Contacts of the helix formed by residues 802 - 814 (chain B) in PDB entry 2XBB
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 HIS 802 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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797B GLY 3.6 21.7 + - - -
798B TYR* 3.6 28.7 - + - -
799B SER* 3.3 31.3 + - - +
801B ASN* 1.3 77.1 - - - +
803B GLN* 1.3 70.7 + - + +
804B VAL* 3.1 39.9 + - + +
805B ILE* 2.9 9.0 + - + +
806B GLN* 2.9 20.1 + - - +
854B GLN* 4.9 6.7 + - - -
875B PRO* 5.8 1.3 - - + -
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Residues in contact with GLN 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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801B ASN 3.3 4.8 + - - -
802B HIS* 1.3 77.9 + - + +
804B VAL* 1.3 64.8 + - + +
806B GLN* 3.2 20.3 + - - +
807B TRP* 2.9 68.8 + - + +
1896B GOL 4.4 6.5 + - - -
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Residues in contact with VAL 804 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
798B TYR* 3.5 15.7 - - + +
802B HIS* 3.1 26.2 + - + +
803B GLN* 1.3 77.4 - - + +
805B ILE* 1.3 56.3 + - - +
807B TRP* 3.3 14.0 + - + +
808B PHE* 3.0 22.9 + - - +
873B LEU* 3.5 26.7 - - + -
874B PRO 4.1 7.0 - - - +
875B PRO* 4.0 14.4 - - + -
876B TYR 3.6 24.2 - - - +
882B LEU* 3.5 10.3 - - + +
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Residues in contact with ILE 805 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
794B TYR* 3.6 22.2 - - + +
798B TYR* 3.7 31.4 - - + -
799B SER 3.1 28.7 - - - +
800B ALA 4.0 8.1 - - - +
802B HIS* 2.9 9.0 + - + +
804B VAL* 1.3 75.6 - - - +
806B GLN* 1.3 66.5 + - - +
808B PHE* 3.1 6.6 + - + +
809B TRP* 3.0 43.4 + - + +
852B VAL* 3.5 32.5 - - + -
873B LEU* 4.5 4.0 - - + -
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Residues in contact with GLN 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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800B ALA 4.0 12.3 - - - +
801B ASN* 3.4 32.9 + - - +
802B HIS 2.9 12.9 + - - +
803B GLN* 3.2 27.8 + - - +
805B ILE* 1.3 76.7 - - - +
807B TRP* 1.3 58.1 + - + +
809B TRP* 3.6 5.9 + - - +
810B LYS* 3.0 29.4 + - - +
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Residues in contact with TRP 807 (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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803B GLN* 2.9 54.3 + - + +
804B VAL* 3.4 15.0 - - + +
806B GLN* 1.3 76.3 - - + +
808B PHE* 1.3 58.2 - - - +
810B LYS* 3.1 11.2 + - + +
811B ALA* 2.8 30.5 + - - +
876B TYR 3.4 14.6 - - - -
877B GLU* 3.2 24.0 - - - -
878B SER* 3.2 26.9 - - - -
879B PHE* 3.6 32.1 - + + -
882B LEU* 3.8 13.9 - - + -
1896B GOL 3.1 42.7 + - - -
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Residues in contact with PHE 808 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
788B TRP* 5.4 0.4 - + - -
804B VAL 3.0 13.3 + - - +
805B ILE* 3.1 13.2 + - + +
807B TRP* 1.3 75.4 - - - +
809B TRP* 1.3 104.5 + + - +
811B ALA* 3.1 5.5 + - - +
812B VAL* 2.9 45.0 + - + +
823B LEU* 4.2 10.3 - - + -
850B PHE* 4.3 17.9 - + - -
852B VAL* 4.5 8.7 - - + -
871B LEU* 3.4 32.3 - - + -
873B LEU* 4.3 14.4 - - + -
882B LEU* 3.6 14.5 - - + +
886B LEU* 4.1 24.0 - - + -
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Residues in contact with TRP 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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785B VAL* 4.5 5.5 - - + +
788B TRP* 3.7 28.3 - + + -
789B ARG* 3.3 56.9 - - + +
792B THR* 3.3 33.0 - - + -
794B TYR* 2.8 20.9 + + - -
800B ALA* 5.5 2.0 - - - -
805B ILE* 3.0 38.2 + - + +
806B GLN* 4.2 5.4 - - - +
808B PHE* 1.3 103.3 - + - +
810B LYS* 1.3 60.4 + - - +
812B VAL* 3.7 18.2 - - + +
813B LEU* 2.8 31.5 + - - +
850B PHE* 4.5 0.9 - + - -
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Residues in contact with LYS 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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806B GLN 3.0 20.1 + - - +
807B TRP* 3.1 12.3 + - + +
809B TRP* 1.3 76.3 - - - +
811B ALA* 1.3 60.2 + - - +
813B LEU* 3.4 13.3 - - + +
814B MET* 3.0 48.2 + - + +
879B PHE* 3.8 29.1 - - + -
1896B GOL 3.5 26.2 + - - +
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Residues in contact with ALA 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 TRP 2.8 13.3 + - - +
808B PHE 3.3 9.0 - - - +
810B LYS* 1.3 73.8 - - - +
812B VAL* 1.3 66.0 - - - +
813B LEU 3.0 1.6 - - - -
814B MET 3.0 11.8 + - - -
815B MET* 3.0 20.3 + - + +
879B PHE* 3.5 9.4 - - + -
882B LEU* 3.8 20.0 - - + -
883B TRP* 3.4 25.4 - - + -
886B LEU* 4.8 8.7 - - + -
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Residues in contact with VAL 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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785B VAL* 3.8 21.3 - - + -
788B TRP* 4.0 23.1 - - + -
808B PHE* 2.9 40.8 + - + +
809B TRP* 3.8 16.2 - - + +
811B ALA* 1.3 76.3 - - + +
813B LEU* 1.3 61.6 + - - +
814B MET 3.4 0.5 + - - -
815B MET* 3.5 19.2 + - + -
820B ARG* 3.1 26.9 + - + +
823B LEU* 3.6 24.5 - - + -
886B LEU* 5.4 0.9 - - + -
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Residues in contact with LEU 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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785B VAL* 3.9 27.3 - - + +
786B ASN* 6.5 0.2 - - - -
809B TRP 2.8 19.3 + - - +
810B LYS* 3.4 15.9 - - + +
812B VAL* 1.3 77.8 - - - +
814B MET* 1.3 66.7 + - + +
815B MET 3.5 0.4 - - - +
820B ARG* 2.8 23.8 + - - +
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Residues in contact with MET 814 (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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810B LYS* 3.0 36.6 - - + +
811B ALA* 3.0 4.9 + - - +
813B LEU* 1.3 83.8 - - + +
815B MET* 1.3 61.1 + - - +
816B ASP 3.9 1.2 + - - -
819B LYS* 5.2 1.6 + - - -
879B PHE* 3.9 20.4 - - - -
883B TRP* 3.6 21.5 - - + -
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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
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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