Contacts of the helix formed by residues 907 - 922 (chain N) in PDB entry 1ZYR
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 GLU 907 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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786N ILE* 4.6 4.5 - - - -
790N TYR* 4.9 2.5 - - + -
905N PRO 3.4 4.4 + - - +
906N GLN* 1.3 73.7 - - - +
908N LYS* 1.3 75.3 + - + +
909N ASN* 3.1 33.0 + - - +
910N SER* 2.6 30.5 + - - +
911N LEU* 3.1 14.7 + - - +
1025N GLN* 4.0 21.4 - - - +
1026N SER* 4.8 2.9 - - - +
1027N GLY 4.6 3.4 - - - +
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Residues in contact with LYS 908 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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780N LYS* 3.9 29.0 - - - +
781N PRO 5.0 2.9 - - - +
782N SER* 4.2 14.8 + - - +
786N ILE* 3.5 17.2 - - + +
907N GLU* 1.3 77.8 - - + +
909N ASN* 1.3 74.4 + - - +
911N LEU* 3.5 3.3 - - - +
912N LYS* 2.8 39.2 + - + +
1027N GLY* 3.3 42.0 + - - +
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Residues in contact with ASN 909 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
907N GLU* 3.1 27.9 + - - +
908N LYS* 1.3 97.2 - - - +
910N SER* 1.3 66.4 + - - +
912N LYS* 3.7 21.2 + - - +
913N ASP* 2.9 31.2 + - - +
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Residues in contact with SER 910 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
901N GLN* 5.7 4.3 - - - +
904N VAL* 5.2 8.1 - - - -
905N PRO 4.4 3.6 - - - -
906N GLN* 2.6 27.4 + - - -
907N GLU* 2.6 37.9 + - - +
909N ASN* 1.3 79.4 - - - +
911N LEU* 1.3 66.3 + - - +
913N ASP* 3.4 4.9 + - - +
914N LEU* 2.9 24.2 + - - +
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Residues in contact with LEU 911 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
781N PRO* 3.1 46.0 - - + +
786N ILE* 3.8 21.8 - - + -
789N LEU* 3.8 19.3 - - + -
882N PHE* 4.5 7.4 - - + -
906N GLN* 3.7 26.2 - - + +
907N GLU 3.1 9.6 + - - +
908N LYS 3.5 2.9 - - - +
910N SER* 1.3 90.5 + - - +
912N LYS* 1.3 59.6 + - - +
913N ASP 2.9 2.0 - - - -
914N LEU* 2.3 35.4 + - + +
915N VAL* 2.8 13.0 + - + +
934N LEU* 4.8 6.5 - - + -
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Residues in contact with LYS 912 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
776N GLU* 3.0 28.7 - - + +
777N PRO* 2.9 39.9 - - + +
780N LYS* 3.4 42.7 - - + +
908N LYS* 2.8 24.7 + - + +
909N ASN* 3.3 25.4 + - - +
911N LEU* 1.3 72.0 - - - +
913N ASP* 1.3 87.8 + - - +
915N VAL* 3.2 2.4 + - - +
916N TYR 3.1 5.2 + - - -
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Residues in contact with ASP 913 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
901N GLN* 6.2 2.0 - - - +
909N ASN* 2.9 11.0 + - - +
910N SER* 3.5 9.2 - - - +
911N LEU 2.7 3.2 + - - -
912N LYS* 1.3 99.5 + - - +
914N LEU* 1.3 67.4 + - - +
915N VAL 2.8 3.1 + - - -
916N TYR* 3.0 13.7 + - - +
917N GLN* 3.0 31.7 + - + +
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Residues in contact with LEU 914 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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882N PHE* 3.5 34.1 - - + -
886N VAL* 4.0 18.4 - - + -
899N LEU* 4.0 32.8 - - + +
900N ILE* 4.0 11.7 - - + -
910N SER 2.9 14.2 + - - +
911N LEU* 2.3 28.4 + - - +
913N ASP* 1.3 68.3 - - - +
915N VAL* 1.3 57.6 + - + +
917N GLN* 4.2 1.6 - - - +
918N ALA* 2.9 23.3 + - + +
930N LEU* 4.0 18.8 - - + -
934N LEU* 4.5 14.6 - - + -
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Residues in contact with VAL 915 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
769N LEU* 5.3 4.0 - - + -
770N LEU* 4.7 8.3 - - + -
777N PRO* 3.8 19.3 - - + -
779N ALA 4.9 2.2 - - - +
780N LYS* 5.0 0.4 - - - -
781N PRO* 4.4 11.7 - - + -
911N LEU 2.8 11.5 + - - +
912N LYS 3.4 8.3 - - - +
913N ASP 2.8 0.6 + - - -
914N LEU* 1.3 76.7 - - + +
916N TYR* 1.3 55.8 + - - +
918N ALA* 2.8 7.8 + - - +
919N PHE* 2.6 34.5 + - + +
927N THR* 3.9 19.1 - - + -
930N LEU* 4.8 2.5 - - + -
931N LEU* 3.4 29.4 - - + -
934N LEU* 4.3 14.8 - - + -
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Residues in contact with TYR 916 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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770N LEU* 4.6 4.9 - - + -
775N GLY* 3.9 28.7 - - - -
776N GLU* 4.6 3.4 - - - -
777N PRO* 3.6 13.2 - - + +
912N LYS 3.1 12.8 + - - +
913N ASP* 3.0 16.8 + - - +
915N VAL* 1.3 71.9 - - - +
917N GLN* 1.3 76.3 + - - +
919N PHE* 2.8 14.4 + - - +
920N LEU* 2.7 65.8 - - + +
1145N TYR* 3.1 40.7 + + - -
1167N SER* 5.8 0.3 - - - -
1168N MET* 3.7 23.9 + - + +
1169N ASP* 5.8 0.4 - - - -
1207N TYR* 5.9 0.3 - - - -
1212N ALA* 5.2 3.2 - - + +
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Residues in contact with GLN 917 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
899N LEU* 4.5 28.0 - - + +
913N ASP* 3.0 15.7 + - + +
914N LEU 4.2 1.8 - - - +
916N TYR* 1.3 97.8 - - - +
918N ALA* 1.3 68.4 + - - +
919N PHE 3.0 0.2 + - - -
920N LEU* 3.1 13.8 + - - +
921N ARG* 2.9 36.9 + - + +
1169N ASP* 4.3 16.6 + - - -
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Residues in contact with ALA 918 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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899N LEU* 4.1 13.4 - - + +
914N LEU* 2.9 22.1 + - + +
915N VAL* 2.8 18.8 + - - +
917N GLN* 1.3 77.0 - - - +
919N PHE* 1.3 62.2 + - - +
922N LEU* 3.2 29.0 + - + +
927N THR* 3.0 16.8 + - - +
930N LEU* 4.0 19.3 - - + -
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Residues in contact with PHE 919 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
769N LEU* 4.3 13.0 - - + -
770N LEU* 3.1 43.3 - - + -
915N VAL 2.6 14.2 + - - +
916N TYR* 2.8 12.3 + - - +
918N ALA* 1.3 75.0 - - - +
920N LEU* 1.3 69.7 + - + +
921N ARG 3.2 0.3 + - - -
922N LEU 3.8 1.7 - - - +
923N GLY* 3.5 26.8 + - - +
924N MET* 3.5 35.4 - - + -
927N THR* 3.0 18.2 + - + +
1211N MET* 4.3 10.8 - - + -
1212N ALA* 3.8 19.1 - - + -
1213N ARG* 3.3 31.2 - - - -
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Residues in contact with LEU 920 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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916N TYR* 2.7 81.6 + - + +
917N GLN* 3.8 15.3 - - - +
919N PHE* 1.3 93.0 - - + +
921N ARG* 1.3 65.7 + - + +
922N LEU 4.5 0.7 - - - +
1167N SER* 6.1 2.0 - - - -
1168N MET 6.0 0.2 - - - +
1169N ASP* 4.4 17.3 - - - +
1212N ALA* 4.9 9.0 - - + -
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Residues in contact with ARG 921 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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895N VAL* 2.8 51.0 + - + +
898N GLU* 3.2 32.2 + - - +
899N LEU* 4.7 12.9 - - + +
917N GLN* 2.9 30.0 + - + +
918N ALA 4.2 0.7 - - - +
920N LEU* 1.3 76.3 - - + +
922N LEU* 1.3 76.7 + - + +
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Residues in contact with LEU 922 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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890N VAL* 3.3 48.2 - - + -
892N ASP* 4.3 17.5 - - + +
895N VAL* 3.5 30.3 - - + -
896N ALA* 6.3 0.2 - - - -
899N LEU* 5.3 5.8 - - + -
918N ALA* 3.2 19.5 + - + +
919N PHE 3.8 3.0 - - - +
920N LEU 4.5 0.9 - - - +
921N ARG* 1.3 84.9 - - + +
923N GLY* 1.3 61.5 + - - +
926N LYS* 3.7 22.7 - - + +
927N THR* 5.8 0.4 - - - +
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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