Contacts of the helix formed by residues 753 - 769 (chain C) in PDB entry 4YZ9
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 753 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680C HIS* 3.7 38.7 - + + +
685C VAL* 4.1 12.2 - - + +
752C THR* 1.3 82.5 - - - +
754C THR* 1.3 86.8 + - + +
756C ASP* 3.0 18.8 + - - +
757C ILE* 3.6 16.4 + - + +
820C ARG 5.0 4.6 + - - -
821C PRO 4.8 1.6 - - - -
822C SER* 4.0 33.1 + - - -
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Residues in contact with THR 754 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741C GLU* 4.2 4.0 + - - -
752C THR* 2.8 18.3 + - - +
753C TYR* 1.3 105.9 - - + +
755C VAL* 1.3 62.8 + - - +
756C ASP 3.3 0.2 - - - -
757C ILE* 3.3 14.0 + - - +
758C PHE 3.4 5.2 + - - -
817C PRO* 3.6 38.0 - - + +
818C GLN* 5.6 1.6 - - - +
820C ARG* 3.0 32.9 + - + +
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Residues in contact with VAL 755 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685C VAL* 5.0 0.4 - - + -
687C ARG* 4.3 15.0 - - + +
738C ILE* 5.5 1.1 - - + -
739C ALA* 4.2 9.3 - - + +
741C GLU* 3.4 22.7 - - + +
742C MET* 3.5 42.8 - - + -
751C PRO* 4.3 10.8 - - + -
752C THR* 3.3 15.0 + - - +
753C TYR 3.1 0.6 + - - -
754C THR* 1.3 80.6 + - - +
756C ASP* 1.3 70.3 + - - +
758C PHE* 3.4 5.7 + - - +
759C SER* 3.3 24.9 + - - +
820C ARG* 4.2 1.8 - - - +
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Residues in contact with ASP 756 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676C LEU* 3.8 16.3 - - + +
680C HIS* 3.0 26.7 + - - +
685C VAL* 3.5 10.5 - - - +
686C HIS* 2.9 32.8 + - - +
687C ARG* 2.8 29.7 + - - -
689C LEU* 3.9 7.2 - - + +
753C TYR 3.0 7.6 + - - +
755C VAL* 1.3 75.8 - - - +
757C ILE* 1.3 59.4 + - - +
759C SER* 3.7 6.7 + - - -
760C ALA* 2.8 30.8 + - - +
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Residues in contact with ILE 757 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673C THR* 6.4 0.2 - - + -
676C LEU* 4.4 7.0 - - + -
680C HIS* 4.1 16.6 - - + -
753C TYR* 3.7 17.9 - - + +
754C THR* 3.3 13.0 + - - +
755C VAL 3.2 0.6 - - - -
756C ASP* 1.3 75.6 - - - +
758C PHE* 1.3 60.4 + - - +
760C ALA* 3.3 5.1 + - + +
761C GLY* 2.8 25.6 + - - -
812C MET* 3.7 34.8 - - + +
820C ARG* 4.0 11.0 - - + -
821C PRO* 3.3 29.4 - - + +
822C SER* 4.5 0.4 - - - -
823C ALA* 3.8 24.0 - - - +
826C VAL* 4.8 3.1 - - + -
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Residues in contact with PHE 758 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
737C TRP 4.0 7.9 - - - -
738C ILE 3.5 19.1 - - - -
739C ALA* 3.5 18.6 - - + -
740C PRO* 3.8 10.8 - - + -
754C THR 3.4 2.8 + - - -
755C VAL 3.7 7.6 - - - +
756C ASP 3.3 0.4 - - - -
757C ILE* 1.3 79.1 - - - +
759C SER* 1.3 63.6 + - - +
761C GLY* 3.3 2.6 + - - -
762C CYS* 3.2 32.7 + - - -
775C PHE* 3.3 33.9 - + - -
785C ILE* 3.9 19.7 - - + -
812C MET 3.4 11.3 + - - -
813C ILE* 3.4 36.9 - - + +
815C MET* 5.9 0.2 - - - -
820C ARG* 3.8 29.4 - - - +
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Residues in contact with SER 759 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687C ARG 5.5 2.1 + - - -
689C LEU* 3.4 35.0 + - - +
737C TRP* 2.7 30.3 + - - -
738C ILE* 4.6 2.6 - - - -
755C VAL* 3.3 16.8 + - - +
756C ASP* 3.7 7.9 + - - -
757C ILE 3.3 0.2 - - - -
758C PHE* 1.3 77.1 - - - +
760C ALA* 1.3 63.5 + - - +
762C CYS* 3.1 9.2 + - - +
763C VAL* 3.0 25.2 + - - +
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Residues in contact with ALA 760 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672C THR* 6.0 4.0 - - + -
673C THR* 5.8 3.4 - - + +
676C LEU* 4.5 9.4 - - + -
689C LEU* 4.0 16.8 - - + +
756C ASP 2.8 22.3 + - - +
757C ILE* 3.7 8.3 - - + +
759C SER* 1.3 72.9 - - - +
761C GLY* 1.3 58.8 + - - +
763C VAL* 2.8 9.2 + - - +
764C PHE* 2.8 47.4 + - + -
812C MET* 5.1 4.0 - - - -
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Residues in contact with GLY 761 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
757C ILE 2.8 19.6 + - - -
758C PHE 3.3 2.9 + - - -
759C SER 3.3 0.2 - - - -
760C ALA* 1.3 70.9 - - - +
762C CYS* 1.3 61.0 + - - +
764C PHE* 3.3 3.5 + - - +
765C TYR* 3.2 18.2 + - - +
809C ILE* 3.9 10.4 - - - +
812C MET* 3.6 26.1 - - - -
813C ILE* 3.7 16.2 - - - -
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Residues in contact with CYS 762 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
736C GLY 5.0 0.9 - - - -
737C TRP* 3.6 24.6 - - + -
758C PHE* 3.2 33.1 + - - -
759C SER* 3.1 9.9 + - - +
761C GLY* 1.3 75.7 - - - +
763C VAL* 1.3 57.9 + - - +
765C TYR* 3.4 2.8 + - - +
766C TYR* 2.9 28.4 + - - +
773C HIS* 3.9 24.2 - - - +
774C PRO* 3.9 17.5 - - + +
775C PHE* 4.1 4.5 - - - -
813C ILE* 4.0 10.5 - - - -
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Residues in contact with VAL 763 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649C LEU* 3.4 31.6 - - + -
669C LEU* 4.4 10.8 - - + -
672C THR* 5.4 3.8 - - + -
689C LEU* 5.0 2.0 - - + -
690C LYS* 4.1 7.9 - - - +
691C PRO* 4.0 25.8 - - + -
694C ILE* 3.7 19.1 - - + -
737C TRP* 4.0 2.9 - - + -
759C SER 3.0 15.4 + - - +
760C ALA* 2.8 11.7 + - - +
762C CYS* 1.3 74.3 - - - +
764C PHE* 1.3 66.1 + - + +
766C TYR* 3.1 6.9 + - + +
767C VAL* 2.9 22.9 + - - +
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Residues in contact with PHE 764 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669C LEU* 3.7 32.5 - - + -
672C THR* 5.9 4.0 - - + -
673C THR* 3.2 28.3 - - + -
760C ALA* 2.8 39.0 + - + -
761C GLY 3.4 8.7 - - - +
762C CYS 3.3 0.2 - - - -
763C VAL* 1.3 75.4 - - + +
765C TYR* 1.3 62.6 + - - +
767C VAL* 3.2 1.7 + - - +
768C ILE* 3.0 30.5 + - - +
808C LEU* 4.0 11.2 - - + -
809C ILE* 4.0 14.6 - - + -
812C MET* 3.7 17.7 - - + -
826C VAL* 4.0 8.7 - - + -
831C PHE* 3.6 20.9 - + - -
832C PHE* 3.6 26.2 - + - -
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Residues in contact with TYR 765 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
761C GLY 3.2 6.8 + - - +
762C CYS 3.9 0.7 - - - +
764C PHE* 1.3 78.6 - - - +
766C TYR* 1.3 52.5 + - - +
768C ILE* 4.5 1.8 - - - +
769C SER* 2.4 55.3 + - - -
772C SER* 3.9 4.7 - - - -
773C HIS 3.6 24.7 - - - -
774C PRO* 3.4 38.6 - - + -
791C SER 3.4 9.9 + - - -
792C LEU* 3.3 39.8 - - + -
793C ASP 3.7 0.5 + - - -
794C CYS* 3.1 40.0 + - + +
795C LEU* 4.1 19.3 - - + -
809C ILE* 4.0 14.0 - - + +
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Residues in contact with TYR 766 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649C LEU* 4.2 5.2 - - + -
650C GLN* 3.4 20.8 + - + +
653C VAL* 3.5 29.4 - - + +
654C GLU* 3.3 26.5 + - - +
691C PRO* 3.8 32.5 - - + -
737C TRP* 4.2 17.5 - + + -
762C CYS 2.9 19.2 + - - +
763C VAL* 3.1 8.3 + - - +
765C TYR* 1.3 76.1 - - - +
767C VAL* 1.3 65.4 + - + +
770C GLU* 3.2 2.8 + - - -
771C GLY* 2.9 50.7 + - - -
772C SER 3.2 25.1 + - - +
773C HIS* 5.6 0.9 - - + -
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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
----------------------------------------------------------
649C LEU* 3.8 33.0 - - + -
652C TYR* 4.9 7.4 - - + -
653C VAL* 4.1 14.9 - - + +
665C PRO* 3.7 35.4 - - + +
668C LEU* 4.9 1.3 - - + -
669C LEU* 3.8 26.9 - - + -
763C VAL 2.9 18.8 + - - +
764C PHE 3.8 3.1 - - - +
766C TYR* 1.3 75.0 - - + +
768C ILE* 1.3 66.3 + - + +
770C GLU* 3.3 15.2 + - - +
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Residues in contact with ILE 768 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
665C PRO* 6.1 2.7 - - + -
666C ILE* 6.4 0.4 - - + -
669C LEU* 4.4 6.3 - - + -
764C PHE* 3.0 20.7 + - + +
765C TYR* 4.0 3.1 - - + +
767C VAL* 1.3 79.9 - - + +
769C SER* 1.3 60.6 + - - +
770C GLU* 3.1 14.1 + - - +
795C LEU* 3.7 26.7 - - + -
802C ASP* 4.7 7.4 - - - +
805C ALA* 4.1 4.9 - - + -
809C ILE* 3.7 24.5 - - + -
831C PHE* 3.6 36.3 - - + -
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Residues in contact with SER 769 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
765C TYR* 2.4 40.1 + - - -
766C TYR 3.5 0.5 + - - -
768C ILE* 1.3 72.0 - - - +
770C GLU* 1.3 70.9 + - - +
771C GLY 3.6 0.2 + - - -
772C SER* 3.1 39.7 + - - -
794C CYS* 3.8 32.1 - - - +
795C LEU* 6.1 0.9 - - - -
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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