Contacts of the helix formed by residues 799 - 813 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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796B HIS* 3.4 25.7 + - + +
797B PRO 3.4 0.4 - - - -
798B GLU* 1.3 77.9 - - - +
800B HIS* 1.3 68.0 + - - +
801B GLU* 3.5 24.6 - - - +
802B ASP* 3.1 30.8 + - - +
803B VAL* 3.0 21.8 + - - +
938B PRO* 4.0 1.3 - - - -
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Residues in contact with HIS 800 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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798B GLU 4.0 0.4 + - - -
799B LYS* 1.3 73.5 - - - +
801B GLU* 1.3 85.4 + - + +
803B VAL* 3.2 2.4 + - - +
804B ILE* 3.2 37.6 + - + +
835B LEU* 6.3 0.4 - - + -
838B GLN* 3.2 30.5 - - - -
934B THR* 3.5 51.5 + - + +
935B SER* 4.9 3.6 - - - +
937B PHE 4.9 1.1 - - - -
938B PRO* 3.6 30.9 - - + +
941B LEU* 3.6 24.9 - - + +
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Residues in contact with GLU 801 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
799B LYS* 3.3 28.0 - - - +
800B HIS* 1.3 98.8 + - - +
802B ASP* 1.3 72.1 + - - +
804B ILE* 3.5 4.4 + - - +
805B ALA* 3.1 23.1 + - - +
831B PHE* 5.4 1.6 - - - -
835B LEU* 5.7 4.5 - - - +
931B CYS* 5.5 7.1 - - - -
934B THR* 5.3 2.1 + - - -
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Residues in contact with ASP 802 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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768B ILE* 5.8 2.6 - - - +
794B CYS 3.5 7.8 - - - +
795B LEU* 3.4 29.6 - - + +
796B HIS* 3.1 40.8 + - - +
799B LYS* 3.1 38.0 + - + +
801B GLU* 1.3 77.7 - - - +
803B VAL* 1.3 60.1 + - - +
805B ALA* 3.8 1.5 - - - +
806B ARG* 2.9 28.3 + - - +
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Residues in contact with VAL 803 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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796B HIS 3.9 1.6 - - - +
797B PRO* 3.0 35.9 - - + +
799B LYS 3.0 19.7 + - - +
800B HIS 3.2 6.5 + - - +
802B ASP* 1.3 74.6 - - - +
804B ILE* 1.3 67.6 + - + +
806B ARG* 3.0 18.2 + - + +
807B GLU* 3.0 14.4 + - + +
938B PRO* 4.0 14.1 - - + +
939B HIS* 3.9 25.8 - - + +
942B ALA* 4.0 20.2 - - + -
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Residues in contact with ILE 804 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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800B HIS* 3.2 35.5 + - + +
801B GLU* 4.0 3.8 - - - +
803B VAL* 1.3 76.9 - - + +
805B ALA* 1.3 63.7 + - - +
806B ARG 3.3 0.2 + - - -
807B GLU* 3.3 10.6 + - + +
808B LEU* 3.4 9.7 + - - +
829B HIS* 3.5 11.9 - - + -
830B PRO* 3.8 15.3 - - + +
831B PHE* 3.5 34.8 - - + +
938B PRO 5.5 0.2 - - - +
941B LEU* 3.9 18.4 - - + -
942B ALA* 3.7 37.2 - - + +
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Residues in contact with ALA 805 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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768B ILE* 4.0 26.9 - - + -
795B LEU* 4.2 14.4 - - + -
801B GLU 3.1 17.5 + - - +
802B ASP* 3.8 5.8 - - - +
804B ILE* 1.3 78.0 - - - +
806B ARG* 1.3 62.0 + - - +
808B LEU* 3.5 2.5 + - - +
809B ILE* 3.0 29.8 + - + +
831B PHE* 4.0 19.7 - - + -
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Residues in contact with ARG 806 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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792B LEU* 3.6 45.5 + - + +
793B ASP* 4.4 10.3 + - - +
795B LEU* 2.9 51.3 + - + +
796B HIS 4.9 0.6 - - - -
797B PRO* 4.8 14.1 - - - +
802B ASP 2.9 18.5 + - - +
803B VAL* 3.0 11.4 + - + +
805B ALA* 1.3 74.6 - - - +
807B GLU* 1.3 66.1 + - - +
809B ILE* 3.3 1.9 + - - +
810B GLU* 3.0 44.4 + - - +
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Residues in contact with GLU 807 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
803B VAL* 3.0 12.6 + - + +
804B ILE* 3.3 11.4 + - + +
806B ARG* 1.3 78.4 - - - +
808B LEU* 1.3 61.8 + - - +
810B GLU* 3.8 14.9 - - - +
811B LYS* 3.4 35.8 + - - +
829B HIS* 3.4 21.3 - - + +
942B ALA* 5.0 13.6 - - + +
945B TYR* 6.1 0.9 - - + -
946B ARG* 3.0 38.4 + - + +
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Residues in contact with LEU 808 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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764B PHE* 3.9 16.8 - - + -
804B ILE 3.4 3.7 + - - +
805B ALA* 4.0 5.8 - - - +
806B ARG 3.3 0.6 - - - -
807B GLU* 1.3 77.2 - - - +
809B ILE* 1.3 68.3 + - + +
811B LYS* 3.1 8.5 + - + +
812B MET* 3.0 40.1 + - + +
821B PRO* 4.6 8.1 - - + -
826B VAL* 3.9 37.2 - - + +
829B HIS* 3.5 42.6 - - + -
831B PHE* 3.8 27.1 - - + -
946B ARG* 5.8 0.2 - - - +
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Residues in contact with ILE 809 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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761B GLY 4.1 11.7 - - - +
764B PHE* 4.1 9.4 - - + -
765B TYR* 4.0 35.9 - - + +
768B ILE* 4.3 18.8 - - + -
792B LEU* 4.0 16.8 - - + -
795B LEU* 4.3 7.4 - - + -
805B ALA* 3.0 24.9 + - - +
806B ARG* 3.3 3.8 + - - +
808B LEU* 1.3 75.6 - - + +
810B GLU* 1.3 59.4 + - - +
812B MET* 2.8 36.9 + - + +
813B ILE* 3.0 32.5 + - + +
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Residues in contact with GLU 810 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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792B LEU* 4.2 12.3 - - + +
806B ARG* 3.0 42.9 + - - +
807B GLU* 3.8 18.8 - - - +
809B ILE* 1.3 78.1 - - - +
811B LYS* 1.3 63.4 + - + +
813B ILE* 3.8 13.3 - - + +
814B ALA* 3.3 21.5 + - - +
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Residues in contact with LYS 811 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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807B GLU* 3.4 29.3 + - - +
808B LEU* 3.1 10.4 + - + +
809B ILE 3.1 1.0 - - - -
810B GLU* 1.3 83.7 - - + +
812B MET* 1.3 61.1 + - - +
814B ALA* 3.4 13.2 - - - +
819B LYS* 3.6 16.8 - - + +
820B ARG* 3.4 21.0 - - - -
821B PRO* 3.9 15.9 - - + -
946B ARG* 3.3 46.6 - - - +
949B GLU* 5.6 0.4 + - - -
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Residues in contact with MET 812 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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757B ILE* 3.5 30.9 - - + +
758B PHE* 3.5 10.2 - - - -
760B ALA* 4.9 2.9 - - - -
761B GLY* 3.6 24.2 - - - -
764B PHE* 3.7 32.1 - - + -
808B LEU* 3.0 28.5 + - + +
809B ILE* 2.8 27.4 + - + +
811B LYS* 1.3 77.5 - - - +
813B ILE* 1.3 57.3 + - - +
814B ALA 3.2 1.8 - - - -
820B ARG* 3.4 23.6 - - - +
821B PRO* 4.2 8.1 - - + -
826B VAL* 3.9 24.7 - - + -
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Residues in contact with ILE 813 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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758B PHE* 3.3 38.7 - - + +
761B GLY* 3.7 31.2 - - - -
762B CYS* 3.7 12.3 - - - +
774B PRO* 4.2 11.7 - - + -
775B PHE* 4.5 9.0 - - + -
790B CYS* 3.6 30.7 - - - -
792B LEU* 4.3 2.2 - - + -
809B ILE* 3.0 29.4 + - + +
810B GLU* 3.8 11.7 - - + +
812B MET* 1.3 74.0 - - - +
814B ALA* 1.3 68.9 + - - +
815B MET* 3.4 2.8 + - - +
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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