Contacts of the helix formed by residues 925 - 944 (chain A) in PDB entry 5LUQ
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 GLN 925 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
922A SER* 2.2 34.6 + - - +
924A ARG* 1.3 91.5 - - + +
926A THR* 1.3 66.4 + - + +
928A VAL* 3.3 14.9 - - - +
929A ALA* 3.5 10.7 + - - +
930A ALA 4.2 0.5 + - - -
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Residues in contact with THR 926 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
916A GLU 5.6 2.0 - - - -
919A LEU* 3.6 34.6 - - + +
920A THR* 5.1 1.0 + - - -
921A ALA* 4.3 5.5 + - + -
922A SER* 2.5 58.6 + - - +
923A ASP* 3.3 2.9 + - - -
925A GLN* 1.3 70.6 - - + +
927A LYS* 1.3 68.0 + - - +
930A ALA* 2.6 38.5 + - - +
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Residues in contact with LYS 927 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
916A GLU 5.8 3.4 - - - -
922A SER 3.9 1.2 + - - -
923A ASP* 2.7 40.8 + - + +
924A ARG* 4.7 1.0 - - - +
925A GLN 3.7 0.2 - - - -
926A THR* 1.3 80.6 + - - +
928A VAL* 1.3 78.8 + - + +
930A ALA* 4.9 0.4 - - - -
931A CYS* 2.7 45.5 + - + +
976A VAL* 3.3 47.3 - - + +
977A ASP* 3.5 23.6 - - - +
980A THR* 5.3 3.4 - - + +
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Residues in contact with VAL 928 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
924A ARG 3.0 26.2 - - - +
925A GLN* 3.3 10.3 - - - +
927A LYS* 1.3 106.4 - - + +
929A ALA* 1.3 73.6 + - + +
931A CYS* 3.1 4.6 - - - -
932A GLU* 2.9 34.9 + - + +
980A THR* 6.0 3.4 - - - +
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Residues in contact with ALA 929 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
925A GLN 3.5 9.0 + - - +
928A VAL* 1.3 83.1 - - + +
930A ALA* 1.3 54.7 + - - +
932A GLU* 4.3 4.7 - - - -
933A LEU* 2.7 40.2 + - - +
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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
----------------------------------------------------------
916A GLU* 3.4 48.9 - - + +
917A LEU* 6.0 0.2 - - - -
919A LEU* 5.5 0.4 - - + -
925A GLN 4.2 1.0 + - - -
926A THR* 2.6 28.0 + - - +
927A LYS* 4.9 0.7 - - - -
929A ALA* 1.3 79.9 - - - +
931A CYS* 1.3 55.8 + - - +
933A LEU* 3.3 6.3 - - - +
934A LEU* 2.9 24.6 + - - +
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Residues in contact with CYS 931 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
917A LEU* 4.7 17.9 - - + -
927A LYS* 2.7 32.4 + - + +
928A VAL* 3.1 8.7 - - - -
930A ALA* 1.3 74.7 - - - +
932A GLU* 1.3 72.5 + - - +
933A LEU 3.1 1.3 - - - -
934A LEU* 3.1 6.7 + - - +
935A HIS* 2.8 28.2 + - - +
969A LEU* 5.4 1.5 - - + +
977A ASP* 4.5 8.3 - - - +
980A THR* 3.8 17.7 - - - -
984A TYR* 2.6 40.6 + - + +
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Residues in contact with GLU 932 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
928A VAL* 2.9 20.1 + - + +
929A ALA* 4.3 3.8 - - - -
931A CYS* 1.3 82.8 - - - +
933A LEU* 1.3 53.4 + - - +
935A HIS* 3.2 14.5 + - - +
936A SER* 2.7 39.5 + - - -
980A THR* 4.8 5.1 + - + +
984A TYR* 2.7 27.8 + - - +
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Residues in contact with LEU 933 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
906A PHE* 6.0 3.1 - - + -
909A VAL* 5.7 0.9 - - + -
913A ARG* 4.5 15.7 - - - +
916A GLU* 5.5 0.9 - - - +
929A ALA 2.7 21.9 + - - +
930A ALA* 3.3 6.3 - - - +
932A GLU* 1.3 73.7 - - - +
934A LEU* 1.3 58.6 + - - +
936A SER* 2.6 34.1 + - - -
937A MSE 2.9 34.0 + - + +
940A PHE* 6.2 0.7 - - + -
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Residues in contact with LEU 934 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
910A PHE* 5.3 4.0 - - + +
913A ARG* 3.3 43.3 - - + +
914A VAL* 4.4 2.0 - - + +
916A GLU* 4.7 0.2 - - - +
917A LEU* 4.2 17.0 - - + -
930A ALA 2.9 19.8 + - - +
931A CYS* 3.1 7.4 + - - +
933A LEU* 1.3 71.2 - - - +
935A HIS* 1.3 65.1 + - - +
937A MSE 3.5 14.7 - - + +
938A VAL* 2.8 29.8 + - + +
962A TYR* 2.9 50.9 - - + +
965A THR* 5.2 0.2 - - - +
969A LEU* 3.8 10.8 - - + -
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Residues in contact with HIS 935 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
931A CYS 2.8 8.9 + - - -
932A GLU* 3.2 22.3 + - - +
934A LEU* 1.3 76.5 - - - +
936A SER* 1.3 67.3 + - - +
938A VAL* 2.9 24.6 - - + +
939A MSE 3.0 15.8 + - - +
966A PHE* 4.5 9.2 - + - -
983A LEU* 5.0 9.1 - - + +
984A TYR* 3.2 44.3 - + + -
987A LEU* 3.0 46.9 - - + +
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Residues in contact with SER 936 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
932A GLU* 2.7 25.5 + - - -
933A LEU* 2.6 20.8 + - - +
935A HIS* 1.3 75.2 + - - +
937A MSE 1.3 53.0 + - - -
939A MSE 2.3 37.3 + - - +
940A PHE* 2.8 26.0 - - - -
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Residues in contact with MSE 937 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
893A SER* 4.5 1.5 + - - -
906A PHE* 3.3 36.6 - - + -
909A VAL* 3.2 31.4 - - + +
910A PHE* 4.2 19.7 - - + -
913A ARG* 3.8 18.8 - - + -
933A LEU* 2.9 37.2 + - + +
934A LEU* 3.5 21.3 - - + +
936A SER* 1.3 73.8 - - - +
938A VAL* 1.3 63.5 + - + +
940A PHE* 3.2 17.4 + - - +
941A MSE 3.0 24.7 + - - +
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Residues in contact with VAL 938 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
910A PHE* 6.2 0.4 - - + -
934A LEU* 2.8 25.9 + - + +
935A HIS* 2.9 18.2 - - + +
937A MSE 1.3 73.2 - - + +
939A MSE 1.3 70.4 + - + +
941A MSE 3.1 15.5 - - + +
942A LEU* 2.8 23.2 + - + +
962A TYR* 3.4 44.4 - - + +
966A PHE* 4.2 11.0 - - + -
987A LEU* 6.4 0.4 - - + -
991A LEU* 4.1 25.6 - - + -
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Residues in contact with MSE 939 (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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935A HIS* 3.0 16.3 + - + +
936A SER* 2.3 31.7 + - - +
938A VAL* 1.3 72.6 - - + +
940A PHE* 1.3 64.9 + - + +
942A LEU* 3.0 44.1 - - + +
943A GLY* 2.9 18.0 + - - -
987A LEU* 4.2 26.2 - - + -
991A LEU* 4.7 2.0 - - + -
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Residues in contact with PHE 940 (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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893A SER* 2.9 25.8 - - - +
894A PHE 4.5 10.1 - - - +
895A ALA* 4.9 12.3 - - + -
906A PHE* 5.0 11.2 - + - -
933A LEU* 6.2 0.9 - - + -
936A SER* 2.8 45.8 - - - -
937A MSE 3.2 14.6 - - - +
938A VAL 3.2 0.2 - - - -
939A MSE 1.3 78.6 - - + +
941A MSE 1.3 54.5 + - - +
943A GLY* 2.6 22.3 + - - -
944A LYS* 2.9 18.0 + - + +
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Residues in contact with MSE 941 (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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892A LEU* 4.0 10.5 - - + -
893A SER* 3.9 12.1 + - - -
910A PHE* 3.4 35.0 - - + -
937A MSE 3.0 12.2 + - - +
938A VAL* 3.1 30.7 - - + +
940A PHE* 1.3 79.2 - - - +
942A LEU* 1.3 62.9 + - - +
943A GLY 3.2 0.7 + - - -
944A LYS* 4.0 2.7 - - - +
945A ALA* 3.6 8.7 - - - +
958A MSE 2.9 54.4 - - + +
959A TYR* 3.8 39.2 - - + +
962A TYR* 4.1 22.2 - - + -
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Residues in contact with LEU 942 (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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938A VAL* 2.8 13.9 + - + +
939A MSE 3.0 39.7 - - + +
941A MSE 1.3 80.8 - - - +
943A GLY* 1.3 62.5 + - - +
945A ALA* 4.0 8.5 - - - +
946A THR* 5.0 0.9 + - - -
959A TYR* 5.7 11.9 - - + -
991A LEU* 3.4 37.5 - - + -
994A TRP* 5.2 19.0 + - + +
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Residues in contact with GLY 943 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
939A MSE 2.9 8.3 + - - -
940A PHE* 2.6 14.7 + - - -
942A LEU* 1.3 76.5 - - - +
944A LYS* 1.3 51.7 + - - +
945A ALA 2.5 20.3 + - - -
946A THR* 2.8 20.5 + - - -
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Residues in contact with LYS 944 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
892A LEU 4.7 5.1 - - - +
893A SER* 5.4 10.5 - - - +
894A PHE* 5.3 14.8 - - + +
896A VAL* 5.8 6.5 - - - +
940A PHE* 2.9 16.7 + - + +
941A MSE 4.0 4.7 - - - +
943A GLY* 1.3 67.9 - - - -
945A ALA* 1.3 57.8 + - - +
946A THR 3.8 0.4 - - - +
947A GLN* 4.6 27.3 - - + +
949A PRO* 5.7 5.7 - - + +
951A GLY* 4.2 12.6 - - - -
958A MSE 4.3 5.5 - - - +
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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
------------------------------------------------------------
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