Contacts of the helix formed by residues 799 - 813 (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 LYS 799 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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871A LYS* 4.7 9.2 - - + +
876A GLU* 3.3 36.7 + - - +
877A ASN* 3.4 29.5 + - - +
796C HIS* 3.4 23.8 + - + +
797C PRO 3.5 0.2 - - - -
798C GLU* 1.3 77.0 - - - +
800C HIS* 1.3 55.3 + - - +
801C GLU* 3.5 32.2 - - - +
802C ASP* 3.0 29.9 + - + +
803C VAL* 2.8 34.4 + - - +
938C PRO* 3.8 2.2 - - - -
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Residues in contact with HIS 800 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
799C LYS* 1.3 72.6 - - - +
801C GLU* 1.3 94.2 + - + +
803C VAL* 3.1 2.1 + - - +
804C ILE* 3.0 36.7 + - + +
835C LEU* 6.5 0.4 - - + -
838C GLN* 3.0 28.7 + - - -
934C THR* 3.4 47.0 + - + +
935C SER* 5.1 2.8 - - - +
937C PHE 5.2 0.2 + - - -
938C PRO* 3.5 27.5 + - - +
941C LEU* 3.5 40.2 + - + +
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Residues in contact with GLU 801 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
876A GLU 5.4 3.2 - - - +
666C ILE* 6.3 4.3 - - + -
799C LYS* 3.5 34.0 - - - +
800C HIS* 1.3 95.4 - - + +
802C ASP* 1.3 60.8 + - - +
804C ILE* 3.6 5.7 + - - +
805C ALA* 3.0 27.8 + - - +
831C PHE* 5.0 3.6 - - - -
835C LEU* 6.2 0.2 - - - +
931C CYS* 5.6 6.1 - - - -
934C THR* 5.5 1.0 + - - -
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Residues in contact with ASP 802 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
768C ILE* 4.7 7.8 - - - +
794C CYS 4.2 3.5 - - - +
795C LEU* 3.7 23.5 - - + +
796C HIS* 2.9 43.0 + - - +
799C LYS* 3.0 36.0 + - + +
801C GLU* 1.3 78.0 - - - +
803C VAL* 1.3 61.6 + - - +
805C ALA* 3.8 5.8 - - - +
806C ARG* 2.9 28.9 + - - +
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Residues in contact with VAL 803 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
796C HIS 4.0 1.6 - - - +
797C PRO* 3.0 33.4 - - + +
799C LYS 2.8 26.6 + - - +
800C HIS 3.7 3.8 - - - +
802C ASP* 1.3 70.0 - - - +
804C ILE* 1.3 67.3 + - + +
806C ARG* 3.3 9.5 + - - +
807C GLU* 3.3 19.8 + - - +
938C PRO* 4.0 13.5 - - + +
939C HIS* 3.8 24.0 - - + +
942C ALA* 3.8 24.4 - - + +
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Residues in contact with ILE 804 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
800C HIS* 3.0 34.0 + - + +
801C GLU* 3.9 5.2 - - - +
803C VAL* 1.3 75.8 - - + +
805C ALA* 1.3 64.2 + - - +
807C GLU* 3.1 14.1 + - + +
808C LEU 3.4 8.3 + - - -
829C HIS* 3.6 12.9 - - + -
830C PRO* 3.7 15.7 - - + +
831C PHE* 3.5 36.3 - - + +
941C LEU* 3.9 17.9 - - + -
942C ALA* 3.7 37.2 - - + +
945C TYR* 5.8 0.4 - - + -
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Residues in contact with ALA 805 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
768C ILE* 4.1 17.0 - - + -
795C LEU* 4.3 7.0 - - + -
801C GLU 3.0 19.4 + - - +
802C ASP* 3.8 8.1 - - - +
803C VAL 3.3 0.2 - - - -
804C ILE* 1.3 77.0 - - - +
806C ARG* 1.3 57.4 + - - +
808C LEU* 3.4 2.5 + - - +
809C ILE* 2.9 37.8 + - + +
831C PHE* 3.8 30.3 - - + -
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Residues in contact with ARG 806 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
792C LEU* 3.5 46.4 + - + +
793C ASP* 3.8 20.0 + - - +
795C LEU* 3.3 44.0 + - + +
796C HIS 5.2 0.6 - - - -
797C PRO* 5.2 10.4 - - - +
802C ASP 2.9 18.7 + - - +
803C VAL* 3.6 8.3 - - - +
804C ILE 3.2 0.2 - - - -
805C ALA* 1.3 76.7 - - - +
807C GLU* 1.3 62.5 + - - +
809C ILE* 4.2 2.2 - - - +
810C GLU* 3.2 42.4 + - - +
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Residues in contact with GLU 807 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
803C VAL 3.3 8.9 + - - +
804C ILE* 3.1 12.3 + - + +
806C ARG* 1.3 80.5 - - - +
808C LEU* 1.3 61.2 + - - +
810C GLU* 3.8 13.6 - - - +
811C LYS* 3.1 56.0 + - - +
829C HIS* 2.6 36.4 + - + +
942C ALA* 5.6 10.3 - - + -
945C TYR* 4.4 15.5 - - - -
946C ARG* 5.1 9.0 - - - +
949C GLU* 5.5 1.0 - - - +
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Residues in contact with LEU 808 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
764C PHE* 4.0 27.1 - - + -
804C ILE 3.4 3.5 + - - +
805C ALA* 3.9 6.3 - - - +
806C ARG 3.3 0.4 - - - -
807C GLU* 1.3 78.1 - - - +
809C ILE* 1.3 67.8 + - + +
811C LYS* 3.0 18.4 + - + +
812C MET* 3.1 29.6 + - + +
821C PRO* 4.7 7.2 - - + -
826C VAL* 4.0 28.5 - - + +
829C HIS* 3.5 43.6 + - + +
831C PHE* 3.9 26.9 - - + -
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Residues in contact with ILE 809 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
761C GLY 3.9 15.9 - - - +
764C PHE* 4.0 18.6 - - + -
765C TYR* 4.0 19.3 - - + +
768C ILE* 3.7 28.7 - - + -
774C PRO* 5.2 0.2 - - + -
792C LEU* 3.8 23.8 - - + -
795C LEU* 4.2 14.6 - - + -
805C ALA* 2.9 26.8 + - + +
806C ARG* 4.2 3.6 - - - +
808C LEU* 1.3 75.3 - - + +
810C GLU* 1.3 59.4 + - - +
812C MET* 3.0 26.3 + - + +
813C ILE* 3.1 21.4 + - + +
831C PHE* 6.3 0.2 - - + -
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Residues in contact with GLU 810 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
790C CYS* 5.9 3.6 - - - -
792C LEU* 4.0 15.1 - - + +
806C ARG* 3.2 37.9 + - - +
807C GLU* 3.8 15.3 - - - +
809C ILE* 1.3 78.6 - - - +
811C LYS* 1.3 66.2 + - + +
813C ILE* 3.9 11.8 - - + +
814C ALA* 3.3 21.3 + - - +
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Residues in contact with LYS 811 (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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807C GLU* 3.1 45.5 + - - +
808C LEU* 3.0 13.7 + - + +
810C GLU* 1.3 84.2 - - + +
812C MET* 1.3 60.1 + - - +
814C ALA* 3.4 17.1 - - - +
819C LYS* 3.6 8.5 - - - +
820C ARG* 3.5 15.6 - - - -
821C PRO* 4.0 18.2 - - + -
825C HIS* 5.9 8.2 + - + -
829C HIS* 5.2 5.7 + - + +
945C TYR* 5.2 5.5 - - - -
949C GLU* 4.6 12.7 + - - -
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Residues in contact with MET 812 (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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757C ILE* 3.7 29.1 - - + +
758C PHE* 3.4 18.0 + - - -
760C ALA* 4.9 3.1 - - - -
761C GLY* 3.6 24.2 - - - -
764C PHE* 3.7 32.1 - - + -
808C LEU* 3.4 15.7 - - + +
809C ILE* 3.0 27.6 + - - +
811C LYS* 1.3 76.8 - - - +
813C ILE* 1.3 58.4 + - - +
814C ALA 3.2 1.8 - - - -
820C ARG* 3.4 17.0 - - - +
821C PRO* 4.1 13.9 - - + -
826C VAL* 3.9 27.1 - - + -
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Residues in contact with ILE 813 (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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758C PHE* 3.4 38.4 - - + +
761C GLY* 3.7 31.2 - - - -
762C CYS* 3.8 9.2 - - - +
774C PRO* 3.9 24.7 - - + -
775C PHE* 4.3 8.4 - - + -
790C CYS* 4.1 26.9 - - + -
792C LEU* 4.4 5.4 - - + -
809C ILE* 3.1 23.5 + - + +
810C GLU* 3.9 10.3 - - - +
812C MET* 1.3 74.0 - - - +
814C ALA* 1.3 68.5 + - - +
815C MET* 3.4 2.1 + - - -
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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
------------------------------------------------------------
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