Contacts of the helix formed by residues 923 - 942 (chain A) in PDB entry 1WER
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 SER 923 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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822A MET* 4.6 7.6 + - - -
824A SER 4.9 5.0 + - - -
921A SER 3.6 1.8 + - - -
922A PRO* 1.3 75.1 - - - +
924A PRO* 1.3 69.0 - - - +
925A ILE* 3.9 6.0 + - - +
926A ALA* 3.2 21.9 + - - +
927A ALA* 2.8 26.4 + - - +
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Residues in contact with PRO 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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922A PRO 4.6 0.9 - - - +
923A SER* 1.3 86.9 - - - +
925A ILE* 1.3 64.5 + - + +
927A ALA* 3.3 7.5 + - + +
928A ARG* 3.1 23.7 + - - +
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Residues in contact with ILE 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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824A SER 4.4 10.5 - - - +
825A LYS* 3.7 25.8 - - + +
826A GLN 3.9 23.8 - - - +
827A SER* 4.0 21.5 - - - +
923A SER* 3.3 6.1 + - - +
924A PRO* 1.3 78.7 - - + +
926A ALA* 1.3 63.3 + - - +
928A ARG* 3.4 5.9 + - - +
929A THR* 3.1 30.1 + - - +
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Residues in contact with ALA 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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821A ILE* 3.7 28.6 - - + +
822A MET* 3.8 25.1 - - + +
824A SER 5.3 1.1 + - - +
922A PRO* 3.8 7.0 - - + -
923A SER* 3.2 22.9 + - - +
925A ILE* 1.3 79.0 - - - +
927A ALA* 1.3 58.4 + - - +
929A THR* 3.3 2.6 + - - -
930A LEU* 2.9 33.4 + - - +
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Residues in contact with ALA 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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922A PRO* 3.9 16.5 - - + +
923A SER 2.8 17.5 + - - +
924A PRO* 3.3 9.2 + - + +
926A ALA* 1.3 75.9 - - - +
928A ARG* 1.3 63.0 + - - +
930A LEU* 3.4 8.0 + - - +
931A ILE* 3.2 31.3 + - + +
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Residues in contact with ARG 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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827A SER* 6.0 0.4 - - - +
828A CYS 5.6 0.7 - - - +
829A GLU* 2.8 38.3 + - + +
831A SER* 2.8 28.7 + - - +
834A LYS* 3.6 20.5 - - - +
924A PRO 3.1 16.2 + - - +
925A ILE* 3.7 7.0 - - - +
926A ALA 3.3 0.2 - - - -
927A ALA* 1.3 74.5 - - - +
929A THR* 1.3 66.6 + - - +
931A ILE* 3.2 29.0 + - - +
932A LEU* 3.0 54.6 + - + +
935A LYS* 5.4 1.6 - - - +
952A TYR* 3.8 16.4 + - - -
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Residues in contact with THR 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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821A ILE* 3.8 27.6 - - + -
826A GLN 4.5 2.6 + - - -
828A CYS* 3.7 46.2 + - - +
847A HIS* 5.6 0.2 - - - +
851A ILE* 3.8 14.8 - - + -
925A ILE* 3.1 21.9 + - - +
926A ALA* 3.6 4.5 - - - -
928A ARG* 1.3 76.8 - - - +
930A LEU* 1.3 57.0 + - - +
932A LEU* 3.1 3.1 + - - +
933A VAL* 2.8 38.0 + - + +
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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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818A ILE* 4.4 14.4 - - + -
821A ILE* 4.2 19.5 - - + -
822A MET* 3.5 30.3 - - + -
909A ILE* 3.4 39.7 - - + +
910A LEU* 4.6 9.2 - - + +
912A PRO* 3.8 14.6 - - + -
922A PRO* 3.9 15.0 - - + -
926A ALA 2.9 18.6 + - - +
927A ALA* 3.6 6.7 - - - +
928A ARG 3.3 0.2 - - - -
929A THR* 1.3 76.4 - - - +
931A ILE* 1.3 57.5 + - + +
933A VAL* 4.5 1.1 - - - -
934A ALA* 2.9 33.0 + - - +
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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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910A LEU* 4.0 22.0 - - + +
927A ALA* 3.2 19.4 + - + +
928A ARG* 3.2 33.2 + - - +
930A LEU* 1.3 77.9 - - + +
932A LEU* 1.3 57.1 + - - +
934A ALA* 3.5 1.7 + - - +
935A LYS* 3.0 45.3 + - - +
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Residues in contact with LEU 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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828A CYS* 3.2 35.7 - - + +
829A GLU* 4.3 3.1 - - - -
830A LEU* 4.3 9.9 - - + -
848A LEU* 4.4 14.8 - - + -
928A ARG* 3.0 61.2 + - + +
929A THR* 3.9 3.6 - - - +
931A ILE* 1.3 73.2 - - - +
933A VAL* 1.3 57.3 + - - +
935A LYS* 3.6 12.9 - - - +
936A SER* 2.8 37.4 + - - -
952A TYR* 4.7 2.2 - - + -
953A MET* 3.8 28.2 - - + +
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Residues in contact with VAL 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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821A ILE* 4.3 8.1 - - + -
848A LEU* 3.9 19.3 - - + -
851A ILE* 3.9 22.0 - - + -
852A LEU* 4.1 11.8 - - + +
855A LEU* 3.5 31.0 - - + -
909A ILE* 4.1 14.1 - - + -
929A THR* 2.8 29.2 + - + +
930A LEU* 3.8 4.0 - - - +
932A LEU* 1.3 74.0 - - - +
934A ALA* 1.3 59.6 + - - +
936A SER* 3.2 3.5 + - - -
937A VAL* 2.9 31.0 + - + +
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Residues in contact with ALA 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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906A CYS* 4.0 11.1 - - + +
909A ILE* 3.8 19.3 - - + -
910A LEU* 3.7 34.1 - - + -
930A LEU 2.9 18.3 + - - +
931A ILE 3.8 0.4 - - - +
933A VAL* 1.3 77.0 - - - +
935A LYS* 1.3 57.8 + - - +
937A VAL* 3.8 5.3 - - - +
938A GLN* 2.9 31.5 + - - +
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Residues in contact with LYS 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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928A ARG* 5.4 1.8 - - - +
931A ILE* 3.0 34.5 + - - +
932A LEU* 3.6 16.8 - - - +
934A ALA* 1.3 77.0 - - - +
936A SER* 1.3 61.5 + - - +
938A GLN* 3.4 5.9 + - - +
939A ASN* 3.2 20.8 + - - +
946A PHE* 3.6 17.2 - - + -
950A GLU* 3.8 23.5 + - - +
952A TYR* 5.5 6.5 - - + -
953A MET* 4.0 20.9 - - + -
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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
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848A LEU* 4.4 2.3 - - - +
852A LEU* 3.6 29.4 - - - +
932A LEU 2.8 21.9 + - - -
933A VAL 3.2 4.2 + - - -
935A LYS* 1.3 72.7 - - - +
937A VAL* 1.3 65.7 + - - +
939A ASN* 3.4 4.0 + - - +
940A LEU* 3.1 22.9 + - - +
946A PHE* 4.1 10.7 - - - -
953A MET* 3.7 11.3 - - - +
956A VAL* 3.7 19.2 - - - +
959A PHE* 4.6 2.8 - - - -
960A ILE* 4.4 4.2 - - - +
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Residues in contact with VAL 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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852A LEU* 4.2 10.5 - - + -
855A LEU* 3.9 27.4 - - + -
856A VAL* 5.0 13.0 - - + -
859A ILE* 4.8 3.8 - - + -
901A PHE* 3.7 34.1 - - + -
905A ILE* 4.6 6.7 - - + -
906A CYS* 4.0 9.2 - - - -
909A ILE* 4.5 2.9 - - + -
933A VAL* 2.9 21.5 + - + +
934A ALA* 3.9 5.2 - - - +
936A SER* 1.3 75.6 - - - +
938A GLN* 1.3 58.7 + - - +
940A LEU* 3.3 10.1 + - + +
941A ALA* 2.8 27.4 + - - +
959A PHE* 5.6 0.9 - - + -
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Residues in contact with GLN 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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897A SER* 5.0 0.9 + - - -
901A PHE* 4.7 0.2 - - - +
902A LEU* 3.3 48.8 + - + +
906A CYS* 3.5 23.2 - - + +
934A ALA 2.9 18.4 + - - +
935A LYS* 3.8 6.5 - - - +
936A SER 3.3 0.2 - - - -
937A VAL* 1.3 76.3 - - - +
939A ASN* 1.3 59.0 + - - +
941A ALA* 3.2 10.9 + - - +
942A ASN* 2.9 46.8 + - - +
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Residues in contact with ASN 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 LYS* 3.2 15.8 + - - +
936A SER 3.8 1.1 - - - +
937A VAL 3.3 0.2 - - - -
938A GLN* 1.3 78.2 - - - +
940A LEU* 1.3 56.7 + - - +
942A ASN* 3.1 5.9 + - - +
943A LEU 2.9 21.8 + - - -
944A VAL* 2.9 48.7 + - - +
945A GLU 3.6 3.4 + - - -
946A PHE* 3.5 46.3 - - + +
950A GLU* 5.1 2.3 - - - +
960A ILE* 3.7 13.0 - - + -
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Residues in contact with LEU 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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856A VAL* 3.8 19.3 - - + -
860A PHE* 4.6 7.0 - - + -
936A SER 3.1 13.8 + - - +
937A VAL* 3.6 10.1 - - + +
939A ASN* 1.3 74.3 - - - +
941A ALA* 1.3 57.4 + - - +
943A LEU* 2.9 19.8 + - - +
959A PHE* 3.7 28.0 - - + -
960A ILE* 3.7 41.0 - - + +
963A ASN* 3.7 29.8 - - + +
964A LYS* 3.9 8.3 - - + +
967A MET* 3.5 19.5 - - + +
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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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894A ARG* 5.9 0.3 - - - -
897A SER* 2.9 32.3 + - - +
901A PHE* 3.6 26.7 - - + -
937A VAL 2.8 20.5 + - - +
938A GLN* 3.4 16.4 - - - +
940A LEU* 1.3 73.8 - - - +
942A ASN* 1.3 59.6 + - - +
943A LEU* 3.6 5.9 + - - +
967A MET* 3.2 19.0 - - + +
971A LEU* 4.3 1.7 - - - +
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Residues in contact with ASN 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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894A ARG* 5.5 8.4 - - - +
897A SER* 4.6 4.2 + - - -
902A LEU* 6.2 0.2 - - - +
938A GLN* 2.9 45.5 + - - +
939A ASN* 3.1 7.6 + - - +
941A ALA* 1.3 77.3 - - - +
943A LEU* 1.3 72.2 + - - +
944A VAL* 3.3 23.2 + - + +
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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