Contacts of the helix formed by residues 811 - 820 (chain B) in PDB entry 6AHU
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 LEU 811 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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806B LEU* 3.8 26.5 - - + -
808B SER* 3.1 10.4 + - - +
810B LYS* 1.3 78.8 - - + +
812B LEU* 1.3 60.7 + - - +
813B LYS 3.2 0.9 - - - -
814B GLN* 3.3 27.9 + - - +
815B LEU* 3.2 29.9 + - + +
848B ILE* 4.8 21.1 - - + -
851B HIS* 6.0 0.7 - - - +
852B PHE* 3.9 30.1 - - + -
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Residues in contact with LEU 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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806B LEU* 3.8 34.3 - - + +
807B ARG* 4.3 5.8 - - - -
808B SER 3.1 23.5 + - - +
809B ARG* 4.0 6.7 - - + -
810B LYS 3.4 0.4 - - - -
811B LEU* 1.3 75.6 - - - +
813B LYS* 1.3 59.7 + - - +
815B LEU* 3.8 16.5 - - + +
816B SER* 3.1 28.1 + - - -
857B VAL* 4.2 15.3 - - + -
858B TRP* 5.0 8.7 - - - +
1022B ILE* 4.7 8.5 - - + +
1024B VAL* 3.8 48.5 - - + +
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Residues in contact with LYS 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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809B ARG* 3.3 17.6 + - - +
810B LYS* 3.9 15.9 - - - +
811B LEU 3.2 0.6 - - - -
812B LEU* 1.3 78.8 - - - +
814B GLN* 1.3 61.9 + - + +
816B SER* 3.6 7.2 + - - -
817B ALA* 3.5 17.3 + - - +
1024B VAL* 5.0 11.2 - - + +
13G ALA* 3.8 14.7 - - + +
14G GLU* 3.2 42.9 + - - +
15G LEU* 3.7 26.5 - - + +
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Residues in contact with GLN 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 4.3 10.5 + - - +
811B LEU* 3.3 30.7 + - - +
812B LEU 3.3 0.4 - - - -
813B LYS* 1.3 79.1 - - + +
815B LEU* 1.3 63.4 + - + +
817B ALA* 3.1 15.3 + - - +
818B TRP* 3.1 27.7 + - - +
848B ILE* 4.1 16.8 - - + +
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Residues in contact with LEU 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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806B LEU* 4.5 10.5 - - + -
811B LEU* 3.2 17.7 + - + +
812B LEU* 3.6 26.2 + - + +
813B LYS 3.4 0.2 - - - -
814B GLN* 1.3 76.7 - - + +
816B SER* 1.3 63.2 + - - +
817B ALA 3.5 0.2 + - - -
818B TRP* 3.6 13.5 + - + +
819B CYS* 3.5 27.2 + - - +
848B ILE* 5.8 10.3 - - + -
857B VAL* 4.9 6.1 - - + -
987B LEU* 3.8 30.5 - - + -
990B LEU* 5.7 8.5 - - + -
991B LEU* 4.8 18.2 - - + -
994B LEU* 5.5 4.5 - - + -
1022B ILE* 4.3 14.4 - - + +
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Residues in contact with SER 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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812B LEU 3.1 19.2 + - - -
813B LYS* 3.8 8.5 - - - -
814B GLN 3.2 0.4 - - - -
815B LEU* 1.3 76.9 - - - +
817B ALA* 1.3 59.6 + - - +
820B GLY* 3.0 24.7 + - - +
821B PRO* 3.3 7.6 - - - +
1022B ILE* 3.0 29.9 + - - +
1023B GLU* 4.9 0.9 - - - -
1024B VAL 4.8 9.5 + - - -
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Residues in contact with ALA 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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813B LYS 3.5 9.6 + - - +
814B GLN* 3.1 14.1 + - - +
816B SER* 1.3 77.6 - - - +
818B TRP* 1.3 65.6 + - + +
821B PRO* 3.4 26.9 - - + +
837B GLN 5.6 6.1 - - - +
838B GLN* 5.2 10.4 + - - +
1002B ARG* 5.0 1.0 + - - -
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Residues in contact with TRP 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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814B GLN* 3.1 33.9 + - + +
815B LEU* 3.6 16.1 + - + +
816B SER 3.4 0.2 - - - -
817B ALA* 1.3 82.1 - - + +
819B CYS* 1.3 61.7 + - - +
821B PRO 3.9 4.9 - - - +
838B GLN* 5.8 5.2 - - - -
839B GLY 3.4 24.7 - - - -
840B LEU* 3.7 32.1 - - + -
841B THR* 4.1 9.2 - - - -
842B ARG* 6.3 0.2 - - + -
845B CYS* 4.1 27.7 - - - -
991B LEU* 5.4 2.5 - - + -
994B LEU* 3.8 26.9 - - + +
1002B ARG* 3.2 65.1 + - - +
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Residues in contact with CYS 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 LEU* 3.5 9.5 + - - +
818B TRP* 1.3 79.8 - - - +
820B GLY* 1.3 67.0 + - - +
821B PRO 4.6 1.6 - - - -
822B SER* 4.7 6.1 - - - -
990B LEU* 4.8 11.7 - - - -
994B LEU* 3.7 34.5 - - - -
1002B ARG* 5.5 2.5 - - - -
1003B GLY* 4.7 9.5 + - - +
1020B ILE* 3.2 34.0 - - + +
1021B ALA* 4.7 0.2 - - - -
1022B ILE* 3.8 33.4 - - + +
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Residues in contact with GLY 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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816B SER* 3.0 17.1 + - - +
819B CYS* 1.3 81.8 - - - +
821B PRO* 1.3 67.9 - - - +
822B SER* 3.2 7.3 + - - -
1019B ARG* 5.2 2.6 + - - -
1021B ALA* 4.4 19.0 - - - +
1022B ILE 5.2 1.1 - - - -
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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
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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