Contacts of the helix formed by residues 779 - 788 (chain C) in PDB entry 1ZM9
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 GLY 779 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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535C GLU* 2.7 22.7 + - - -
777C SER 3.2 0.4 + - - -
778C PHE* 1.3 73.2 - - - +
780C PHE* 1.3 65.7 + - - +
781C THR* 3.3 3.1 - - - -
782C GLY* 3.1 15.1 + - - -
783C GLU* 3.1 20.0 + - - +
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Residues in contact with PHE 780 (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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731C VAL* 4.5 15.7 - - + -
733C ILE* 4.6 3.6 - - + -
746C VAL* 3.6 30.1 - - + -
747C LEU* 3.7 30.1 - - + -
750C LYS* 4.3 15.9 - - + +
772C LEU* 3.6 32.5 - - + -
776C GLU 4.9 0.4 - - - -
777C SER* 3.1 21.4 + - - +
778C PHE 3.1 4.3 - - - -
779C GLY* 1.3 75.5 - - - +
781C THR* 1.3 63.9 + - - +
783C GLU* 3.0 9.4 + - - +
784C LEU* 2.8 55.5 + - + +
794C PRO* 5.4 4.0 - - + -
796C MET* 4.8 13.2 - - + -
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Residues in contact with THR 781 (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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110C ASP* 2.5 42.3 - - + +
779C GLY* 3.3 1.0 - - - -
780C PHE* 1.3 82.9 - - - +
782C GLY* 1.3 62.4 + - - +
784C LEU* 4.0 6.7 - - - +
785C ARG* 3.1 28.8 + - - +
794C PRO* 4.8 22.5 - - + +
796C MET* 5.7 3.6 - - - -
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Residues in contact with GLY 782 (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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779C GLY* 3.1 12.9 + - - -
781C THR* 1.3 79.1 - - - +
783C GLU* 1.3 57.7 + - - +
785C ARG* 3.0 25.6 - - - +
786C GLN* 3.6 5.4 + - - +
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Residues in contact with GLU 783 (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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746C VAL* 4.4 13.8 - - + +
749C LYS* 4.4 11.3 - - - +
750C LYS* 3.2 33.4 + - - -
778C PHE 4.2 5.7 - - - +
779C GLY* 3.1 12.1 + - - +
780C PHE* 3.0 7.3 + - - +
782C GLY* 1.3 72.3 - - - +
784C LEU* 1.3 65.2 - - - +
785C ARG 3.0 2.8 + - - -
786C GLN* 3.4 7.0 + - - +
787C ALA* 3.2 21.3 + - - +
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Residues in contact with LEU 784 (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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733C ILE* 4.0 19.3 - - + -
742C GLY 4.7 3.8 - - - +
743C ILE* 3.7 31.0 - - + -
746C VAL* 4.6 12.5 - - + +
780C PHE* 2.8 35.3 + - + +
781C THR* 4.0 6.3 - - - +
783C GLU* 1.3 73.1 - - - +
785C ARG* 1.3 65.1 + - - +
787C ALA* 4.3 2.9 - - + -
788C THR* 3.2 35.9 + - + -
792C ALA* 4.2 13.0 - - + -
794C PRO* 3.2 37.0 - - + -
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Residues in contact with ARG 785 (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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108C HIS* 3.1 34.8 + - - -
109C VAL* 4.7 11.5 - - - +
110C ASP* 3.9 12.5 + - - -
138C GLN* 5.6 5.4 - - - +
781C THR* 3.1 17.1 + - - +
782C GLY* 3.0 16.2 - - - +
783C GLU 3.0 0.2 - - - -
784C LEU* 1.3 80.5 - - - +
786C GLN* 1.3 68.4 + - - +
788C THR* 5.1 0.2 - - - -
789C GLY* 3.5 1.4 + - - -
790C GLY* 3.2 46.7 + - - +
792C ALA 5.9 1.2 + - - -
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Residues in contact with GLN 786 (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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782C GLY 3.6 4.5 + - - +
783C GLU* 3.4 9.2 + - - +
785C ARG* 1.3 81.5 - - - +
787C ALA* 1.3 67.0 + - - +
789C GLY* 3.4 8.7 + - - -
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Residues in contact with ALA 787 (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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742C GLY* 4.0 20.2 - - - +
745C SER* 5.5 2.0 - - - +
746C VAL* 3.6 24.9 - - + -
783C GLU 3.2 14.0 + - - +
784C LEU* 3.7 4.7 - - - +
785C ARG 3.2 0.2 + - - -
786C GLN* 1.3 84.5 - - - +
788C THR* 1.3 61.2 + - + +
789C GLY 3.3 2.8 + - - -
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Residues in contact with THR 788 (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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735C CYS* 4.3 0.2 - - - -
739C ALA* 3.2 39.3 - - - +
742C GLY* 3.8 3.6 - - - -
743C ILE* 3.6 37.7 - - + +
784C LEU* 3.2 16.8 + - + -
787C ALA* 1.3 76.2 - - - +
789C GLY* 1.3 52.8 + - - +
790C GLY* 2.7 16.2 + - - -
791C GLN* 2.8 19.2 + - - +
792C ALA* 2.9 28.1 + - + +
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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