Contacts of the helix formed by residues 844 - 852 (chain B) in PDB entry 3B7B
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 844 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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835B VAL 4.4 3.4 - - - -
836B ASN* 3.8 26.2 - - - +
837B CYS 3.8 1.1 - - - -
838B GLN* 4.1 3.1 - - + +
842B GLY 3.9 0.8 + - - +
843B TRP* 1.3 78.2 - - - +
845B PRO* 1.3 76.7 - - - +
846B MET* 3.7 10.8 + - - +
847B ILE* 3.1 36.9 + - + +
848B TRP* 3.2 14.8 + - - -
866B SER* 5.5 0.7 - - - -
867B ASP 5.5 2.4 + - - +
870B ILE* 3.7 36.5 - - + +
878B CYS* 5.9 0.2 - - - +
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Residues in contact with PRO 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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812B LEU* 3.9 24.9 - - + +
813B HIS* 3.9 23.6 - - + +
816B ALA* 3.6 19.9 - - + +
834B ASP 5.2 0.2 - - - +
835B VAL 3.0 28.5 - - - +
837B CYS 3.4 13.5 - - - +
844B THR* 1.3 81.0 - - - +
846B MET* 1.3 63.5 + - - +
848B TRP* 3.1 11.7 + - + +
849B ALA* 2.9 18.9 + - - +
861B LEU* 3.7 18.6 - - + -
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Residues in contact with MET 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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835B VAL 5.1 0.4 + - - -
844B THR* 3.1 8.9 + - - +
845B PRO* 1.3 80.0 - - - +
847B ILE* 1.3 56.7 + - - +
849B ALA* 3.0 3.1 + - - +
850B THR* 2.8 34.2 + - - +
858B VAL* 4.0 24.2 - - + +
861B LEU* 3.5 16.4 - - + +
862B LEU* 3.9 14.8 - - + -
866B SER* 3.2 36.7 + - - +
867B ASP 4.0 3.6 - - - +
868B ILE* 3.7 39.9 - - + -
878B CYS* 3.8 19.3 - - + -
894B LEU* 4.0 9.9 - - + -
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Residues in contact with ILE 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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842B GLY 4.5 1.8 - - - +
843B TRP* 3.4 36.6 - - + -
844B THR* 3.1 34.7 + - + +
846B MET* 1.3 76.3 - - - +
848B TRP* 1.3 61.9 + - - +
850B THR* 3.3 2.7 + - - -
851B GLU* 3.0 21.7 + - - +
870B ILE* 5.1 5.2 - - + +
871B ARG 5.7 0.2 - - - -
872B ASP* 4.3 11.2 - - + +
876B ASN 4.6 7.2 - - - +
877B ILE 4.9 0.2 - - - -
878B CYS* 4.1 25.4 - - + +
881B TRP* 3.3 41.2 - - + +
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Residues in contact with TRP 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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809B SER* 4.2 8.9 + - - -
813B HIS* 3.8 27.4 + - + +
816B ALA 4.2 1.8 - - - -
817B LYS* 3.9 42.4 - - + +
839B ASP* 3.2 28.2 + - - -
843B TRP* 3.6 37.3 - + + +
844B THR 3.2 22.5 + - - -
845B PRO* 3.1 8.3 + - + +
847B ILE* 1.3 76.5 - - - +
849B ALA* 1.3 64.3 + - - +
851B GLU* 3.1 11.3 + - - +
852B TYR* 3.3 48.9 - + - -
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Residues in contact with ALA 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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816B ALA 3.4 19.9 + - - +
845B PRO 2.9 12.1 + - - +
846B MET 3.4 9.0 - - - +
848B TRP* 1.3 77.2 - - - +
850B THR* 1.3 59.1 + - - +
852B TYR* 3.5 1.7 + - - -
853B LYS 3.2 2.3 + - - -
854B HIS* 3.0 31.6 + - - +
857B LEU* 4.0 25.8 - - + -
858B VAL* 3.8 17.9 - - + -
861B LEU* 4.2 2.2 - - + -
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Residues in contact with THR 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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846B MET* 2.8 19.9 + - - +
847B ILE* 3.7 5.2 - - - -
848B TRP 3.1 0.2 - - - -
849B ALA* 1.3 72.8 - - - +
851B GLU* 1.3 64.9 + - - +
852B TYR 3.1 2.6 + - - -
853B LYS* 3.3 8.0 + - - -
858B VAL* 3.8 10.7 - - - +
878B CYS* 3.3 21.7 - - - -
881B TRP* 4.1 4.5 - - + -
882B ALA* 3.5 36.1 - - + +
885B SER* 3.3 13.4 + - - -
890B ILE* 3.7 27.2 - - + +
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Residues in contact with GLU 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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843B TRP* 3.7 32.2 - - + -
847B ILE 3.0 12.1 + - - +
848B TRP* 3.1 10.9 + - - +
850B THR* 1.3 77.9 - - - +
852B TYR* 1.3 90.8 + - + +
853B LYS* 3.9 3.1 + - - +
881B TRP* 4.4 14.6 - - + +
884B PHE* 4.0 24.5 - - + -
885B SER* 3.9 17.5 - - - -
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Residues in contact with TYR 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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817B LYS* 3.5 40.7 - - + -
848B TRP* 3.3 36.1 + + - -
849B ALA 3.5 0.4 + - - -
850B THR 3.1 0.4 - - - -
851B GLU* 1.3 102.6 + - + +
853B LYS* 1.3 73.1 + - - +
854B HIS* 3.1 36.0 + - + +
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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