Contacts of the helix formed by residues 910 - 931 (chain A) in PDB entry 4X7J
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 910 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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903A ARG* 5.5 0.4 - - - +
906A ILE 4.0 3.5 + - - -
907A GLU* 4.0 9.1 + - - +
908A GLU 3.7 2.6 - - - -
909A ARG* 1.3 75.7 - - - +
911A ARG* 1.3 88.3 + - - +
912A SER* 3.1 33.1 + - - -
913A VAL* 3.0 27.7 + - + +
914A CYS* 3.0 19.8 + - - -
1081A ASP 4.6 0.7 - - - +
1082A PHE* 4.0 7.2 - - + +
1083A PRO* 6.3 1.3 - - + -
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Residues in contact with ARG 911 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
909A ARG 3.4 4.0 + - - -
910A GLU* 1.3 81.9 + - - +
912A SER* 1.3 59.8 + - - +
914A CYS* 3.3 2.4 + - - +
915A LEU* 2.9 47.5 + - + +
1018A LEU* 4.3 10.3 - - + +
1047A TYR* 3.7 32.2 + - + +
1049A CYS* 4.4 9.1 - - - +
1050A GLU* 2.7 35.3 + - - +
1076A VAL* 3.9 22.8 + - - +
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Residues in contact with SER 912 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
910A GLU* 3.1 19.2 + - - -
911A ARG* 1.3 80.6 - - - +
913A VAL* 1.3 56.3 + - - +
915A LEU* 3.9 2.1 - - - +
916A HIS* 3.0 29.8 + - - +
1080A LEU* 4.1 21.8 - - - +
1081A ASP 3.3 33.6 + - - -
1082A PHE* 4.0 3.1 - - - -
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Residues in contact with VAL 913 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
899A TRP* 4.4 16.2 - - + -
903A ARG* 4.8 10.1 - - - +
909A ARG* 6.0 0.4 - - - -
910A GLU* 3.0 28.6 + - + +
912A SER* 1.3 76.2 - - - +
914A CYS* 1.3 59.7 + - - +
916A HIS* 3.3 3.9 + - + +
917A ILE* 3.0 43.1 + - + +
1082A PHE* 3.6 43.7 - - + -
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Residues in contact with CYS 914 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
899A TRP* 5.1 7.2 - - - -
909A ARG* 3.6 27.4 - - - -
910A GLU 3.0 16.7 + - - +
911A ARG 3.6 6.3 - - - +
913A VAL* 1.3 78.9 - - - +
915A LEU* 1.3 57.5 + - - +
917A ILE* 3.3 8.7 + - - +
918A PHE* 2.8 29.3 + - - +
1014A LEU* 5.7 0.9 - - - -
1017A LEU* 3.3 42.0 - - + +
1018A LEU* 3.8 18.4 - - + -
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Residues in contact with LEU 915 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
911A ARG* 2.9 36.8 + - + +
912A SER* 4.0 1.3 - - - +
914A CYS* 1.3 74.3 - - - +
916A HIS* 1.3 56.7 + - - +
918A PHE* 4.3 2.9 - - - -
919A LEU* 2.8 36.4 + - - +
1014A LEU* 4.1 14.8 - - + -
1018A LEU* 4.9 4.5 - - + -
1050A GLU* 3.6 28.0 - - + +
1076A VAL* 3.6 43.5 - - + +
1077A PHE* 3.7 15.6 - - + -
1080A LEU* 3.8 22.9 - - + -
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Residues in contact with HIS 916 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
912A SER 3.0 19.1 + - - +
913A VAL* 3.5 5.8 - - + +
915A LEU* 1.3 74.9 - - - +
917A ILE* 1.3 69.3 + - + +
919A LEU* 3.9 6.5 - - - +
920A GLN* 3.2 52.5 + - + +
1080A LEU* 3.7 17.7 - - + +
1082A PHE* 3.8 29.2 - + + -
1085A LYS* 3.2 29.9 + - - +
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Residues in contact with ILE 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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896A LEU* 4.1 21.8 - - + -
899A TRP* 3.5 46.0 - - + -
913A VAL* 3.0 22.4 + - + +
914A CYS* 3.7 6.7 - - - +
916A HIS* 1.3 79.5 - - + +
918A PHE* 1.3 66.4 + - - +
920A GLN* 3.3 12.7 + - - +
921A ILE* 3.3 30.4 + - + +
945A PHE* 4.5 15.5 - - + -
951A VAL* 4.2 13.4 - - + +
1017A LEU* 4.2 8.7 - - + -
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Residues in contact with PHE 918 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
914A CYS 2.8 18.0 + - - +
915A LEU* 3.8 3.8 - - - +
916A HIS 3.4 0.2 - - - -
917A ILE* 1.3 76.6 - - - +
919A LEU* 1.3 56.5 + - - +
921A ILE* 3.0 8.4 + - + +
922A ALA* 2.9 30.5 + - + -
1010A LEU* 3.3 54.7 - - + -
1013A ILE* 4.5 5.8 - - + -
1014A LEU* 3.6 42.0 - - + -
1017A LEU* 3.8 14.1 - - + +
1057A MET* 4.2 11.2 - - + -
1071A ILE* 3.8 17.3 - - + -
1077A PHE* 3.5 31.9 - + - -
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Residues in contact with LEU 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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915A LEU 2.8 22.3 + - - +
916A HIS* 3.9 9.2 - - - +
917A ILE 3.3 0.2 - - - -
918A PHE* 1.3 77.2 - - - +
920A GLN* 1.3 58.9 + - + +
922A ALA* 3.3 3.3 + - + +
923A GLU* 2.9 54.7 + - - +
1072A ILE* 4.0 30.5 - - + +
1077A PHE* 3.9 33.2 - - + +
1080A LEU* 4.3 18.4 - - + -
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Residues in contact with GLN 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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648A HIS* 5.5 0.3 - - - -
650A GLY* 4.9 5.1 - - - -
916A HIS* 3.2 45.0 + - + +
917A ILE* 3.3 5.5 + - - +
918A PHE 3.2 0.2 - - - -
919A LEU* 1.3 78.6 - - + +
921A ILE* 1.3 59.6 + - - +
923A GLU* 3.6 14.6 + - - +
924A ALA* 3.1 22.9 + - - +
949A ASP 4.5 2.8 + - - +
950A VAL* 3.9 17.4 - - - +
951A VAL* 3.1 56.7 + - + +
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Residues in contact with ILE 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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896A LEU* 3.9 28.5 - - + -
917A ILE* 3.4 23.8 - - + +
918A PHE* 3.0 13.3 + - + +
920A GLN* 1.3 76.3 - - - +
922A ALA* 1.3 56.1 + - - +
924A ALA* 3.2 5.0 + - - +
925A VAL* 2.9 31.1 + - - +
938A LEU* 4.3 9.2 - - + -
943A ILE* 3.9 24.9 - - + -
951A VAL* 4.0 13.9 - - + -
953A VAL* 4.2 14.8 - - + -
1010A LEU* 3.6 22.7 - - + -
1013A ILE* 4.0 14.8 - - + -
1017A LEU* 4.5 0.9 - - + -
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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 PHE* 2.9 36.6 + - + +
919A LEU* 3.7 6.1 - - - +
921A ILE* 1.3 77.8 - - - +
923A GLU* 1.3 51.8 + - - +
925A VAL* 3.3 5.2 + - - +
926A GLU* 2.8 33.1 + - - +
1010A LEU* 4.2 14.1 - - + +
1068A ALA* 4.1 5.5 - - + +
1071A ILE* 4.4 8.7 - - + -
1072A ILE* 3.7 19.0 - - + +
1077A PHE* 6.0 0.2 - - + -
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Residues in contact with GLU 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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648A HIS* 3.8 15.5 + - + +
919A LEU* 2.9 43.1 + - + +
920A GLN* 3.8 15.0 - - - +
922A ALA* 1.3 71.9 - - - +
924A ALA* 1.3 61.7 + - - +
926A GLU* 3.3 9.3 + - - +
927A PHE* 2.9 28.1 + - - +
1072A ILE* 4.0 25.5 - - + +
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Residues in contact with ALA 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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648A HIS* 4.0 12.2 - - - -
650A GLY* 3.7 30.3 - - - +
651A ILE* 4.3 4.9 - - + +
920A GLN 3.1 15.5 + - - +
921A ILE 3.4 8.1 - - - +
923A GLU* 1.3 71.3 - - - +
925A VAL* 1.3 66.1 + - - +
927A PHE* 3.3 3.6 + - - +
928A LEU* 3.1 29.3 + - - +
953A VAL* 3.9 17.7 - - + -
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Residues in contact with VAL 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 ILE 2.9 17.9 + - - +
922A ALA 3.3 8.0 + - - +
924A ALA* 1.3 77.7 - - + +
926A GLU* 1.3 61.0 + - - +
928A LEU* 3.3 10.7 + - + +
929A HIS* 3.0 52.8 + - + +
935A HIS* 5.8 1.1 - - + -
938A LEU* 3.8 35.9 - - + -
953A VAL* 5.4 2.9 - - + -
1006A ASP* 4.0 13.0 - - + +
1007A ILE* 4.7 0.7 - - + -
1010A LEU* 4.1 19.7 - - + -
1068A ALA* 4.3 5.2 - - + -
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Residues in contact with GLU 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 ALA 2.8 20.5 + - - +
923A GLU* 3.3 11.1 + - - +
925A VAL* 1.3 71.5 - - - +
927A PHE* 1.3 69.9 + - - +
929A HIS* 3.5 3.8 + - + +
930A SER* 3.0 30.2 + - - -
1068A ALA* 3.7 12.5 - - + +
1069A ILE* 3.8 46.6 - - + +
1072A ILE* 4.4 14.1 - - + +
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Residues in contact with PHE 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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646A LEU* 3.9 30.5 - - + -
647A GLU 3.6 32.5 - - - -
648A HIS* 3.5 44.2 - + + +
651A ILE* 3.9 13.7 - - + -
923A GLU 2.9 10.8 + - - +
924A ALA 3.5 7.2 - - - +
925A VAL 3.3 0.2 - - - -
926A GLU* 1.3 81.6 + - - +
928A LEU* 1.3 67.1 + - + +
930A SER* 2.7 26.4 + - - -
931A LYS* 3.2 44.1 - - + +
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Residues in contact with LEU 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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646A LEU* 3.9 13.7 - - + -
651A ILE* 3.8 19.1 - - + -
924A ALA 3.1 17.1 + - - +
925A VAL* 3.3 12.5 + - + +
927A PHE* 1.3 82.9 - - + +
929A HIS* 1.3 62.6 + - + +
931A LYS* 3.1 10.0 + - - -
933A LEU* 2.9 48.5 + - + +
934A MET* 5.1 0.9 - - - -
935A HIS* 4.3 29.6 - - + +
953A VAL* 4.7 4.9 - - + -
1006A ASP* 5.7 0.4 - - - +
1101A 3Z1 3.6 38.4 - - - -
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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
----------------------------------------------------------
925A VAL* 3.0 37.3 + - + +
926A GLU* 3.8 6.1 - - + +
928A LEU* 1.3 77.4 - - + +
930A SER* 1.3 57.1 + - - +
932A GLY* 3.0 18.9 + - - -
933A LEU 3.2 17.7 - - - +
934A MET* 4.2 0.7 - - - -
1003A HIS* 3.1 54.2 + + + +
1006A ASP* 2.9 28.8 + - + +
1007A ILE* 4.2 10.7 - - + +
1067A GLU* 5.2 0.4 + - - -
1068A ALA* 4.4 10.8 + - + +
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Residues in contact with SER 930 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
926A GLU* 3.0 27.1 + - - -
927A PHE* 2.7 24.2 + - - -
929A HIS* 1.3 76.0 - - - +
931A LYS* 1.3 69.0 + - - +
932A GLY 3.3 1.2 + - - -
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Residues in contact with LYS 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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645A LYS 5.4 5.8 + - - -
646A LEU* 4.3 17.5 - - + -
927A PHE* 3.2 48.0 - - + +
928A LEU* 3.1 9.0 + - - +
930A SER* 1.3 86.8 - - - +
932A GLY* 1.3 61.8 + - - +
933A LEU* 3.3 15.4 + - + +
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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