Contacts of the helix formed by residues 802 - 811 (chain B) in PDB entry 1P43
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 ASP 802 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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753B PHE* 3.5 20.0 - - + -
756B GLY* 4.7 3.5 - - - +
758B TYR* 2.5 38.6 + - - +
775B GLY* 5.4 0.5 - - - -
798B PHE* 4.5 0.2 - - + -
799B ALA* 3.1 21.0 + - + +
801B ASP* 1.3 74.8 - - - +
803B TRP* 1.3 63.6 + - - +
804B GLU* 3.4 3.1 + - - +
805B ALA* 3.0 29.1 + - + +
806B TRP* 3.1 14.3 - - - -
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Residues in contact with TRP 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 ASP* 3.0 33.8 + - + +
802B ASP* 1.3 73.6 - - - +
804B GLU* 1.3 64.9 + - - +
806B TRP* 2.9 20.0 + - - +
807B SER* 3.0 16.0 + - - -
822B LEU* 3.7 40.2 - - + -
829B ARG* 3.7 40.4 - - + -
832B THR* 3.7 22.8 - - + +
833B ALA* 3.5 24.9 - - + -
836B LYS* 3.4 41.7 - - + +
838B ALA* 4.2 9.1 - - + +
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Residues in contact with GLU 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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802B ASP* 3.3 2.4 + - - +
803B TRP* 1.3 78.5 - - - +
805B ALA* 1.3 62.7 + - - +
807B SER* 3.4 11.1 + - - -
808B HIS* 2.9 35.6 + - + +
836B LYS* 5.7 0.2 - - - +
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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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775B GLY* 4.5 13.9 - - - -
776B PRO* 6.4 0.2 - - - -
798B PHE* 3.5 30.5 - - + -
802B ASP* 3.0 33.9 + - - +
804B GLU* 1.3 78.1 - - - +
806B TRP* 1.3 62.0 + - - +
808B HIS* 3.7 6.5 + - - +
809B PHE* 3.2 24.9 + - - +
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Residues in contact with TRP 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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796B ASP* 3.5 25.4 - - - -
797B PRO* 3.5 26.9 - - + -
798B PHE* 3.1 38.3 + - + +
799B ALA 2.9 19.5 + - - -
802B ASP 3.1 28.3 - - - -
803B TRP* 2.9 7.0 + - - +
805B ALA* 1.3 76.4 - - - +
807B SER* 1.3 60.0 + - - +
809B PHE* 3.2 3.9 + - - +
810B PHE* 2.8 31.9 + - - +
817B ILE* 3.7 16.4 - - + -
818B VAL 3.6 10.3 - - - -
819B ALA* 3.9 6.5 - - - -
822B LEU* 3.7 31.2 - - + +
838B ALA* 3.2 40.8 - - + +
839B ALA* 4.0 8.7 - - + -
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Residues in contact with SER 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 TRP 3.0 11.6 + - - -
804B GLU* 3.8 18.1 + - - -
806B TRP* 1.3 77.7 - - - +
808B HIS* 1.3 64.5 + - - +
810B PHE* 3.4 2.3 + - - +
811B LYS* 3.3 26.5 + - - +
836B LYS* 2.7 36.8 + - - +
837B LYS* 3.7 12.9 - - - +
838B ALA* 4.3 0.9 - - - -
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Residues in contact with HIS 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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775B GLY 5.1 1.3 - - - -
776B PRO* 4.1 40.1 + - + +
779B ALA* 4.4 9.8 - - + +
798B PHE* 6.2 0.2 - + - -
804B GLU* 2.9 29.6 + - + +
805B ALA* 3.8 6.1 - - - +
807B SER* 1.3 78.3 - - - +
809B PHE* 1.3 69.3 + - - +
811B LYS* 3.3 33.5 + - - +
812B THR* 4.3 2.9 + - - +
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Residues in contact with PHE 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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779B ALA* 3.8 20.0 - - + -
782B TYR* 3.7 30.1 - + + -
783B HIS* 3.7 28.0 - + - -
786B MET* 3.9 16.6 - - - -
794B ILE* 4.5 2.7 - - + -
797B PRO* 4.3 18.6 - - + -
798B PHE* 3.3 34.3 - + + -
805B ALA 3.2 4.6 + - - +
806B TRP* 3.7 2.7 - - - +
808B HIS* 1.3 83.6 - - - +
810B PHE* 1.3 64.9 + - - +
811B LYS 3.1 0.9 + - - -
812B THR* 3.1 6.6 + - - -
813B ALA* 3.0 23.6 + - + -
817B ILE* 3.6 32.5 - - + -
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Residues in contact with PHE 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 TRP 2.8 17.7 + - - +
807B SER 3.8 1.1 - - - +
808B HIS 3.3 0.2 - - - -
809B PHE* 1.3 75.4 - - + +
811B LYS* 1.3 64.7 + - - +
812B THR 3.1 1.0 + - - -
813B ALA* 3.4 15.6 + - + +
814B GLY 4.8 0.9 + - - -
815B ILE 4.9 2.7 - - - -
817B ILE* 4.0 18.4 - - + -
837B LYS* 3.3 41.3 - - + +
838B ALA 3.8 4.3 - - - +
839B ALA* 3.5 25.1 - - - -
840B ASP* 3.5 44.0 - - + -
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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 SER* 3.3 14.6 - - - +
808B HIS* 3.3 30.5 + - - +
809B PHE 3.1 0.4 + - - -
810B PHE* 1.3 80.2 - - + +
812B THR* 1.3 68.8 + - + +
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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