Contacts of the helix formed by residues 782 - 792 (chain C) in PDB entry 4YOC
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 782 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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692C TYR* 3.5 7.8 - - - -
733C ILE* 5.3 6.5 - - + -
735C TYR* 3.3 24.0 - - - +
745C ARG* 5.5 3.4 - - - +
769C GLN* 3.3 10.3 - - - +
780C LEU 3.2 1.6 - - - +
781C PRO* 1.3 89.9 - - + +
783C ALA* 1.3 60.6 + - - +
784C LYS* 3.8 5.7 + - - +
785C GLU* 3.3 31.4 + - - +
786C TYR* 3.0 26.2 + - - +
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Residues in contact with ALA 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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692C TYR* 3.6 16.9 - - + -
735C TYR* 4.2 13.4 - - + -
743C THR* 4.5 0.9 - - + -
767C VAL* 3.8 30.5 - - + -
768C PHE 6.2 0.2 - - - -
769C GLN* 2.9 16.4 + - + +
782C THR* 1.3 70.4 - - - +
784C LYS* 1.3 60.5 + - - +
786C TYR* 3.5 5.8 - - - +
787C PHE* 2.9 44.2 + - + -
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Residues in contact with LYS 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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1101A ASN* 3.5 27.2 + - - +
1104A ARG* 6.0 0.8 - - - +
735C TYR* 3.8 24.5 - - + +
742C LEU* 5.6 1.2 - - - +
743C THR* 3.0 43.9 + - - +
744C GLU* 5.1 0.4 - - - +
745C ARG* 5.7 2.9 - - + +
782C THR* 3.1 8.0 - - - +
783C ALA* 1.3 79.6 - - - +
785C GLU* 1.3 60.9 + - + +
787C PHE* 3.3 2.4 + - - +
788C ARG* 2.9 51.8 + - - +
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Residues in contact with GLU 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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779C GLU 4.2 5.2 - - - +
780C LEU* 3.6 13.6 - - + +
781C PRO* 3.3 30.7 - - - +
782C THR* 3.3 24.9 + - - +
784C LYS* 1.3 76.3 - - + +
786C TYR* 1.3 60.3 - - - +
788C ARG* 3.5 18.8 - - - +
789C ASP* 2.9 31.9 + - - +
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Residues in contact with TYR 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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579C GLN* 2.4 49.0 + - - +
692C TYR* 3.6 30.3 - + + +
697C ARG 3.9 19.3 - - - -
699C LEU* 3.8 26.0 - - + +
780C LEU* 3.9 22.1 - - + +
782C THR 3.0 14.1 + - - +
783C ALA* 3.5 7.9 - - - +
784C LYS 3.2 0.4 - - - -
785C GLU* 1.3 77.6 - - - +
787C PHE* 1.3 76.0 + + - +
789C ASP* 3.8 1.6 - - - +
790C LEU* 2.9 43.8 + - + +
793C ARG* 3.9 19.4 + - - -
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Residues in contact with PHE 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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580C GLY 4.1 9.0 - - - -
581C ASN* 3.3 36.7 + - - +
690C LYS* 5.0 0.2 - - + -
699C LEU* 3.6 32.5 - - + -
737C GLU* 3.6 22.4 - - + -
739C LYS 5.9 0.2 - - - +
741C ASN* 4.6 10.8 + - - +
743C THR* 3.4 30.3 - - + +
767C VAL* 3.9 28.5 - - + -
783C ALA* 2.9 25.5 + - + +
784C LYS 3.9 0.7 - - - +
786C TYR* 1.3 90.4 - + - +
788C ARG* 1.3 57.4 + - - +
790C LEU* 3.8 6.8 - - + +
791C TYR* 2.9 28.6 + - - +
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Residues in contact with ARG 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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1098A ASP* 3.3 37.9 + - - +
1099A PRO 4.9 6.5 + - - -
1101A ASN* 5.3 2.4 + - - -
1104A ARG* 5.9 3.6 - - - +
741C ASN* 4.5 14.6 + - - +
784C LYS* 2.9 47.7 + - - +
785C GLU* 3.5 18.3 - - - +
787C PHE* 1.3 74.5 - - - +
789C ASP* 1.3 66.9 + - - +
791C TYR* 3.0 18.4 + - - +
792C HIS* 3.2 18.4 + - + -
816C ARG* 3.8 24.7 - - - +
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Residues in contact with ASP 789 (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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780C LEU* 3.8 23.5 - - + +
785C GLU 2.9 17.4 + - - +
786C TYR 3.9 2.5 - - - +
788C ARG* 1.3 76.6 - - - +
790C LEU* 1.3 56.5 + - - +
792C HIS* 3.4 5.7 + - - +
793C ARG* 2.7 61.9 + - - +
814C SER* 5.7 4.5 + - - -
816C ARG* 5.5 3.4 - - - +
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Residues in contact with LEU 790 (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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579C GLN* 3.6 23.6 - - + +
580C GLY* 3.7 16.4 - - - -
581C ASN* 4.3 10.1 - - - +
786C TYR* 2.9 33.4 + - + +
787C PHE* 3.8 15.5 - - + +
789C ASP* 1.3 76.4 + - - +
791C TYR* 1.3 64.2 + - - +
793C ARG* 3.2 47.9 + - + +
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Residues in contact with TYR 791 (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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1066A GLU* 2.6 43.5 + - + +
581C ASN* 5.6 3.1 - - - +
740C PRO* 3.9 25.6 - - + -
741C ASN* 3.6 43.3 - - + +
787C PHE 2.9 18.4 + - - +
788C ARG* 3.0 7.2 + - - +
790C LEU* 1.3 77.7 - - - +
792C HIS* 1.3 77.4 + + - +
793C ARG 3.8 2.4 + - - +
815C ASN* 4.0 8.4 + - - -
862C ARG* 4.4 6.0 + - - -
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Residues in contact with HIS 792 (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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1064A TYR* 5.7 1.2 + - - -
1066A GLU* 4.5 7.2 - - + -
1098A ASP* 4.6 2.6 + - - -
741C ASN* 4.8 4.6 + - - -
788C ARG* 3.2 26.7 + - + +
789C ASP* 3.4 5.4 + - - +
790C LEU 3.1 0.6 - - - -
791C TYR* 1.3 100.6 - + - +
793C ARG* 1.3 64.0 + - - +
814C SER* 3.4 17.9 - - - +
815C ASN* 2.7 55.3 + - + +
816C ARG* 3.0 50.9 + - + +
862C ARG* 4.5 10.3 + - - -
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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