Contacts of the helix formed by residues 908 - 921 (chain A) in PDB entry 4Q0W
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 908 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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883A GLU* 5.1 7.5 + - - +
906A THR 3.8 2.1 + - - +
907A GLU* 1.3 76.8 - - - +
909A LYS* 1.3 59.9 + - - +
910A PHE* 3.4 10.7 + - - +
911A GLU* 2.9 43.7 + - - +
912A LYS* 2.9 28.7 + - - +
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Residues in contact with LYS 909 (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 ASN* 1.3 77.5 - - - +
910A PHE* 1.3 58.7 + - - +
912A LYS* 3.2 5.2 + - + +
913A ASP* 2.5 70.4 + - - +
13C C 2.8 27.0 + - - -
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Residues in contact with PHE 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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879A GLU* 3.5 46.7 - - + -
880A VAL* 4.7 1.1 - - + -
883A GLU* 3.6 47.6 - - + +
884A PHE* 4.0 9.0 - + - -
908A ASN* 3.4 8.8 + - - +
909A LYS* 1.3 79.3 - - - +
911A GLU* 1.3 66.7 - - + +
913A ASP* 3.8 4.8 - - - +
914A LEU* 2.8 63.2 + - + +
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Residues in contact with GLU 911 (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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883A GLU* 5.3 4.7 - - + +
884A PHE* 4.0 17.4 - - + -
893A TRP* 3.2 43.9 + - + +
907A GLU* 3.1 33.6 - - + +
908A ASN* 2.9 26.2 + - - +
910A PHE* 1.3 88.1 - - + +
912A LYS* 1.3 59.8 + - - +
914A LEU* 4.4 1.3 - - - -
915A ARG* 2.9 26.3 + - - +
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Residues in contact with LYS 912 (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 GLU* 3.6 19.4 + - + +
908A ASN 2.9 18.6 + - - +
909A LYS* 3.8 4.7 - - + +
911A GLU* 1.3 76.0 - - - +
913A ASP* 1.3 65.6 + - - +
915A ARG* 3.9 2.2 - - - +
916A LYS* 3.1 23.6 + - - +
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Residues in contact with ASP 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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909A LYS* 2.5 58.7 + - - +
910A PHE* 3.8 5.2 + - + +
912A LYS* 1.3 77.7 - - - +
914A LEU* 1.3 65.8 + - - +
916A LYS* 3.3 6.8 + - - +
917A LYS* 3.1 22.0 + - - +
12C C 5.5 7.9 + - - +
13C C 4.0 6.1 + - - -
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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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872A MET* 4.2 20.9 - - + -
876A SER* 5.9 2.5 - - - -
880A VAL* 4.3 9.9 - - + -
884A PHE* 3.8 21.3 - - + -
890A PHE* 3.9 13.0 - - + -
893A TRP* 3.9 7.2 - - + -
910A PHE* 2.8 51.9 + - + +
911A GLU 4.0 3.1 - - - +
913A ASP* 1.3 71.7 - - - +
915A ARG* 1.3 63.0 + - - +
917A LYS* 3.1 11.7 + - + +
918A LEU* 3.0 46.1 + - + +
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Residues in contact with ARG 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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893A TRP* 3.0 44.1 + - + +
894A TYR* 2.8 31.5 + - + +
897A GLY* 3.5 14.4 - - - -
898A GLN* 2.9 36.9 + - - +
904A GLN* 3.6 23.5 - - - -
907A GLU* 3.0 32.6 + - - +
911A GLU 2.9 18.0 + - - +
912A LYS* 3.9 4.5 - - - +
914A LEU* 1.3 77.5 - - - +
916A LYS* 1.3 63.2 + - - +
918A LEU* 3.1 7.3 + - - +
919A VAL* 2.9 31.3 + - + +
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Residues in contact with LYS 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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912A LYS 3.1 16.2 + - - +
913A ASP* 3.6 7.6 - - - +
915A ARG* 1.3 78.8 - - - +
917A LYS* 1.3 57.5 + - - +
919A VAL* 3.5 20.4 + - - +
920A ASN* 3.0 41.7 + - + +
12C C 3.6 25.1 - - - +
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Residues in contact with LYS 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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871A GLY* 2.8 41.0 + - - -
872A MET* 4.2 11.9 - - + -
876A SER* 3.3 20.0 + - - -
913A ASP 3.1 13.2 + - - +
914A LEU* 3.4 15.9 - - + +
916A LYS* 1.3 76.4 - - - +
918A LEU* 1.3 60.5 + - + +
920A ASN* 3.4 5.3 + - - +
921A ASN* 2.9 39.2 + - - +
12C C 5.2 4.7 + - - +
7D G 4.9 2.2 + - - -
8D A 4.0 10.6 - - - -
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Residues in contact with LEU 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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869A LEU* 5.0 3.8 - - + -
870A LYS 5.5 1.3 - - - +
872A MET* 4.2 22.4 - - + -
890A PHE* 3.7 39.3 - - + -
893A TRP* 3.9 8.3 - - + -
894A TYR* 3.6 40.4 - - + -
914A LEU* 3.0 26.1 + - + +
915A ARG 3.1 2.2 + - - +
917A LYS* 1.3 76.7 - - + +
919A VAL* 1.3 62.7 + - - +
921A ASN* 3.2 2.9 + - - +
922A GLU 3.0 4.2 + - - -
923A ILE* 2.9 51.1 + - + +
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Residues in contact with VAL 919 (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 TYR* 4.0 9.2 - - + +
898A GLN* 3.7 35.0 - - - +
915A ARG* 2.9 24.0 + - + +
916A LYS* 3.8 17.0 - - - +
918A LEU* 1.3 74.8 - - - +
920A ASN* 1.3 56.5 + - - +
922A GLU* 2.7 29.7 + - - +
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Residues in contact with ASN 920 (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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870A LYS* 5.4 2.1 + - - -
916A LYS* 3.0 33.8 + - + +
917A LYS* 3.8 5.8 - - - +
919A VAL* 1.3 78.4 - - - +
921A ASN* 1.3 66.1 + - - +
922A GLU* 3.3 10.4 + - - +
11C A 3.0 39.7 + - - +
12C C 5.9 0.7 - - - +
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Residues in contact with ASN 921 (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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870A LYS* 3.4 56.4 + - + +
871A GLY* 3.6 14.5 - - - -
917A LYS* 2.9 35.8 + - - +
918A LEU* 3.8 3.8 - - - +
919A VAL 3.1 0.2 - - - -
920A ASN* 1.3 84.7 - - - +
922A GLU* 1.3 70.3 + - - +
923A ILE* 3.2 21.9 + - + +
11C A 5.6 0.7 + - - +
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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