Contacts of the helix formed by residues 912 - 921 (chain A) in PDB entry 5IYB
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 912 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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910A LYS* 4.0 2.2 - - - +
911A PRO* 1.3 82.9 - - - +
913A ASN* 1.3 64.5 + - - +
914A LYS* 4.3 6.3 - - - +
915A ALA* 3.1 27.1 + - - +
916A PHE* 3.2 16.1 + - - +
963A ARG* 3.7 4.3 + - - -
1325A ASP* 3.3 32.1 - - - -
1327A GLU* 4.4 0.2 - - - +
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Residues in contact with ASN 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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912A SER* 1.3 72.4 - - - +
914A LYS* 1.3 58.0 + - - +
916A PHE* 3.5 4.9 + - - +
917A GLU* 3.0 33.2 + - - +
963A ARG* 3.9 18.1 + - - +
967A ARG* 4.5 2.3 + - - -
1324A GLU 4.3 11.1 + - - +
1325A ASP* 2.9 24.4 + - - +
1326A GLY* 3.5 13.4 - - - -
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Residues in contact with LYS 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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912A SER* 3.3 6.0 + - - +
913A ASN* 1.3 76.9 - - - +
915A ALA* 1.3 59.2 + - - +
917A GLU* 3.5 7.3 + - - +
918A LYS* 2.9 33.0 + - + +
1325A ASP* 5.4 1.3 + - - +
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Residues in contact with ALA 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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910A LYS* 3.6 26.6 - - - +
912A SER* 3.1 22.4 + - - +
914A LYS* 1.3 74.8 - - - +
916A PHE* 1.3 61.4 + - - +
918A LYS* 3.4 7.3 + - - +
919A LYS* 2.9 32.7 + - - +
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Residues in contact with PHE 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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908A THR* 4.1 14.6 - - + -
910A LYS* 4.0 11.8 - - + +
912A SER 3.2 6.1 + - - +
913A ASN* 3.8 4.3 - - - +
915A ALA* 1.3 78.1 - - - +
917A GLU* 1.3 63.7 + - + +
919A LYS* 4.5 0.2 - - - -
920A PHE* 3.0 68.5 + + - +
956A PHE* 3.7 28.5 - + - -
959A MET* 4.2 22.4 - - + -
960A ARG* 4.4 11.7 - - + -
963A ARG* 3.0 64.8 - - - +
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Residues in contact with GLU 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 ASN* 3.0 21.8 + - - +
914A LYS* 3.8 6.3 - - - +
916A PHE* 1.3 78.1 - - + +
918A LYS* 1.3 64.0 + - - +
921A ARG* 3.0 69.3 + - - +
956A PHE* 4.1 19.1 - - + -
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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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914A LYS* 2.9 21.0 + - + +
915A ALA* 3.7 8.7 - - - +
917A GLU* 1.3 79.0 - - - +
919A LYS* 1.3 61.7 + - - +
921A ARG 4.4 0.2 - - - +
1052A ARG* 3.5 28.8 + - - +
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Residues in contact with LYS 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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910A LYS* 6.0 4.7 - - + -
915A ALA 2.9 18.6 + - - +
916A PHE* 4.5 0.2 - - - -
918A LYS* 1.3 79.4 - - - +
920A PHE* 1.3 83.3 + - + +
1052A ARG* 3.0 24.5 + - - +
1053A ARG* 4.3 22.5 - - - +
1056A GLU* 4.1 20.1 + - - +
1057A GLU* 3.9 22.9 + - - +
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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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907A ALA* 4.5 24.7 - - + -
908A THR* 5.1 2.5 - - + -
910A LYS* 5.2 5.2 - - + -
916A PHE* 3.0 50.3 + + + +
919A LYS* 1.3 99.2 - - + +
921A ARG* 1.3 64.3 + - - +
922A PHE 3.3 2.9 + - - -
956A PHE* 4.1 17.4 - - + -
959A MET* 5.0 8.1 - - + -
1047A SER* 3.4 32.3 - - - -
1050A CYS* 3.6 19.0 - - + -
1052A ARG* 3.5 14.1 - - - +
1053A ARG* 3.9 25.8 - - + +
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Residues in contact with ARG 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 GLU* 3.0 51.1 + - - +
918A LYS 4.4 0.5 - - - +
919A LYS 3.8 0.2 - - - -
920A PHE* 1.3 76.4 - - - +
922A PHE* 1.3 63.1 + - - +
923A ASP* 4.4 1.6 - - - +
924A TYR* 5.7 6.1 - - - +
925A THR* 6.1 3.6 - - - +
953A GLU* 3.9 21.7 + - - +
956A PHE* 3.5 43.5 - - + -
1052A ARG* 2.7 33.8 + - - -
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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