - -
1016A LEU* 3.4 38.8 - - + +
1017A LEU* 4.2 15.9 - - + -
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Residues in contact with LEU 914 (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 ARG* 3.0 58.3 + - + +
911A SER* 4.0 5.6 - - - +
913A CYS* 1.3 71.7 - - - +
915A HIS* 1.3 57.0 + - - +
917A PHE* 3.8 3.9 - - - +
918A LEU* 2.8 37.9 + - - +
1013A LEU* 4.0 22.9 - - + -
1017A LEU* 4.3 9.9 - - + -
1049A GLU* 4.2 13.0 - - + +
1075A VAL* 3.8 19.7 - - + +
1076A PHE* 4.0 25.4 - - + -
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Residues in contact with HIS 915 (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 SER 2.9 19.2 + - - +
912A VAL* 3.6 9.4 - - + +
914A LEU* 1.3 74.6 - - - +
916A ILE* 1.3 64.5 + - + +
918A LEU* 3.7 11.8 + - - +
919A GLN* 3.1 55.5 + - + +
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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
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895A LEU* 3.9 24.0 - - + -
898A TRP* 3.6 47.6 - - + +
912A VAL* 3.0 25.4 + - + +
913A CYS* 3.4 7.6 - - - +
914A LEU 3.2 0.2 - - - -
915A HIS* 1.3 79.0 - - + +
917A PHE* 1.3 65.6 + - - +
919A GLN* 3.2 13.7 + - - +
920A ILE* 3.3 25.9 + - + +
944A PHE* 4.7 6.3 - - + -
950A VAL* 4.2 27.0 - - + +
1016A LEU* 4.2 7.4 - - + -
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Residues in contact with PHE 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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913A CYS 2.9 15.7 + - - +
914A LEU* 3.2 4.7 + - - +
916A ILE* 1.3 75.5 - - - +
918A LEU* 1.3 57.6 + - - +
920A ILE* 3.2 13.0 + - + +
921A ALA* 2.8 33.0 + - + -
1009A LEU* 3.2 56.5 - - + -
1012A ILE* 4.6 5.8 - - + -
1013A LEU* 3.7 41.7 - - + -
1016A LEU* 3.8 12.1 - - + -
1056A MET* 4.5 3.6 - - + -
1070A ILE* 3.8 29.2 - - + -
1076A PHE* 3.6 25.4 - + - -
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Residues in contact with LEU 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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914A LEU 2.8 21.7 + - - +
915A HIS* 3.9 12.8 - - - +
916A ILE 3.2 0.2 - - - -
917A PHE* 1.3 75.6 - - - +
919A GLN* 1.3 56.9 + - + +
921A ALA* 3.2 5.0 + - + +
922A GLU* 2.8 51.8 + - - +
1071A ILE* 4.2 36.1 - - + +
1076A PHE* 4.2 36.6 - - + +
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Residues in contact with GLN 919 (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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647A HIS* 5.4 0.3 - - - -
649A GLY* 4.8 5.6 - - - -
915A HIS* 3.1 50.5 + - + +
916A ILE* 3.2 8.1 + - - +
918A LEU* 1.3 75.0 - - + +
920A ILE* 1.3 64.9 + - - +
922A GLU* 3.5 13.7 + - - +
923A ALA* 3.1 23.2 + - - +
948A ASP 5.2 3.0 + - - -
949A VAL* 3.7 13.3 - - - +
950A VAL* 3.1 50.7 + - + +
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Residues in contact with ILE 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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895A LEU* 4.1 16.6 - - + -
916A ILE* 3.5 22.2 - - + +
917A PHE* 3.2 13.4 + - + +
919A GLN* 1.3 77.5 - - - +
921A ALA* 1.3 62.2 + - - +
923A ALA* 3.1 5.6 + - - +
924A VAL* 3.0 22.6 + - + +
937A LEU* 4.4 9.4 - - + -
942A ILE* 4.1 29.2 - - + -
950A VAL* 3.9 15.7 - - + +
952A VAL* 4.0 22.7 - - + +
1009A LEU* 3.8 21.8 - - + -
1012A ILE* 4.3 13.5 - - + -
1016A LEU* 4.8 0.2 - - + -
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Residues in contact with ALA 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 PHE* 2.8 37.9 + - + +
918A LEU* 3.6 7.0 - - + +
920A ILE* 1.3 76.4 - - - +
922A GLU* 1.3 57.1 + - - +
924A VAL* 3.5 2.5 + - - +
925A GLU* 2.9 23.6 + - - +
1009A LEU* 4.5 16.1 - - + +
1067A ALA* 4.3 4.9 - - + +
1070A ILE* 4.5 7.9 - - + -
1071A ILE* 3.4 24.0 - - + +
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Residues in contact with GLU 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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647A HIS* 3.7 15.5 + - + +
918A LEU* 2.8 42.8 + - + +
919A GLN* 3.9 16.1 - - - +
921A ALA* 1.3 72.6 - - - +
923A ALA* 1.3 63.5 + - - +
925A GLU* 3.5 2.8 + - - +
926A PHE* 3.1 22.9 + - - +
1071A ILE* 3.6 30.3 - - + +
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Residues in contact with ALA 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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647A HIS* 3.9 11.4 - - - +
649A GLY* 3.5 32.3 - - - +
650A ILE* 4.6 3.7 - - + +
919A GLN 3.1 13.8 + - - +
920A ILE 3.1 9.4 + - - +
922A GLU* 1.3 76.4 - - - +
924A VAL* 1.3 62.5 + - - +
926A PHE* 3.4 5.7 + - - +
927A LEU* 3.2 28.5 + - - +
952A VAL* 3.9 16.8 - - + +
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Residues in contact with VAL 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 ILE* 3.0 13.4 + - + +
921A ALA* 3.7 9.2 - - - +
923A ALA* 1.3 73.9 - - - +
925A GLU* 1.3 65.2 + - - +
927A LEU* 3.2 9.5 + - + +
928A HIS* 2.9 54.7 + - + +
934A HIS* 5.1 5.2 - - + -
937A LEU* 3.5 36.3 - - + -
952A VAL* 4.7 2.5 - - + -
1005A ASP* 4.0 10.3 - - + +
1006A ILE* 5.0 0.4 - - + -
1009A LEU* 4.3 16.4 - - + -
1067A ALA* 4.4 7.6 - - + -
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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 ALA 2.9 17.8 + - - +
922A GLU 3.8 3.9 - - - +
923A ALA 3.4 0.2 - - - -
924A VAL* 1.3 77.2 - - - +
926A PHE* 1.3 60.6 + - - +
928A HIS* 3.4 4.6 + - + +
929A SER* 3.0 39.7 + - - -
1067A ALA* 3.8 9.8 - - + +
1068A ILE* 3.8 46.8 - - + +
1071A ILE* 3.5 18.4 - - + +
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Residues in contact with PHE 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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645A LEU* 3.7 29.8 - - + -
646A GLU 3.5 26.0 - - - -
647A HIS* 3.3 33.7 - + + +
650A ILE* 3.5 33.2 - - + -
922A GLU 3.1 9.7 + - - +
923A ALA 3.5 6.7 - - - +
924A VAL 3.2 0.2 - - - -
925A GLU* 1.3 81.1 + - - +
927A LEU* 1.3 63.0 + - + +
929A SER* 2.8 22.4 + - - -
930A LYS* 3.3 36.8 - - - +
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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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645A LEU* 3.9 14.4 - - + -
650A ILE* 3.7 24.2 - - + -
923A ALA 3.2 14.1 + - - +
924A VAL* 3.2 12.6 + - + +
926A PHE* 1.3 78.1 - - + +
928A HIS* 1.3 66.1 + - + +
930A LYS* 3.0 12.6 + - - +
932A LEU* 2.9 43.5 + - + +
933A MET 4.7 0.7 - - - -
934A HIS* 4.2 38.4 - - + +
952A VAL* 4.9 3.6 - - + -
955A PHE* 3.8 28.3 - - + -
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Residues in contact with HIS 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 VAL* 2.9 38.8 + - + +
925A GLU* 3.7 6.5 - - + +
927A LEU* 1.3 77.2 - - + +
929A SER* 1.3 56.4 + - - +
931A GLY* 2.9 19.1 + - - -
932A LEU 3.3 16.8 - - - -
933A MET* 4.3 0.9 - - - -
1002A HIS* 3.2 53.1 + + + +
1005A ASP* 2.9 27.7 + - + -
1006A ILE* 4.1 10.1 - - + +
1066A GLU* 6.0 0.2 - - - -
1067A ALA* 4.3 11.6 + - + +
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Residues in contact with SER 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 GLU* 3.0 28.9 + - - -
926A PHE* 2.8 25.1 + - - -
928A HIS* 1.3 76.3 - - - +
930A LYS* 1.3 67.9 + - - +
931A GLY 3.3 0.6 + - - -
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Residues in contact with LYS 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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645A LEU* 4.4 17.5 - - + -
926A PHE* 3.3 39.9 - - + +
927A LEU* 3.0 9.7 + - - +
929A SER* 1.3 83.8 + - - +
931A GLY* 1.3 60.5 + - - +
932A LEU* 4.3 18.5 - - + +
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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