Contacts of the helix formed by residues 912 - 919 (chain A) in PDB entry 6ZGI
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 THR 912 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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906A PHE* 4.7 3.1 - - - -
907A ASN* 4.3 6.3 - - - +
910A GLY 5.8 0.7 - - - +
911A VAL* 1.3 80.6 - - - +
913A GLN* 1.3 65.2 + - - +
914A ASN* 2.8 24.3 + - - -
915A VAL* 3.3 22.5 + - - +
916A LEU 4.1 1.6 + - - -
1106A GLN* 3.3 30.8 + - + +
1111A GLU* 4.6 1.3 + - - +
1121C PHE* 4.8 11.4 - - + -
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Residues in contact with GLN 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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903A ALA* 4.1 21.9 - - + +
904A TYR* 4.3 20.6 - - - -
906A PHE* 5.4 0.9 - - - -
907A ASN* 2.9 35.3 + - - +
911A VAL 3.8 0.4 + - - -
912A THR* 1.3 72.0 - - - +
914A ASN* 1.3 66.8 + - - +
916A LEU* 3.0 9.0 + - - +
917A TYR* 3.0 42.2 + - + -
1089C PHE* 4.2 8.9 - - + +
1090C PRO* 3.9 33.2 + - - +
1091C ARG 5.7 1.0 + - - -
1093C GLY 4.9 5.5 + - - -
1107C ARG* 4.4 5.5 - - - +
1121C PHE* 5.1 6.6 - - + -
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Residues in contact with ASN 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 THR* 2.8 25.5 + - - -
913A GLN* 1.3 77.2 - - - +
915A VAL* 1.3 67.5 + - - +
917A TYR* 4.3 2.7 - - - +
918A GLU* 2.9 43.3 + - - +
1111A GLU* 3.0 29.8 + - - +
1089C PHE* 4.1 29.0 - - + -
1121C PHE* 3.9 13.7 - - + -
1123C SER* 3.5 28.5 + - - +
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Residues in contact with VAL 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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718A PHE* 4.0 20.9 - - + -
906A PHE* 4.6 4.0 - - + -
911A VAL* 3.7 23.6 - - + -
912A THR* 3.5 27.1 - - - +
914A ASN* 1.3 85.3 - - - +
916A LEU* 1.3 62.7 + - - +
918A GLU* 4.7 2.5 - - - -
919A ASN* 2.8 42.1 + - - +
1106A GLN* 4.7 2.7 - - - +
1109A PHE* 4.1 31.4 - - + -
1111A GLU* 4.6 3.1 - - - +
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Residues in contact with LEU 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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800A PHE* 5.7 2.0 - - + -
899A ALA* 3.5 29.2 - - + +
902A MET* 3.6 27.8 - - + -
903A ALA* 3.5 21.5 - - + +
906A PHE* 4.0 26.5 - - + -
912A THR 4.1 1.2 + - - -
913A GLN 3.0 8.4 + - - +
915A VAL* 1.3 80.1 - - - +
917A TYR* 1.3 75.4 + - + +
919A ASN 3.2 1.6 + - - -
920A GLN* 3.1 31.5 + - + +
923A ILE* 3.8 28.0 - - + -
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Residues in contact with TYR 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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899A ALA* 4.4 14.4 - - + -
900A MET* 3.7 24.4 - - + +
903A ALA* 3.6 26.3 - - + +
904A TYR* 6.0 0.7 - - - -
913A GLN* 3.0 38.4 + - + +
914A ASN* 3.4 3.1 + - - +
916A LEU* 1.3 89.9 - - + +
918A GLU* 1.3 61.2 + - + +
920A GLN* 4.0 23.4 + - - +
1079C PRO* 3.7 36.0 + - + +
1089C PHE* 3.8 31.2 - + + -
1128C VAL* 4.2 12.5 - - - +
1129C VAL* 4.4 21.3 - - + -
1130C ILE* 5.1 2.7 + - - +
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Residues in contact with GLU 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 ASN* 2.9 36.2 + - + +
915A VAL* 4.3 4.2 - - - +
917A TYR* 1.3 79.5 - - + +
919A ASN* 1.3 66.7 + - - +
920A GLN 3.4 1.3 + - - -
1111A GLU* 5.2 0.5 - - - +
1089C PHE* 5.3 1.8 - - + -
1123C SER* 3.3 28.4 + - - +
1124C GLY* 4.9 4.0 - - - -
1128C VAL* 3.7 42.8 - - + +
1129C VAL* 5.2 2.9 - - + -
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Residues in contact with ASN 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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718A PHE* 4.0 23.4 - - + -
915A VAL* 2.8 34.6 + - - +
916A LEU 3.2 5.4 + - - -
918A GLU* 1.3 84.1 + - - +
920A GLN* 1.3 64.6 + - - +
921A LYS 3.3 2.2 - - - -
922A LEU* 3.3 20.8 + - + +
923A ILE* 3.1 23.9 + - + +
1109A PHE* 4.9 5.6 - - - -
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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