Contacts of the helix formed by residues 912 - 919 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1121B PHE* 4.8 12.1 - - + -
906C PHE* 4.7 2.8 - - - -
907C ASN* 4.3 5.8 - - - -
910C GLY 5.8 0.9 - - - +
911C VAL* 1.3 80.5 - - - +
913C GLN* 1.3 66.1 + - - +
914C ASN* 2.8 24.6 + - - +
915C VAL* 3.3 23.0 + - - +
916C LEU 4.1 1.6 + - - -
1106C GLN* 3.3 30.1 + - + +
1111C GLU* 4.6 1.2 + - - +
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Residues in contact with GLN 913 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1079B PRO 5.5 0.2 - - - +
1089B PHE* 4.2 7.8 - - + +
1090B PRO* 3.8 33.7 + - - +
1091B ARG 5.7 1.0 + - - -
1093B GLY 4.9 5.3 + - - -
1107B ARG* 4.4 4.8 - - - +
1121B PHE* 5.1 7.1 - - + -
903C ALA* 4.1 21.0 - - + +
904C TYR* 4.3 21.2 - - - -
906C PHE* 5.4 0.9 - - - -
907C ASN* 2.9 35.6 + - - +
911C VAL 3.8 0.6 + - - -
912C THR* 1.3 72.4 - - - +
914C ASN* 1.3 67.2 + - - +
916C LEU* 3.0 9.1 + - - +
917C TYR* 3.0 41.1 + - + -
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Residues in contact with ASN 914 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1089B PHE* 4.0 30.1 - - + -
1121B PHE* 3.9 12.7 - - - -
1123B SER* 3.5 28.2 + - - +
912C THR* 2.8 25.8 + - - -
913C GLN* 1.3 78.6 - - - +
915C VAL* 1.3 67.5 + - - +
917C TYR* 4.3 2.7 - - - +
918C GLU* 2.9 42.7 + - - +
1111C GLU* 3.0 29.8 + - - +
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Residues in contact with VAL 915 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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718C PHE* 4.0 20.2 - - + -
906C PHE* 4.6 4.7 - - + -
911C VAL* 3.7 23.3 - - + -
912C THR* 3.5 27.8 - - - +
913C GLN 3.1 0.2 - - - -
914C ASN* 1.3 85.7 - - - +
916C LEU* 1.3 62.4 + - - +
918C GLU* 4.7 2.7 - - - -
919C ASN* 2.8 41.8 + - - +
923C ILE* 4.7 0.2 - - - +
1106C GLN* 4.7 2.5 - - - +
1109C PHE* 4.1 30.7 - - + -
1111C GLU* 4.6 3.4 - - - +
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Residues in contact with LEU 916 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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800C PHE* 5.7 2.2 - - + -
899C ALA* 3.5 29.2 - - + +
902C MET* 3.6 28.3 - - + -
903C ALA* 3.5 21.5 - - + +
906C PHE* 4.0 26.8 - - + -
912C THR 4.1 1.0 + - - -
913C GLN 3.0 9.3 + - - +
915C VAL* 1.3 79.8 - - - +
917C TYR* 1.3 75.2 + - + +
919C ASN 3.2 1.4 + - - -
920C GLN* 3.1 31.5 + - + +
923C ILE* 3.8 27.8 - - + -
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Residues in contact with TYR 917 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1079B PRO* 3.7 35.6 + - + +
1089B PHE* 3.8 31.0 - + + -
1128B VAL 4.2 12.3 - - - +
1129B VAL* 4.4 21.4 - - + -
1130B ILE* 5.1 2.6 + - - +
899C ALA* 4.4 14.4 - - + -
900C MET* 3.7 23.9 - - + +
903C ALA* 3.6 26.4 - - + +
904C TYR* 6.0 0.9 - - - -
913C GLN* 3.0 39.0 + - + +
914C ASN* 3.4 3.3 + - - +
916C LEU* 1.3 91.9 - - + +
918C GLU* 1.3 60.8 + - - +
920C GLN* 4.0 22.7 + - - +
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Residues in contact with GLU 918 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1089B PHE* 5.3 1.3 - - + -
1123B SER* 3.3 28.9 + - - +
1124B GLY* 4.9 3.6 - - - -
1128B VAL* 3.7 42.8 - - + +
1129B VAL* 5.2 3.1 - - + -
914C ASN* 2.9 34.7 + - + +
915C VAL* 4.3 4.2 - - - +
917C TYR* 1.3 80.6 - - + +
919C ASN* 1.3 66.6 + - - +
920C GLN 3.4 1.8 + - - -
1111C GLU* 5.2 0.7 - - - +
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Residues in contact with ASN 919 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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718C PHE* 4.0 23.5 - - + -
915C VAL* 2.8 35.6 + - - +
916C LEU 3.2 4.8 + - - -
918C GLU* 1.3 85.7 + - - +
920C GLN* 1.3 64.2 + - - +
921C LYS 3.3 2.7 - - - -
922C LEU* 3.3 20.9 + - + +
923C ILE* 3.1 22.9 + - + +
1109C PHE* 4.9 5.7 - - - -
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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