Contacts of the helix formed by residues 841 - 852 (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 THR 841 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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818B TRP* 4.1 8.2 - - - -
839B GLY 4.0 4.4 + - - -
840B LEU* 1.3 80.4 + - - +
842B ARG* 1.3 62.1 + - - +
843B GLU* 4.0 7.9 - - + +
844B ALA* 3.7 32.6 + - + +
845B CYS* 3.5 19.9 + - - -
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Residues in contact with ARG 842 (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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818B TRP* 6.3 0.2 - - + -
840B LEU* 4.5 27.3 - - + +
841B THR* 1.3 71.5 - - - +
843B GLU* 1.3 65.1 + - + +
844B ALA 3.3 0.2 - - - -
845B CYS* 3.4 11.0 + - - +
846B LEU* 3.4 28.4 + - + +
995B SER* 2.6 51.9 + - - +
998B PRO* 4.1 21.8 - - - +
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Residues in contact with GLU 843 (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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841B THR* 3.3 8.1 - - + +
842B ARG* 1.3 78.8 - - + +
844B ALA* 1.3 62.8 + - - +
846B LEU* 3.5 13.5 + - + +
847B SER* 3.4 18.7 + - - -
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Residues in contact with ALA 844 (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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841B THR* 3.7 24.9 - - + +
842B ARG 3.3 0.4 - - - -
843B GLU* 1.3 75.9 - - - +
845B CYS* 1.3 66.4 + - - +
846B LEU 3.3 0.2 - - - -
847B SER* 3.4 8.9 + - - -
848B ILE* 3.3 28.5 + - + +
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Residues in contact with CYS 845 (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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818B TRP* 4.1 27.1 - - - -
841B THR 3.5 16.8 + - - -
842B ARG* 3.4 12.7 + - + +
843B GLU 3.3 0.4 - - - -
844B ALA* 1.3 79.1 - - - +
846B LEU* 1.3 62.9 + - + +
848B ILE* 3.4 17.9 + - - +
849B LEU* 3.4 20.1 + - - +
991B LEU* 3.7 36.0 - - + +
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Residues in contact with LEU 846 (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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719B VAL* 5.3 11.7 - - + -
842B ARG* 3.4 15.3 + - + +
843B GLU* 3.5 14.8 + - + +
844B ALA 3.3 0.2 - - - -
845B CYS* 1.3 79.4 - - + +
847B SER* 1.3 60.1 + - - +
848B ILE 3.3 0.2 - - - -
849B LEU* 3.4 22.1 + - + +
850B GLY* 3.3 18.0 + - - -
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Residues in contact with SER 847 (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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843B GLU 3.4 11.2 + - - -
844B ALA* 3.7 12.1 - - - -
845B CYS 3.3 0.6 - - - -
846B LEU* 1.3 78.3 - - - +
848B ILE* 1.3 64.0 + - - +
850B GLY* 3.7 2.2 + - - +
851B HIS* 3.2 23.2 + - - +
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Residues in contact with ILE 848 (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* 5.0 5.2 - - + -
811B LEU* 4.8 25.8 - - + -
814B GLN* 4.1 20.2 - - + +
815B LEU* 5.8 10.8 - - + -
844B ALA* 3.3 17.9 + - + +
845B CYS* 3.7 17.0 - - + +
846B LEU 3.3 0.4 - - - -
847B SER* 1.3 76.9 - - - +
849B LEU* 1.3 61.0 + - + +
851B HIS* 3.2 5.7 + - + +
852B PHE* 3.0 31.4 + - + +
987B LEU* 4.8 16.9 - - + +
991B LEU* 5.4 5.6 - - + -
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Residues in contact with LEU 849 (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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719B VAL* 5.6 7.6 - - + -
720B GLN* 5.5 9.4 + - - +
845B CYS 3.4 14.6 - - - +
846B LEU* 3.4 27.0 + - + +
847B SER 3.3 0.4 - - - -
848B ILE* 1.3 78.8 - - + +
850B GLY* 1.3 58.5 + - - +
852B PHE 3.3 19.9 - - - +
853B PRO* 3.6 9.0 - - - +
987B LEU* 3.7 35.0 - - + -
988B THR* 3.7 30.7 - - + +
991B LEU* 3.8 26.2 - - + -
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Residues in contact with GLY 850 (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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720B GLN* 5.5 6.7 - - - +
846B LEU 3.3 11.8 + - - -
847B SER* 3.7 3.8 + - - -
848B ILE 3.3 0.2 - - - -
849B LEU* 1.3 77.5 - - - +
851B HIS* 1.3 62.2 + - - +
853B PRO* 4.0 9.8 - - - +
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Residues in contact with HIS 851 (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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300B TYR* 6.1 1.6 - + - -
847B SER* 3.2 19.6 + - - +
848B ILE* 3.2 8.0 + - + +
850B GLY* 1.3 79.7 - - - +
852B PHE* 1.3 102.0 + + + +
853B PRO* 3.3 8.5 - - - +
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Residues in contact with PHE 852 (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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274B THR* 6.3 0.4 - - + -
300B TYR* 3.3 33.9 - + - -
302B ARG* 4.6 13.0 - - + -
804B CYS* 6.1 3.6 - - + -
806B LEU* 3.6 31.4 - - + -
808B SER* 4.9 7.9 - - - -
811B LEU* 3.9 23.3 - - + -
848B ILE* 3.0 16.1 + - + +
849B LEU* 3.3 13.2 - - - +
851B HIS* 1.3 111.1 - + - +
853B PRO* 1.3 66.4 - - + +
854B ARG 3.8 0.9 + - - -
855B ALA* 4.1 19.0 - - + +
987B LEU* 4.6 5.3 - - + +
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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