Contacts of the helix formed by residues 916 - 922 (chain A) in PDB entry 2X36
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 916 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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891A PRO* 3.5 5.9 - - - +
892A VAL 3.0 41.3 + - - +
895A ILE* 3.4 28.8 - - + +
912A LEU* 4.7 2.7 - - + -
913A PRO* 2.7 35.3 + - + +
915A GLU* 1.3 75.5 + - - +
917A LYS* 1.3 66.6 + - - +
918A LYS 3.1 3.4 - - - +
919A ASP* 2.5 30.8 + - - +
920A PHE* 3.2 21.5 + - - +
935A PHE* 4.1 2.1 - - - -
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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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913A PRO 3.9 0.6 + - - -
914A ALA* 3.0 23.1 + - + +
915A GLU 3.3 1.4 - - - -
916A ASN* 1.3 77.9 - - - +
918A LYS* 1.3 57.7 + - - +
920A PHE* 3.1 4.0 + - - +
921A TYR* 3.0 60.8 + - + -
935A PHE* 3.6 37.5 - - + -
935F PHE 5.6 1.6 + - - -
937F GLU* 3.5 25.9 + - + +
941F GLU* 3.3 26.6 + - - +
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Residues in contact with LYS 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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915A GLU 4.7 7.8 + - - +
916A ASN 3.1 0.6 - - - -
917A LYS* 1.3 77.4 - - - +
919A ASP* 1.3 78.5 + - - +
920A PHE 3.1 1.3 - - - -
921A TYR* 4.0 7.7 - - - +
922A ASP* 3.3 40.6 + - - +
891C PRO* 3.9 38.3 + - + +
892C VAL 5.1 6.7 - - - -
888F LYS* 6.2 6.5 - - + +
937F GLU* 6.5 0.7 - - + -
938F HIS* 5.3 7.3 + - + +
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Residues in contact with ASP 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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892A VAL 4.6 0.3 - - - +
895A ILE* 3.8 23.5 - - + +
915A GLU 4.4 1.9 - - - +
916A ASN* 2.5 40.6 + - - +
918A LYS* 1.3 92.5 - - - +
920A PHE* 1.3 61.7 + - - +
922A ASP* 3.4 15.6 - - - +
923A LEU* 3.4 19.4 - - - +
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Residues in contact with PHE 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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895A ILE* 4.4 2.9 - - + -
899A THR* 3.8 29.2 - - + -
910A ILE* 4.7 4.9 - - + -
912A LEU* 4.1 15.3 - - + -
916A ASN 3.2 10.5 + - - +
917A LYS 3.1 8.9 + - - +
919A ASP* 1.3 78.1 - - - +
921A TYR* 1.3 80.3 + + - +
923A LEU* 3.4 30.1 - - + +
928A THR* 3.2 46.1 + - + +
931A LEU* 4.5 3.1 - - + -
933A VAL* 3.3 35.0 - - + -
935A PHE* 3.7 23.8 - + + -
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Residues in contact with TYR 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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917A LYS* 3.0 48.1 + - + +
918A LYS* 3.8 3.3 + - - +
920A PHE* 1.3 86.4 - + - +
922A ASP* 1.3 56.7 + - - +
923A LEU 3.0 18.1 + - - +
928A THR* 6.2 0.9 - - + -
935A PHE* 3.8 21.8 - + - -
828F HIS* 5.9 1.6 + - - -
937F GLU* 6.1 0.4 - - + -
938F HIS* 3.6 45.0 + + + +
940F ARG* 3.6 33.1 - - + +
941F GLU* 3.5 38.3 - - + +
944F ASP* 5.9 0.9 - - - -
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Residues in contact with ASP 922 (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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918A LYS* 3.3 33.2 + - - +
919A ASP* 3.4 15.4 - - - +
920A PHE 3.3 1.0 - - - -
921A TYR* 1.3 76.3 - - - +
923A LEU* 1.3 60.4 + - - +
924A ALA 4.4 0.2 + - - -
851C LYS* 5.0 12.8 - - - +
886F THR* 5.3 7.4 - - - +
938F HIS* 5.1 9.0 - - + -
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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