Contacts of the helix formed by residues 1007 - 1026 (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 THR1007 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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968A ARG* 4.2 0.4 - - - -
1005A GLY 4.0 0.4 + - - +
1006A LYS* 1.3 77.1 - - - +
1008A GLU* 1.3 59.4 - - - +
1009A GLU* 3.5 8.9 + - - +
1010A GLU* 3.1 36.1 + - - +
1011A ALA* 2.8 26.5 + - - +
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Residues in contact with GLU1008 (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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965A THR* 4.3 25.7 - - + +
968A ARG* 3.4 25.1 + - - +
969A ARG* 3.3 36.2 + - - +
1007A THR* 1.3 74.1 - - - +
1009A GLU* 1.3 60.5 + - - +
1011A ALA* 3.8 0.6 - - + +
1012A LEU* 3.0 34.7 + - + +
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Residues in contact with GLU1009 (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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1007A THR* 3.1 9.0 + - - +
1008A GLU* 1.3 84.9 - - - +
1010A GLU* 1.3 61.7 + - + +
1012A LEU* 3.6 13.5 + - - +
1013A LYS* 3.2 21.8 + - - +
1016A ARG* 5.4 3.5 + - - -
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Residues in contact with GLU1010 (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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1006A LYS* 3.6 28.4 - - + +
1007A THR* 3.1 40.2 + - - +
1009A GLU* 1.3 74.6 - - + +
1011A ALA* 1.3 66.0 + - - +
1013A LYS* 3.0 8.9 + - - +
1014A HIS* 2.9 24.6 + - - +
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Residues in contact with ALA1011 (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* 4.1 7.0 + - + -
965A THR* 6.6 0.2 - - + -
968A ARG* 3.3 41.1 - - - +
1003A ALA* 3.9 14.4 - - + +
1006A LYS* 3.8 10.0 - - - +
1007A THR 2.8 20.8 + - - +
1008A GLU* 3.8 3.6 - - + +
1010A GLU* 1.3 73.2 - - - +
1012A LEU* 1.3 57.4 + - - +
1014A HIS* 3.5 3.0 + - - +
1015A PHE* 2.8 28.6 + - - +
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Residues in contact with LEU1012 (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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961A GLU* 3.9 31.0 - - + +
964A TYR* 4.9 3.8 - - + -
965A THR* 3.9 29.8 - - + +
1008A GLU* 3.0 24.1 + - + +
1009A GLU* 3.9 14.6 - - - +
1011A ALA* 1.3 74.0 - - - +
1013A LYS* 1.3 60.5 + - - +
1015A PHE* 3.3 10.7 + - + +
1016A ARG* 2.8 67.9 + - - +
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Residues in contact with LYS1013 (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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1009A GLU 3.2 11.5 + - - +
1010A GLU* 3.0 11.3 + - - +
1012A LEU* 1.3 75.8 - - - +
1014A HIS* 1.3 66.2 + - - +
1016A ARG* 3.2 15.7 + - + +
1017A VAL* 3.1 43.6 + - + +
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Residues in contact with HIS1014 (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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887A TYR* 4.6 8.8 + - - -
964A TYR* 5.2 3.8 - - - -
1000A ASP 4.9 8.7 + - - -
1001A SER 6.0 0.2 - - - -
1003A ALA* 4.7 12.3 - - + -
1006A LYS* 4.1 28.4 + - - -
1010A GLU 2.9 15.2 + - - +
1011A ALA* 3.5 5.8 - - - +
1013A LYS* 1.3 78.4 - - - +
1015A PHE* 1.3 63.2 - - - +
1017A VAL* 3.2 10.3 + - - +
1018A LYS* 3.2 52.7 + - + +
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Residues in contact with PHE1015 (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* 4.4 2.9 - - + -
887A TYR* 4.2 14.4 - + - -
932A PHE* 3.7 40.6 - + - -
960A CYS* 4.2 17.9 - - + -
961A GLU* 4.0 31.6 - - + -
964A TYR* 3.7 48.2 - + + -
1011A ALA 2.8 21.0 + - - +
1012A LEU* 3.5 7.9 - - + +
1014A HIS* 1.3 75.4 - - - +
1016A ARG* 1.3 59.5 + - - +
1018A LYS* 3.2 9.9 + - + +
1019A PHE* 2.9 45.1 + + + +
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Residues in contact with ARG1016 (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* 4.2 9.6 + - - +
961A GLU* 2.7 46.9 + - + +
1009A GLU* 5.4 3.8 + - - -
1012A LEU* 2.8 50.2 + - - +
1013A LYS* 3.2 14.6 + - + +
1015A PHE* 1.3 73.3 - - - +
1017A VAL* 1.3 58.4 + - + +
1019A PHE* 3.3 7.1 + - - +
1020A ASN* 2.8 40.5 + - - +
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Residues in contact with VAL1017 (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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1013A LYS* 3.1 41.5 + - + +
1014A HIS* 3.5 10.8 - - - +
1015A PHE 3.2 0.2 - - - -
1016A ARG* 1.3 74.2 - - + +
1018A LYS* 1.3 58.3 + - + +
1020A ASN* 3.3 7.5 + - - +
1021A GLU* 2.8 59.2 + - + +
1024A ARG* 5.0 3.5 + - - +
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Residues in contact with LYS1018 (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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887A TYR* 3.6 32.3 - - + +
929A ARG* 6.0 7.9 - - - +
931A PRO* 5.7 3.4 - - + -
932A PHE* 3.9 18.8 + - + +
1014A HIS* 3.2 38.6 + - + +
1015A PHE* 3.2 10.9 + - + +
1017A VAL* 1.3 79.9 - - + +
1019A PHE* 1.3 57.0 + - - +
1021A GLU* 3.4 32.8 + - - +
1022A ALA* 2.9 27.2 + - - +
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Residues in contact with PHE1019 (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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932A PHE* 3.5 35.2 - + + +
934A LEU* 3.7 10.2 - - + +
953A PHE* 3.7 30.3 - + - -
956A PHE* 3.9 11.0 - + - -
957A ARG* 3.3 54.3 - - + -
960A CYS* 4.0 19.3 - - + -
1015A PHE* 2.9 32.4 + + + +
1016A ARG* 3.5 8.1 - - - +
1018A LYS* 1.3 75.5 - - - +
1020A ASN* 1.3 60.6 + - - +
1022A ALA* 3.0 9.6 + - - +
1023A LEU* 3.0 25.0 + - + +
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Residues in contact with ASN1020 (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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957A ARG* 2.7 39.9 + - - +
1016A ARG* 2.8 24.8 + - - +
1017A VAL* 3.7 6.2 - - - +
1019A PHE* 1.3 74.2 - - - +
1021A GLU* 1.3 66.4 + - - +
1023A LEU* 3.3 10.0 + - - +
1024A ARG* 3.1 47.8 + - - +
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Residues in contact with GLU1021 (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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1017A VAL* 2.8 39.5 + - + +
1018A LYS* 3.4 31.0 + - - +
1020A ASN* 1.3 73.9 - - - +
1022A ALA* 1.3 62.2 + - - +
1024A ARG* 3.4 27.3 + - - +
1025A GLU* 3.2 24.4 + - - +
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Residues in contact with ALA1022 (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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932A PHE* 3.1 44.6 - - + +
934A LEU* 3.8 18.7 + - + +
1018A LYS 2.9 13.5 + - - +
1019A PHE 3.2 11.7 - - - +
1021A GLU* 1.3 78.0 - - - +
1023A LEU* 1.3 54.6 + - - +
1025A GLU* 3.7 7.5 + - - +
1026A SER* 3.2 23.4 + - - -
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Residues in contact with LEU1023 (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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934A LEU* 3.7 9.6 - - + +
939A VAL* 5.0 8.1 - - + -
943A GLN* 6.2 0.7 - - - +
953A PHE* 3.5 44.0 - - + -
957A ARG* 4.5 12.1 - - - +
1019A PHE* 3.0 11.2 + - + +
1020A ASN* 3.6 12.6 - - - +
1021A GLU 3.3 0.2 - - - -
1022A ALA* 1.3 75.2 - - - +
1024A ARG* 1.3 66.3 + - - +
1026A SER* 3.0 28.0 + - - +
1027A TRP 4.2 0.3 + - - -
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Residues in contact with ARG1024 (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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1017A VAL* 5.0 3.8 + - - +
1020A ASN* 3.1 39.4 + - - +
1021A GLU* 3.4 37.1 + - - +
1023A LEU* 1.3 76.1 - - + +
1025A GLU* 1.3 63.2 + - - +
1026A SER 3.1 1.4 + - - -
1027A TRP 3.4 15.8 + - - -
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Residues in contact with GLU1025 (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 ILE* 6.3 3.1 - - + -
934A LEU 5.4 0.2 - - - -
1021A GLU 3.2 15.5 + - - +
1022A ALA* 3.7 8.5 - - - +
1024A ARG* 1.3 74.3 - - - +
1026A SER* 1.3 56.4 + - - +
1027A TRP* 3.0 20.3 + - - +
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Residues in contact with SER1026 (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* 3.8 17.2 + - - -
935A THR 3.9 1.6 - - - -
936A TYR* 3.6 38.8 + - - +
939A VAL* 4.3 8.0 - - - +
1022A ALA 3.2 13.6 + - - -
1023A LEU* 3.0 26.8 + - - +
1025A GLU* 1.3 75.2 - - - +
1027A TRP* 1.3 70.9 + - - +
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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