Contacts of the helix formed by residues 924 - 944 (chain A) in PDB entry 4UHW
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 GLY 924 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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848A ARG* 4.9 1.2 - - - +
851A TYR* 4.6 3.1 + - - -
886A VAL* 3.8 28.8 - - - +
890A GLY* 4.0 5.9 - - - -
923A PHE* 1.3 73.3 - - - +
925A PHE* 1.3 57.0 + - - +
927A GLN* 3.1 24.2 + - - +
928A ALA* 2.9 32.4 + - - +
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Residues in contact with PHE 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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893A LYS* 3.3 53.1 - - + +
896A ASN* 3.6 16.8 - - + -
922A GLY* 3.5 12.1 - - - +
923A PHE 3.2 3.6 + - - -
924A GLY* 1.3 72.7 - - - +
926A PRO* 1.4 68.1 - - + +
927A GLN 3.1 1.8 - - - -
928A ALA* 4.4 2.5 - - - +
929A ALA* 2.8 52.0 + - + +
1012A LEU* 3.5 16.6 - - + -
1013A LYS 3.4 24.9 - - - -
1014A PHE* 3.7 19.1 - + + -
1270A GLU 5.7 1.1 - - - -
1271A SER 4.9 1.8 - - - -
1274A PHE* 3.4 31.0 - + + -
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Residues in contact with PRO 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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745A MET* 4.0 2.5 - - - -
848A ARG* 3.7 16.6 - - - +
922A GLY* 3.8 19.1 - - - -
924A GLY 3.6 0.4 - - - -
925A PHE* 1.4 96.2 - - + +
927A GLN* 1.3 66.7 + - - +
930A LEU* 3.4 16.6 + - - +
1214A LEU* 3.9 18.4 - - + -
1215A TYR* 2.7 31.8 + - - +
1273A VAL* 3.7 22.9 - - + -
1274A PHE* 4.5 9.8 - - + +
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Residues in contact with GLN 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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745A MET* 3.5 24.6 - - + +
848A ARG* 3.4 26.3 + - - +
849A HIS* 3.0 36.1 + - - +
851A TYR* 3.5 36.9 - - + -
886A VAL* 4.6 2.4 - - - +
924A GLY* 3.1 32.5 + - - +
926A PRO* 1.3 82.5 - - - +
928A ALA* 1.3 65.8 + - - +
930A LEU* 3.4 4.0 + - - +
931A ILE* 3.2 29.1 + - - +
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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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851A TYR* 4.7 2.7 - - + -
872A HIS* 3.9 16.3 + - + +
890A GLY* 3.4 32.1 - - - +
893A LYS 5.0 1.1 - - - -
894A MET* 4.3 7.7 - - - +
924A GLY 2.9 23.1 + - - +
925A PHE* 4.0 3.6 - - - +
927A GLN* 1.3 73.2 - - - +
929A ALA* 1.3 61.9 + - - +
931A ILE* 3.3 19.9 + - - +
932A THR* 3.4 15.9 + - - +
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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
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894A MET* 4.6 3.6 - - - +
896A ASN* 4.5 6.5 - - + -
925A PHE* 2.8 46.3 + - + +
928A ALA* 1.3 71.2 - - - +
930A LEU* 1.3 58.5 + - - +
932A THR* 2.8 23.6 + - - +
933A GLU* 3.0 19.4 + - - +
1274A PHE* 3.3 29.8 - - + -
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Residues in contact with LEU 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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743A ILE* 4.3 15.3 - - + -
745A MET* 3.5 26.2 - - + -
926A PRO 3.4 18.8 + - - +
927A GLN 3.4 5.5 + - - +
928A ALA 3.3 0.4 - - - -
929A ALA* 1.3 74.3 - - - +
931A ILE* 1.3 68.4 + - + +
933A GLU* 4.5 1.8 - - - +
934A SER* 3.0 23.0 + - - -
1215A TYR* 3.8 10.5 - - + +
1274A PHE* 3.8 5.6 - - - -
1277A CYS* 4.2 13.7 - - + -
1280A PHE* 4.0 14.4 - - + -
1281A PHE* 3.7 29.2 - - + -
1304A SER* 3.8 24.0 - - - -
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Residues in contact with ILE 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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743A ILE* 3.5 27.1 - - + +
745A MET* 5.4 5.6 - - + -
851A TYR* 4.8 12.1 - - + -
852A LEU 4.8 1.6 - - - -
853A GLY* 3.8 30.3 - - - +
855A TYR* 4.0 11.7 - - + -
870A MET* 3.4 32.1 - - + -
872A HIS* 4.2 14.4 - - + +
927A GLN 3.2 18.6 - - - +
928A ALA* 3.4 8.5 - - - +
929A ALA 3.3 0.4 - - - -
930A LEU* 1.3 79.4 - - + +
932A THR* 1.3 57.9 + - - +
934A SER* 3.4 3.1 + - - -
935A CYS* 3.1 25.5 + - - +
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Residues in contact with THR 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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868A LEU* 5.1 0.7 - - + -
870A MET* 4.1 14.4 - - + -
894A MET* 3.2 53.6 + - + +
896A ASN* 4.7 5.4 - - - +
898A TYR* 4.9 5.0 - - - -
900A PHE* 4.8 17.1 - - + -
928A ALA 3.4 3.3 + - - +
929A ALA* 2.8 23.2 + - - +
931A ILE* 1.3 77.9 - - - +
933A GLU* 1.3 58.5 + - - +
935A CYS* 3.4 8.7 + - - +
936A ILE* 3.0 32.1 + - - +
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Residues in contact with GLU 933 (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 ASN* 3.3 21.1 + - - -
898A TYR* 2.6 27.7 + - - -
929A ALA 3.0 20.9 + - - +
930A LEU 4.0 1.1 - - - +
932A THR* 1.3 72.5 + - - +
934A SER* 1.3 61.5 + - - +
936A ILE* 3.2 6.7 + - - +
937A THR* 2.9 33.1 + - - +
951A ARG* 2.7 34.0 + - - +
1010A VAL* 4.6 4.0 - - + -
1011A PRO* 4.0 2.1 - - - +
1274A PHE* 3.6 20.8 - - + -
1277A CYS* 4.6 1.3 - - - -
1281A PHE* 3.3 26.9 - - + -
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Residues in contact with SER 934 (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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743A ILE* 4.1 31.6 - - - +
855A TYR* 3.0 17.8 + - - -
930A LEU 3.0 18.1 + - - -
931A ILE 3.5 5.4 - - - -
933A GLU* 1.3 76.2 - - - +
935A CYS* 1.3 61.4 + - - +
937A THR* 3.3 9.8 + - - -
938A GLU* 3.1 28.9 + - - +
1281A PHE* 3.6 9.5 - - - -
1301A THR* 4.7 4.7 - - - +
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Residues in contact with CYS 935 (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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739A LEU* 5.1 0.2 - - - +
855A TYR* 3.7 40.0 + - + -
857A ALA* 3.7 24.7 - - - -
865A ILE* 5.1 5.8 - - - -
868A LEU* 3.8 19.1 - - + -
870A MET* 4.9 2.7 - - + -
900A PHE* 6.3 0.4 - - - -
931A ILE 3.1 13.2 + - - +
932A THR* 3.5 13.0 - - - +
934A SER* 1.3 77.8 + - - +
936A ILE* 1.3 60.8 + - + +
938A GLU* 3.7 2.5 + - - +
939A VAL* 3.2 30.0 + - - +
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Residues in contact with ILE 936 (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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865A ILE* 4.4 17.3 - - + -
898A TYR* 3.3 54.7 - - + +
900A PHE* 5.0 5.6 - - + -
932A THR 3.0 18.0 + - - +
933A GLU* 3.2 11.4 + - - +
935A CYS* 1.3 75.3 - - + +
937A THR* 1.3 61.1 + - - +
939A VAL* 3.0 7.7 + - - +
940A ALA* 2.8 26.3 + - - +
947A PRO* 4.1 7.6 - - + +
950A VAL* 3.7 22.3 - - + +
951A ARG* 3.9 24.0 - - + +
954A ASN* 5.4 2.2 - - + +
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Residues in contact with THR 937 (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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933A GLU 2.9 16.9 + - - +
934A SER* 3.3 11.4 + - - -
936A ILE* 1.3 71.6 - - - +
938A GLU* 1.3 56.0 + - - +
940A ALA* 3.6 9.3 - - - +
941A ALA* 3.0 25.5 + - - +
947A PRO* 3.6 22.7 - - + +
951A ARG* 3.4 28.5 - - - +
1281A PHE* 3.7 27.0 - - + -
1284A HIS* 4.4 21.1 + - - +
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Residues in contact with GLU 938 (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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739A LEU* 3.6 25.9 - - + +
740A GLU 4.2 6.1 - - - +
741A GLY* 4.3 6.3 - - - -
855A TYR* 2.6 25.6 + - - +
934A SER* 3.1 20.3 + - - +
935A CYS 3.8 5.2 - - - +
937A THR* 1.3 76.1 - - - +
939A VAL* 1.3 63.6 + - - +
941A ALA* 3.3 7.9 + - - +
942A LYS* 3.1 27.2 + - - +
1284A HIS* 6.2 2.2 - - + +
1300A LEU 5.1 9.2 - - - +
1301A THR* 4.1 23.3 + - + +
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Residues in contact with VAL 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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739A LEU* 3.8 19.5 - - + -
857A ALA* 4.2 10.8 - - + -
859A PHE* 3.5 41.7 - - + -
863A GLY* 4.1 15.9 - - - +
865A ILE* 4.1 18.6 - - + -
935A CYS* 3.2 15.2 + - - +
936A ILE* 3.0 8.1 + - - +
938A GLU* 1.3 72.5 - - - +
940A ALA* 1.3 65.9 + - - +
942A LYS* 3.2 4.5 + - - +
943A CYS* 3.0 33.8 + - - -
950A VAL* 4.5 3.1 - - + -
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Residues in contact with ALA 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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936A ILE 2.8 19.7 + - - +
937A THR 3.6 6.3 - - - +
939A VAL* 1.3 73.4 - - - +
941A ALA* 1.3 61.7 + - - +
943A CYS* 3.2 2.5 + - - -
944A GLY* 3.1 15.6 + - - -
945A LEU 3.0 31.1 + - - +
947A PRO* 3.6 30.5 - - + -
950A VAL* 3.7 16.6 - - + +
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Residues in contact with ALA 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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937A THR 3.0 15.5 + - - +
938A GLU* 3.4 12.3 - - - +
939A VAL 3.3 0.2 - - - -
940A ALA* 1.3 76.1 - - - +
942A LYS* 1.3 63.1 + - + +
944A GLY* 3.3 13.4 + - - -
945A LEU 5.0 0.4 - - - -
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Residues in contact with LYS 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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737A GLN* 3.7 24.3 + - - +
738A ILE 5.8 1.2 + - - -
739A LEU* 4.0 21.6 - - + +
859A PHE* 3.8 18.6 - - + -
938A GLU* 3.1 18.2 + - - +
939A VAL 3.2 7.6 + - - +
941A ALA* 1.3 76.5 - - + +
943A CYS* 1.3 59.5 + - - +
944A GLY 3.5 0.2 - - - -
1298A GLY* 5.7 8.5 - - - -
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Residues in contact with CYS 943 (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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737A GLN* 4.5 2.9 - - - +
859A PHE* 3.5 30.7 - - - -
860A MET 3.8 5.2 - - - -
861A ASN* 3.7 11.8 - - - +
863A GLY* 3.8 20.4 - - - -
939A VAL* 3.0 20.8 + - - +
940A ALA* 3.9 4.5 - - - +
941A ALA 3.2 0.2 - - - -
942A LYS* 1.3 76.3 - - - +
944A GLY* 1.3 61.6 + - - +
945A LEU* 3.4 27.9 + - + +
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Residues in contact with GLY 944 (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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940A ALA 3.1 5.4 + - - -
941A ALA* 3.3 11.0 + - - -
942A LYS 3.5 0.6 - - - -
943A CYS* 1.3 78.2 - - - +
945A LEU* 1.3 62.3 + - - +
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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