Contacts of the helix formed by residues 810 - 821 (chain B) in PDB entry 1J1C
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 PRO 810 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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655B VAL* 4.1 37.5 - - + -
659B LYS* 5.8 3.1 - - - +
751B LEU* 5.1 2.2 - - + -
806B ARG* 5.3 2.0 - - - +
808B ARG 3.3 8.2 - - - +
809B THR* 1.3 88.6 - - + +
811B PRO* 1.3 66.6 - - + +
812B GLU* 3.8 11.9 - - - +
813B ALA* 2.8 37.7 + - + +
814B ILE* 3.3 5.5 + - - +
839B PHE* 4.7 5.2 - - + -
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Residues in contact with PRO 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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809B THR 3.2 7.8 - - - +
810B PRO* 1.3 82.1 - - + +
812B GLU* 1.3 71.6 + - - +
814B ILE* 3.2 15.9 + - + +
815B ALA* 2.9 28.3 + - - +
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Residues in contact with GLU 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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810B PRO* 3.8 9.4 - - - +
811B PRO* 1.3 95.0 - - - +
813B ALA* 1.3 56.3 + - - +
815B ALA* 3.4 6.6 + - - -
816B LEU* 3.0 24.9 + - - +
837B HIS* 3.3 11.2 - - - -
838B SER* 3.7 24.9 - - - +
839B PHE* 3.7 26.2 - - + +
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Residues in contact with ALA 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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747B LEU* 4.3 2.0 - - - +
751B LEU* 3.8 26.7 - - + -
809B THR* 4.4 3.1 - - + -
810B PRO* 2.8 17.0 + - + +
812B GLU* 1.3 80.6 - - - +
814B ILE* 1.3 57.4 + - - +
816B LEU* 3.4 3.6 + - - +
817B CYS* 3.0 33.2 + - - -
839B PHE* 3.4 35.9 - - + -
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Residues in contact with ILE 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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801B TRP* 3.4 36.6 - - + +
802B THR* 4.1 31.0 - - + +
805B PHE* 3.6 28.7 - - + -
809B THR* 3.9 30.3 - - + +
810B PRO 3.8 7.0 - - - +
811B PRO* 3.2 14.5 + - + +
813B ALA* 1.3 75.4 - - - +
815B ALA* 1.3 64.0 + - - +
817B CYS* 3.4 2.8 + - - +
818B SER* 3.1 22.4 + - - -
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Residues in contact with ALA 815 (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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811B PRO 2.9 16.8 + - - +
812B GLU* 3.6 8.5 - - - +
813B ALA 3.3 0.2 - - - -
814B ILE* 1.3 75.3 - - - +
816B LEU* 1.3 64.3 + - - +
818B SER* 2.9 23.2 + - - -
819B ARG* 3.2 14.5 + - + +
837B HIS* 4.1 12.6 - - + +
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Residues in contact with LEU 816 (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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666B PHE* 4.6 1.8 - - + -
747B LEU* 3.7 18.2 - - + -
812B GLU 3.0 17.2 + - - +
813B ALA 3.6 4.9 - - - +
814B ILE 3.3 0.2 - - - -
815B ALA* 1.3 73.4 - - - +
817B CYS* 1.3 66.7 + - - +
819B ARG* 3.0 11.4 + - - -
820B LEU* 3.1 32.9 + - + +
829B LEU* 3.7 24.7 - - + -
834B ALA* 4.5 6.1 - - + -
837B HIS* 3.7 25.0 + - + +
839B PHE* 3.6 30.5 - - + -
840B PHE* 3.8 21.8 - - + -
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Residues in contact with CYS 817 (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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744B GLY 4.6 2.9 - - - -
747B LEU* 3.6 28.0 - - - -
748B ALA* 4.1 14.4 - - - -
751B LEU* 4.2 2.9 - - - -
801B TRP* 4.1 19.7 - - + -
805B PHE* 3.8 22.4 - - + -
813B ALA 3.0 18.0 + - - +
814B ILE* 3.6 9.9 - - - +
815B ALA 3.3 0.2 - - - -
816B LEU* 1.3 76.1 - - - +
818B SER* 1.3 58.0 + - - +
820B LEU* 2.9 8.0 + - - +
821B LEU* 2.9 34.7 + - + +
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Residues in contact with SER 818 (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 TRP* 3.4 39.4 + - - +
814B ILE 3.1 8.8 + - - -
815B ALA* 2.9 19.8 + - - -
816B LEU 3.3 0.2 - - - -
817B CYS* 1.3 78.1 - - - +
819B ARG* 1.3 64.0 + - - +
820B LEU 3.3 0.2 - - - -
821B LEU 3.9 5.6 - - - +
822B GLU* 3.1 24.1 - - - +
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Residues in contact with ARG 819 (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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815B ALA* 3.2 14.6 + - + +
816B LEU* 3.0 6.7 + - - +
818B SER* 1.3 82.1 + - - +
820B LEU* 1.3 59.7 + - - +
822B GLU* 3.1 23.8 + - - +
827B ALA* 3.0 27.5 + - - +
828B ARG* 3.4 8.8 - - - -
829B LEU* 3.2 64.2 + - + +
837B HIS* 5.2 5.2 - - + +
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Residues in contact with LEU 820 (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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666B PHE* 3.6 33.4 - - + -
740B VAL* 3.6 28.3 - - + +
741B TRP* 4.1 7.8 - - - -
743B ALA 4.8 0.2 - - - -
744B GLY* 3.7 27.6 - - - -
747B LEU* 4.0 11.4 - - + -
816B LEU* 3.1 40.4 + - + +
817B CYS* 2.9 6.1 + - - +
819B ARG* 1.3 79.5 - - - +
821B LEU* 1.3 60.8 + - - +
822B GLU 3.1 6.2 + - - -
828B ARG* 3.3 22.9 + - - +
829B LEU* 4.3 10.5 - - + -
834B ALA* 4.3 7.2 - - + -
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Residues in contact with LEU 821 (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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741B TRP* 3.3 60.1 - - + +
744B GLY* 3.8 26.7 - - - +
745B CYS* 3.9 3.8 - - - +
748B ALA* 4.6 9.4 - - + -
756B ILE* 4.7 0.7 - - + -
757B PHE* 3.8 16.8 - - + -
773B LEU* 3.3 22.4 - - + +
801B TRP* 3.5 32.2 + - + -
817B CYS* 2.9 16.7 + - + +
818B SER 3.9 8.3 - - - +
820B LEU* 1.3 73.9 - - - +
822B GLU* 1.3 59.7 + - - +
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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