Contacts of the strand formed by residues 765 - 770 (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 ILE 765 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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582C ASP* 3.8 15.7 - - - -
583C MET* 3.7 23.8 - - + -
634C ARG* 3.4 31.7 - - - +
688C PHE* 3.4 14.4 - - + +
690C LYS* 3.8 27.6 - - + +
736C GLU* 3.4 10.0 - - - +
737C GLU* 2.9 61.8 + - + +
763C GLY 3.7 4.7 - - - +
764C ASP* 1.3 79.1 - - - +
766C ILE* 1.3 68.3 + - - +
767C VAL* 4.4 0.9 - - + -
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Residues in contact with ILE 766 (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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687C LEU* 3.8 32.8 - - + -
688C PHE 2.9 8.9 + - - -
689C LEU* 3.5 13.5 - - + -
690C LYS 2.9 24.8 + - - +
713C ILE* 4.8 2.5 - - + -
716C LEU* 4.7 2.0 - - + -
720C MET* 3.8 31.4 - - + -
734C LEU* 4.1 11.4 - - + -
735C TYR 3.3 12.6 - - - +
736C GLU* 5.0 1.6 - - - -
746C ILE* 4.4 17.5 - - + -
753C LEU* 4.6 11.7 - - + -
757C LEU* 4.7 11.4 - - + -
764C ASP 4.3 0.2 + - - -
765C ILE* 1.3 76.1 - - - +
767C VAL* 1.3 71.2 + - - +
768C PHE* 4.2 2.0 - - + -
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Residues in contact with VAL 767 (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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690C LYS* 3.3 14.8 - - + +
692C TYR* 4.1 7.4 - - + +
699C LEU* 4.1 22.2 - - + -
733C ILE 3.9 0.3 - - - +
734C LEU* 3.6 0.5 - - - -
735C TYR* 2.8 38.6 + - + +
737C GLU* 3.9 23.6 - - + +
743C THR* 5.0 2.0 - - + -
765C ILE* 4.4 7.2 - - + -
766C ILE* 1.3 77.3 - - - +
768C PHE* 1.3 65.8 + - - +
783C ALA* 3.8 26.9 - - + -
787C PHE* 3.9 22.0 - - + -
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Residues in contact with PHE 768 (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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689C LEU* 4.0 16.8 - - + -
690C LYS 2.9 30.4 + - - -
691C MET* 3.3 35.2 - - + +
692C TYR 2.9 22.5 + - - -
702C CYS* 4.0 11.9 - - + -
720C MET* 3.3 58.3 - - + -
724C ALA* 4.0 3.6 - - + -
726C PHE* 4.3 4.5 - + - -
732C LEU* 3.9 20.0 - - + -
733C ILE 3.2 11.0 - - - +
734C LEU* 3.9 19.5 - - + -
735C TYR* 5.5 0.7 - - - -
766C ILE 4.2 5.4 - - - -
767C VAL* 1.3 78.2 - - - +
769C GLN* 1.3 62.7 + - - +
783C ALA* 6.2 0.2 - - - -
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Residues in contact with GLN 769 (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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691C MET* 5.0 2.5 - - - -
692C TYR* 3.3 28.2 - - + +
694C PRO* 3.4 15.0 - - + +
732C LEU* 3.3 12.2 - - - +
733C ILE* 2.9 50.9 + - + +
735C TYR* 3.6 14.2 - - + -
768C PHE* 1.3 75.1 - - - +
770C LYS* 1.3 65.6 + - - +
775C ASN* 3.8 9.9 - - - +
781C PRO 2.8 26.5 + - - -
782C THR* 3.3 8.3 - - - +
783C ALA* 2.9 27.9 + - - +
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Residues in contact with LYS 770 (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 4.8 1.2 + - - -
694C PRO* 5.6 3.0 - - + +
726C PHE* 3.7 45.2 - - + -
727C ILE* 6.5 1.1 - - - -
730C THR* 4.3 17.3 - - + -
731C SER 3.8 5.2 - - - -
732C LEU* 4.1 1.9 - - - +
733C ILE* 4.1 1.6 - - - +
769C GLN* 1.3 84.0 - - - +
771C ASP* 1.3 60.3 + - - +
772C ASP* 4.3 23.3 + - + +
775C ASN* 3.0 24.6 + - - +
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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