Contacts of the helix formed by residues 949 - 970 (chain A) in PDB entry 2WXL
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 949 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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943A GLN* 3.1 45.2 + - + +
944A GLN* 3.0 27.3 + - - -
946A LYS* 4.0 11.5 - - + +
948A ASN* 1.3 76.3 - - - +
950A SER* 1.3 62.6 + - - +
951A GLU* 3.7 8.5 + - - +
952A LYS* 3.3 26.8 + - - +
953A PHE* 3.0 24.4 + - - +
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Residues in contact with SER 950 (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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943A GLN* 5.6 0.2 - - - +
949A ASN* 1.3 75.7 - - - +
951A GLU* 1.3 59.1 + - - +
953A PHE* 4.3 7.9 - - - -
954A GLU* 2.9 46.1 + - - +
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Residues in contact with GLU 951 (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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949A ASN* 3.1 8.2 - - - +
950A SER* 1.3 83.5 + - - +
952A LYS* 1.3 76.0 + - + +
954A GLU* 4.3 1.4 - - - +
955A ARG* 3.3 30.3 + - + +
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Residues in contact with LYS 952 (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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872A ILE* 5.9 3.4 - - + -
873A GLU* 5.6 7.4 - - - +
876A THR* 5.1 2.0 - - + +
942A ILE* 3.3 29.7 - - + +
943A GLN* 4.4 0.2 - - - -
944A GLN* 3.2 33.9 + - + +
949A ASN* 3.3 29.2 + - - +
951A GLU* 1.3 90.3 + - + +
953A PHE* 1.3 66.2 + - - +
955A ARG* 3.4 20.3 + - + +
956A PHE* 3.1 21.1 + - - +
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Residues in contact with PHE 953 (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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934A LEU* 4.6 2.9 - - + -
939A VAL* 3.9 35.7 - - + -
942A ILE* 4.2 10.1 - - + -
943A GLN* 3.7 15.9 - - + +
949A ASN 3.0 17.7 + - - +
950A SER* 4.1 5.8 - - - +
952A LYS* 1.3 77.3 - - - +
954A GLU* 1.3 79.3 + - + +
956A PHE* 3.1 24.8 + + - +
957A ARG* 2.9 23.3 + - - +
1019A PHE* 3.7 25.6 - + - -
1023A LEU* 3.5 40.4 - - + -
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Residues in contact with GLU 954 (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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950A SER* 2.9 30.5 + - - +
951A GLU* 4.5 1.6 - - - +
953A PHE* 1.3 86.9 - - + +
955A ARG* 1.3 60.8 + - - +
956A PHE 3.2 0.2 - - - -
957A ARG* 2.7 50.2 + - - +
958A GLY* 2.9 24.9 + - - -
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Residues in contact with ARG 955 (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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873A GLU* 3.8 15.7 + - - -
876A THR* 5.9 0.7 - - + -
951A GLU* 3.3 21.7 + - + +
952A LYS* 3.4 25.4 - - + +
954A GLU* 1.3 75.6 - - - +
956A PHE* 1.3 58.7 + - - +
958A GLY* 3.3 3.8 + - - -
959A TYR* 2.6 73.2 + - + +
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Residues in contact with PHE 956 (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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876A THR* 3.7 27.3 - - + +
879A CYS* 4.0 9.2 - - - -
880A ALA* 3.5 29.6 - - + -
883A CYS* 4.5 4.9 - - - -
934A LEU* 3.4 34.5 - - + -
942A ILE* 3.7 31.0 - - + -
952A LYS 3.1 10.4 + - - +
953A PHE* 3.1 24.4 + + - +
955A ARG* 1.3 77.9 - - - +
957A ARG* 1.3 66.4 + - - +
959A TYR* 3.2 12.7 + - - +
960A CYS* 3.1 34.0 + - - -
1019A PHE* 3.9 12.6 - + - -
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Residues in contact with ARG 957 (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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953A PHE* 2.9 16.7 + - + +
954A GLU* 2.7 45.3 + - - +
956A PHE* 1.3 75.7 - - - +
958A GLY* 1.3 57.3 + - - +
960A CYS* 3.1 4.2 + - - +
961A GLU* 2.9 54.8 + - + +
1016A ARG* 4.2 10.0 + - - +
1019A PHE* 3.3 51.5 - - + +
1020A ASN* 2.7 37.0 + - - +
1023A LEU* 4.5 5.5 - - - +
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Residues in contact with GLY 958 (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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954A GLU 2.9 15.1 + - - -
955A ARG* 3.6 5.6 - - - -
956A PHE 3.2 0.2 - - - -
957A ARG* 1.3 75.5 - - - +
959A TYR* 1.3 64.1 + - - +
961A GLU* 3.3 8.4 + - - +
962A ARG* 2.9 29.5 + - - +
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Residues in contact with TYR 959 (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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806A LEU* 4.6 14.4 - - + +
808A LEU* 4.4 6.7 - - + +
873A GLU* 2.7 23.2 + - - -
876A THR* 3.8 24.2 - - + -
877A LEU* 3.6 33.2 - - + -
880A ALA* 3.6 15.5 - - + -
955A ARG* 2.6 66.0 + - + -
956A PHE* 3.2 13.0 + - - +
958A GLY* 1.3 75.7 - - - +
960A CYS* 1.3 56.4 + - - +
962A ARG* 3.5 7.8 + - - +
963A ALA* 2.9 31.9 + - - +
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Residues in contact with CYS 960 (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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880A ALA* 3.8 19.9 - - - +
883A CYS* 4.8 0.4 - - - -
884A VAL* 3.4 18.2 - - + +
932A PHE* 4.2 10.1 - - - -
956A PHE* 3.1 43.2 + - - -
957A ARG 3.4 7.2 - - - +
959A TYR* 1.3 76.7 - - - +
961A GLU* 1.3 56.3 + - - +
963A ALA* 4.6 0.2 - - - -
964A TYR* 2.9 30.3 + - - +
1015A PHE* 4.2 11.4 - - + -
1019A PHE* 4.0 20.4 - - + -
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Residues in contact with GLU 961 (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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957A ARG* 2.9 45.2 + - + +
958A GLY* 3.8 6.8 - - - +
960A CYS* 1.3 69.3 - - - +
962A ARG* 1.3 59.6 - - - +
964A TYR* 3.4 3.1 + - - +
965A THR* 2.9 36.8 + - - +
1012A LEU* 3.9 19.2 - - + +
1015A PHE* 4.0 18.6 - - + -
1016A ARG* 2.7 57.0 + - - +
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Residues in contact with ARG 962 (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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804A GLU* 3.4 25.7 + - - +
805A GLY 4.4 5.1 + - - -
806A LEU* 3.9 33.4 - - + +
958A GLY 2.9 21.4 + - - +
959A TYR* 3.8 8.5 - - - +
961A GLU* 1.3 71.6 - - - +
963A ALA* 1.3 63.3 - - - +
965A THR* 3.2 8.2 + - - +
966A ILE* 3.1 47.9 + - + +
969A ARG* 5.9 0.8 - - - +
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Residues in contact with ALA 963 (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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801A TRP* 2.8 51.6 + - + +
806A LEU* 3.9 3.0 - - - +
808A LEU* 3.7 16.6 - - + -
880A ALA 5.1 0.2 - - - +
884A VAL* 4.2 11.0 - - + -
959A TYR 2.9 18.4 + - - +
960A CYS 3.7 3.6 - - - +
962A ARG* 1.3 76.6 - - - +
964A TYR* 1.3 63.7 + - - +
966A ILE 3.5 0.3 + - - -
967A LEU* 3.2 15.2 + - - +
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Residues in contact with TYR 964 (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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884A VAL* 3.9 10.4 - - + +
887A TYR* 4.2 4.7 + + - -
888A VAL* 4.0 23.8 - - + -
960A CYS 2.9 17.3 + - - +
961A GLU* 3.7 3.8 - - - +
963A ALA* 1.3 77.1 - - - +
965A THR* 1.3 71.4 + - + +
967A LEU* 3.4 4.1 + - - +
968A ARG* 3.2 44.1 + - + +
1001A SER 2.7 29.7 + - - -
1002A LEU* 3.4 19.8 + - + -
1003A ALA* 3.8 9.4 - - - +
1011A ALA 4.1 9.9 + - - -
1012A LEU* 4.9 2.9 - - + -
1014A HIS* 5.2 4.0 - - - -
1015A PHE* 3.7 52.7 - + + +
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Residues in contact with THR 965 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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961A GLU 2.9 26.8 + - - +
962A ARG* 3.2 15.1 + - - +
964A TYR* 1.3 78.3 - - + +
966A ILE* 1.3 61.3 + - - +
968A ARG* 3.5 12.8 + - - +
969A ARG* 3.3 36.0 + - - +
1008A GLU* 4.3 32.3 - - + +
1012A LEU* 3.9 26.9 - - + -
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Residues in contact with ILE 966 (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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800A LEU* 3.8 21.8 - - + +
801A TRP* 3.6 18.8 - - + -
804A GLU* 3.8 39.3 - - + +
806A LEU* 3.9 23.6 - - + -
962A ARG* 3.1 37.2 + - - +
963A ALA 3.8 4.0 - - - +
965A THR* 1.3 73.6 - - - +
967A LEU* 1.3 64.9 + - - +
969A ARG* 3.1 26.7 + - - +
970A HIS* 3.3 22.5 - - + -
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Residues in contact with LEU 967 (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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797A MET* 3.6 56.8 - - + +
800A LEU* 4.6 6.1 - - + -
801A TRP* 3.5 21.5 - - + +
884A VAL* 4.0 24.2 - - + -
888A VAL* 4.2 11.9 - - + -
963A ALA 3.2 12.5 + - - +
964A TYR 3.8 6.5 - - - +
966A ILE* 1.3 74.9 - - - +
968A ARG* 1.3 57.8 + - - +
970A HIS* 2.9 23.3 + - - +
971A GLY* 2.9 11.8 + - - -
974A PHE* 4.0 18.0 - - + -
1002A LEU* 4.2 12.3 - - + -
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Residues in contact with ARG 968 (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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964A TYR* 3.2 33.7 + - + +
965A THR* 3.5 15.1 + - - +
967A LEU* 1.3 78.5 - - - +
969A ARG* 1.3 59.7 + - + +
971A GLY* 2.9 18.3 + - - +
1002A LEU* 2.8 31.7 + - + +
1003A ALA 3.1 11.5 + - - -
1004A LEU* 3.6 28.0 + - + +
1006A LYS 2.8 28.9 + - - -
1007A THR 4.2 0.2 - - - -
1008A GLU* 3.4 35.0 + - - +
1011A ALA* 3.3 23.3 - - - +
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Residues in contact with ARG 969 (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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804A GLU* 3.6 24.2 + - - +
962A ARG* 5.9 1.0 - - - +
965A THR* 3.3 16.5 + - - +
966A ILE* 3.1 33.8 + - - +
968A ARG* 1.3 81.4 - - + +
970A HIS* 1.3 67.6 + - + +
971A GLY 3.4 0.8 + - - -
972A LEU* 5.1 1.4 + - - +
1008A GLU* 3.3 33.5 + - - +
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Residues in contact with HIS 970 (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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800A LEU* 3.8 57.1 + - + +
803A GLN* 5.5 3.7 + - - +
804A GLU* 5.1 9.1 - - - -
966A ILE* 3.3 26.9 + - + +
967A LEU 2.9 9.4 + - - +
969A ARG* 1.3 84.2 + - + +
971A GLY* 1.3 66.0 + - - +
972A LEU* 3.1 3.8 - - - -
973A LEU* 2.9 25.3 + - + +
974A PHE* 3.4 12.8 + - + -
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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
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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