Contacts of the helix formed by residues 909 - 918 (chain A) in PDB entry 3LXK
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 CYS 909 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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907A SER 3.9 0.2 + - - -
908A GLY* 1.3 75.2 - - - -
910A LEU* 1.3 63.3 + - - +
911A ARG* 3.5 26.7 - - - -
912A ASP* 3.3 15.2 + - + +
913A PHE* 3.0 25.3 + - - +
952A ALA 3.6 7.2 - - - -
953A ARG* 3.5 30.7 - - - +
955A ILE 3.4 5.6 - - - -
1125A MI1 4.0 22.8 - - + -
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Residues in contact with LEU 910 (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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908A GLY 3.6 1.2 + - - -
909A CYS* 1.3 72.0 - - - +
911A ARG* 1.3 57.8 + - - +
913A PHE* 4.5 3.4 - - + -
914A LEU* 2.9 61.7 + - + +
929A TYR* 4.2 11.2 - - + -
933A ILE* 4.2 12.1 - - + -
952A ALA* 3.9 9.2 - - + +
955A ILE* 2.8 49.5 + - + +
957A VAL* 3.8 22.2 - - + -
963A VAL* 4.0 13.7 - - + -
1016A VAL* 5.7 0.4 - - + -
1020A LEU* 3.7 23.1 - - + -
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Residues in contact with ARG 911 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
909A CYS* 3.3 17.9 - - - -
910A LEU* 1.3 79.4 - - - +
912A ASP* 1.3 62.3 + - - +
914A LEU* 3.9 0.2 - - - +
915A GLN* 3.3 42.5 + - - +
952A ALA* 3.8 10.6 + - + -
953A ARG* 3.6 38.9 - - - +
1019A GLU* 5.1 5.6 - - - -
1024A CYS* 3.7 31.8 - - + +
1026A LYS* 6.2 1.6 - - - +
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Residues in contact with ASP 912 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
907A SER 4.8 7.4 - - - +
908A GLY* 5.8 0.5 - - - -
909A CYS* 3.3 20.1 + - + +
911A ARG* 1.3 76.5 - - - +
913A PHE* 1.3 65.5 + - - +
915A GLN* 3.3 17.4 + - - +
916A ARG* 3.1 49.5 + - - +
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Residues in contact with PHE 913 (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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907A SER* 4.0 28.9 + - - +
909A CYS 3.0 16.4 + - - +
910A LEU* 3.6 11.9 - - + +
912A ASP* 1.3 77.3 - - - +
914A LEU* 1.3 57.5 + - - +
916A ARG* 3.4 4.2 + - - +
917A HIS* 3.0 69.3 + + - +
921A LEU* 4.0 15.7 - - + -
929A TYR* 3.7 22.0 - - - -
957A VAL* 3.6 41.3 - - + -
960A GLU* 4.1 25.8 - - + -
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Residues in contact with LEU 914 (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* 2.9 43.2 + - + +
911A ARG 3.9 2.7 - - - +
913A PHE* 1.3 72.1 - - + +
915A GLN* 1.3 59.9 + - - +
918A ARG* 3.0 32.7 + - - +
921A LEU* 4.0 17.9 - - + -
926A LEU* 3.8 27.8 - - + -
929A TYR* 4.3 3.1 - - + -
952A ALA* 5.4 0.7 - - + -
1019A GLU 4.1 1.3 - - - +
1020A LEU* 3.8 32.5 - - + +
1023A TYR* 3.8 24.0 - - + +
1024A CYS* 3.8 21.5 - - - -
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Residues in contact with GLN 915 (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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911A ARG* 3.3 32.3 + - - +
912A ASP* 3.3 20.0 + - - +
914A LEU* 1.3 78.3 - - - +
916A ARG* 1.3 64.3 + - + +
918A ARG* 3.8 14.1 - - - +
1023A TYR* 3.6 8.5 - - - +
1024A CYS 3.0 27.3 - - - +
1025A ASP* 5.2 1.8 - - - -
1026A LYS* 3.7 31.3 - - + +
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Residues in contact with ARG 916 (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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907A SER* 5.3 6.9 + - - +
912A ASP* 3.1 46.3 + - - +
913A PHE* 3.9 4.2 - - - +
914A LEU 3.3 0.2 - - - -
915A GLN* 1.3 81.1 - - + +
917A HIS* 1.3 92.6 + - + +
918A ARG* 3.4 3.2 + - - +
919A ALA 5.2 0.5 + - - -
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Residues in contact with HIS 917 (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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913A PHE* 3.0 64.7 + + + +
914A LEU 3.9 1.3 - - - -
916A ARG* 1.3 114.9 + - + +
918A ARG* 1.3 64.4 + - - +
919A ALA 3.3 3.1 - - - -
920A ARG* 2.9 37.8 + - + +
921A LEU* 3.2 28.8 + - + +
960A GLU* 5.6 2.2 + - - +
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Residues in contact with ARG 918 (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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914A LEU 3.0 14.2 + - - +
915A GLN* 3.8 13.0 - - - +
916A ARG 3.4 1.3 - - - +
917A HIS* 1.3 77.4 - - - +
919A ALA* 1.3 60.3 + - + +
920A ARG 3.2 4.3 + - - -
921A LEU 3.4 17.7 + - - +
1022A THR 3.6 22.8 + - - -
1023A TYR* 3.5 52.2 - - + +
1025A ASP* 3.8 20.4 + - - +
1064A PRO* 6.2 2.0 - - - +
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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