Contacts of the helix formed by residues 788 - 805 (chain C) in PDB entry 5Y3R
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 TYR 788 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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746C ARG 5.9 2.9 - - - -
780C ILE* 6.0 1.3 - - + -
784C VAL* 2.8 46.8 - - + +
785C MET* 2.2 37.1 + - + +
787C PRO* 1.3 101.6 - - + +
789C TYR* 1.3 50.3 - - - +
790C LYS 3.0 1.8 - - - -
791C ASP* 2.5 29.6 + - - +
792C ILE* 2.2 43.2 + - + +
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Residues in contact with TYR 789 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
785C MET* 3.0 25.6 + - + +
786C GLN* 2.6 28.1 + - - -
787C PRO* 3.0 14.1 - - + -
788C TYR* 1.3 77.1 - - - +
790C LYS* 1.3 101.5 + - + +
792C ILE* 2.8 15.8 + - - +
793C LEU* 2.3 59.7 + - + +
794C PRO* 2.9 5.9 - - - +
865C GLN* 4.9 7.0 - - - +
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Residues in contact with LYS 790 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
787C PRO* 2.7 27.0 + - + +
789C TYR* 1.3 115.0 + - + +
791C ASP* 1.3 58.4 + - - +
794C PRO* 2.9 28.6 - - - +
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Residues in contact with ASP 791 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
746C ARG 5.2 5.2 - - - +
747C ALA 5.3 2.0 - - - +
749C VAL* 4.5 24.7 - - + +
787C PRO 5.2 0.2 - - - -
788C TYR* 2.5 35.7 + - - +
790C LYS* 1.3 74.4 - - - +
792C ILE* 1.3 74.6 + - + +
794C PRO* 3.1 16.1 - - - +
795C CYS* 3.6 13.6 + - - -
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Residues in contact with ILE 792 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747C ALA 5.9 2.7 - - - +
749C VAL* 6.2 1.6 - - + -
752C LEU* 5.1 4.9 - - + -
776C TRP* 4.2 24.0 - - + -
780C ILE* 4.7 3.8 - - + -
785C MET* 3.4 32.1 - - + -
788C TYR* 2.2 49.9 + - + +
789C TYR* 2.8 8.4 + - - -
791C ASP* 1.3 76.7 - - + +
793C LEU* 1.3 51.7 + - - +
795C CYS* 2.9 13.2 + - - +
796C LEU* 2.6 62.8 + - + +
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Residues in contact with LEU 793 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
789C TYR* 2.3 60.6 + - + +
792C ILE* 1.3 69.9 - - - +
794C PRO* 1.3 59.9 - - + +
795C CYS 3.1 1.0 - - - -
796C LEU* 2.6 44.9 + - + -
797C ASP* 3.4 8.7 + - - +
865C GLN* 3.5 61.2 - - + +
866C ILE* 4.5 7.4 - - + -
868C LYS* 5.4 2.5 - - - +
869C ASN* 3.1 15.3 + - - +
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Residues in contact with PRO 794 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
789C TYR 2.9 24.0 - - - +
790C LYS* 2.9 23.1 - - - +
791C ASP 3.1 6.5 - - - +
793C LEU* 1.3 78.0 - - + +
795C CYS* 1.3 62.9 + - - +
798C GLY* 4.3 1.2 + - - -
799C TYR* 4.6 3.5 - - - -
869C ASN* 3.2 32.8 - - - +
873C VAL* 4.5 8.7 - - - +
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Residues in contact with CYS 795 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
749C VAL* 4.7 15.0 - - - -
752C LEU* 4.1 21.3 - - + -
753C GLN* 4.3 8.1 - - - -
791C ASP 3.9 13.2 - - - -
792C ILE* 2.9 10.7 + - - +
793C LEU 3.1 2.5 - - - -
794C PRO* 1.3 75.8 - - - +
796C LEU* 1.3 71.1 + - + +
798C GLY 3.0 11.4 + - - -
799C TYR* 3.0 41.7 - - + -
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Residues in contact with LEU 796 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
752C LEU* 5.2 6.5 - - + -
776C TRP* 5.0 9.4 - - + -
777C SER* 5.4 3.8 - - - +
785C MET* 4.7 8.3 - - + -
792C ILE* 2.6 44.4 + - + +
793C LEU* 2.6 38.6 + - + +
795C CYS* 1.3 71.4 - - + +
797C ASP* 1.3 59.2 + - - +
799C TYR* 4.8 0.9 - - - -
800C LEU* 2.3 72.4 + - + +
858C MET* 5.1 11.2 - - + -
865C GLN* 5.5 2.7 - - - +
866C ILE* 6.4 0.7 - - + -
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Residues in contact with ASP 797 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
793C LEU* 3.4 5.2 + - - +
796C LEU* 1.3 80.5 - - - +
798C GLY* 1.3 57.6 + - - +
799C TYR 2.7 7.3 + - - -
800C LEU* 4.7 3.0 - - - +
801C LYS* 2.9 27.5 + - - +
859C LEU* 5.2 3.5 - - - +
865C GLN 3.6 4.9 - - - +
866C ILE* 2.5 39.4 - - - +
867C ASN 2.8 0.9 + - - -
868C LYS* 2.3 30.7 + - - -
869C ASN* 3.2 14.1 + - + +
870C LEU* 2.9 31.4 - - + +
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Residues in contact with GLY 798 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
794C PRO 4.6 1.1 - - - -
795C CYS 3.0 6.8 + - - -
797C ASP* 1.3 73.2 - - - +
799C TYR* 1.3 73.2 + - - +
801C LYS* 2.9 23.4 - - - +
869C ASN* 3.1 29.5 - - - +
870C LEU* 3.0 7.7 - - - +
873C VAL* 4.1 13.7 - - - +
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Residues in contact with TYR 799 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
752C LEU* 4.9 7.4 - - + -
753C GLN* 3.1 46.1 + - - -
757C LYS* 5.5 19.5 - - + +
794C PRO 4.6 3.4 - - - -
795C CYS* 3.0 42.6 - - + +
796C LEU* 2.9 2.3 + - - +
797C ASP 2.7 0.8 + - - -
798C GLY* 1.3 97.0 - - - +
800C LEU* 1.3 56.4 + - + +
801C LYS* 2.7 25.5 + - - +
802C THR* 2.9 21.7 + - - -
873C VAL* 5.0 11.4 - - + +
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Residues in contact with LEU 800 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
756C PHE* 5.7 7.0 - - + -
774C GLU* 3.2 32.3 - - - +
777C SER* 4.6 3.1 - - - +
796C LEU* 2.3 69.5 + - + +
797C ASP* 4.5 3.8 - - - +
799C TYR* 1.3 68.5 - - + +
801C LYS* 1.3 57.0 + - - +
802C THR 3.1 0.9 - - - -
803C SER* 2.7 47.0 + - - +
804C ALA* 3.7 2.4 + - - +
855C VAL* 4.7 1.4 - - - +
858C MET* 5.1 10.3 - - + -
859C LEU* 5.1 17.9 - - + +
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Residues in contact with LYS 801 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
757C LYS* 4.3 12.6 - - - +
797C ASP* 2.9 15.8 + - - +
798C GLY 2.9 25.6 - - - +
799C TYR* 2.7 19.6 + - - +
800C LEU* 1.3 77.7 - - - +
802C THR* 1.3 81.6 + - + +
804C ALA* 3.6 12.5 + - - +
805C LEU* 3.9 7.6 + - - +
870C LEU* 3.9 15.9 - - + -
873C VAL* 5.8 0.2 - - - -
874C THR* 3.2 24.5 - - + +
877C ASP* 4.1 15.1 + - - +
3120C LEU* 6.1 3.8 - - + -
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Residues in contact with THR 802 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
757C LYS* 4.6 15.2 + - - +
760C LEU* 3.5 29.5 + - - +
799C TYR 2.9 12.4 + - - -
801C LYS* 1.3 99.6 - - - +
803C SER* 1.3 65.9 + - - +
804C ALA 3.1 2.5 - - - -
805C LEU 3.4 13.5 - - - +
806C SER* 3.0 25.7 + - - -
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Residues in contact with SER 803 (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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760C LEU* 3.5 17.0 - - - +
774C GLU* 4.0 6.9 + - - -
800C LEU* 2.7 46.9 + - - +
802C THR* 1.3 80.2 + - - +
804C ALA* 1.3 62.6 + - - +
806C SER* 4.7 1.2 + - - -
851C ILE* 4.2 6.4 - - - +
852C ARG* 4.0 4.2 - - - -
855C VAL* 3.0 41.0 - - - +
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Residues in contact with ALA 804 (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 LEU 3.7 1.7 + - - +
801C LYS* 3.6 9.6 + - - +
802C THR 3.1 0.8 - - - -
803C SER* 1.3 83.1 - - - +
805C LEU* 1.3 61.0 + - - +
806C SER* 3.5 3.3 + - - -
807C ASP* 4.1 4.3 + - - +
852C ARG* 3.2 43.9 + - + +
855C VAL* 3.8 11.8 - - + +
856C VAL* 5.8 4.0 - - + -
859C LEU* 5.9 2.2 - - + -
3114C TYR* 4.8 17.5 - - + -
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Residues in contact with LEU 805 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
801C LYS 3.9 4.6 + - - +
802C THR* 3.0 25.7 + - - +
804C ALA* 1.3 76.0 - - + +
806C SER* 1.3 56.9 + - - +
807C ASP* 3.5 9.6 - - + +
808C GLU 3.1 43.7 - - - +
809C THR 3.4 9.9 - - - +
852C ARG* 3.4 22.0 - - - +
3114C TYR* 3.1 29.2 - - + +
3115C SER* 3.5 11.9 - - - -
3117C ILE 5.1 2.5 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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