Contacts of the helix formed by residues 850 - 861 (chain B) in PDB entry 5MJA
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 850 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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718B VAL* 3.7 22.2 - - + -
818B MET* 4.4 1.6 - - + -
848B ASP 3.5 7.6 - - - +
849B CYS* 1.3 91.1 - - - +
851B ALA* 1.3 64.5 + - - +
852B ALA 3.3 0.4 - - - -
853B LEU* 3.1 27.6 + - + +
854B HIS* 3.2 10.4 + - - +
887B SER 4.3 4.7 - - - +
888B LEU* 3.6 43.5 - - + +
889B LYS 3.5 20.6 - - - +
890B THR* 4.9 1.3 - - - +
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Residues in contact with ALA 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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845B PRO* 6.4 0.4 - - - -
849B CYS 3.5 2.9 + - - -
850B PRO* 1.3 69.9 - - - +
852B ALA* 1.3 51.2 + - - +
854B HIS* 3.3 9.3 + - - +
855B GLN* 2.8 35.1 + - - +
887B SER 5.5 0.2 + - - -
889B LYS 4.2 4.8 + - - +
890B THR 5.3 1.8 + - - -
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Residues in contact with ALA 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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850B PRO* 3.3 1.1 - - + +
851B ALA* 1.3 78.0 - - - +
853B LEU* 1.3 57.0 + - - +
855B GLN* 3.4 8.1 + - - +
856B LEU* 3.1 21.3 + - - +
881B MET* 3.5 24.9 - - + +
887B SER* 3.4 29.5 + - - +
888B LEU* 5.5 0.2 - - + -
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Residues in contact with LEU 853 (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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722B VAL* 3.7 17.7 - - + -
725B LEU* 4.7 3.4 - - + -
814B MET* 3.4 39.0 - - + +
818B MET* 3.6 44.2 - - + -
849B CYS* 4.0 5.2 - - - -
850B PRO* 3.1 25.8 + - + +
852B ALA* 1.3 77.5 - - - +
854B HIS* 1.4 63.6 + - - +
856B LEU* 3.2 2.9 + - + -
857B MET* 3.2 17.6 + - + +
878B LEU* 3.9 23.8 - - + -
881B MET* 3.9 15.9 - - + +
888B LEU* 4.8 0.9 - - + -
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Residues in contact with HIS 854 (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 LEU 3.1 24.6 + - - -
844B PRO* 4.0 1.3 - - + -
845B PRO* 3.5 51.3 - - + +
849B CYS* 4.0 4.6 - - - -
850B PRO 3.2 11.3 + - - +
851B ALA* 3.3 9.8 + - - +
853B LEU* 1.4 70.9 - - - +
855B GLN* 1.4 61.0 + - - +
857B MET* 3.0 27.5 + - + +
858B LEU* 2.9 58.5 + - + +
861B TRP* 4.7 0.7 - + - -
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Residues in contact with GLN 855 (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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851B ALA 2.8 17.1 + - - +
852B ALA* 3.6 10.1 - - - +
853B LEU 3.3 0.2 - - - -
854B HIS* 1.4 76.3 + - - +
856B LEU* 1.3 55.3 + - - +
858B LEU* 3.2 26.8 + - - +
859B ASP* 2.9 62.1 + - - +
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Residues in contact with LEU 856 (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 MET* 3.7 24.7 - - + -
852B ALA 3.1 13.7 + - - +
853B LEU* 3.4 11.7 - - + +
854B HIS 3.2 0.2 - - - -
855B GLN* 1.3 75.7 - - - +
857B MET* 1.4 60.1 + - - +
859B ASP* 3.3 14.3 + - - +
860B CYS* 3.1 29.4 + - - -
869B PRO* 4.4 12.3 - - + -
874B ILE* 4.3 28.5 - - + -
877B THR* 4.1 28.9 - - + +
878B LEU* 3.8 27.8 - - + -
881B MET* 4.6 3.4 - - + -
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Residues in contact with MET 857 (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 GLY* 3.9 4.5 - - - +
814B MET* 3.7 36.8 - - + -
815B TRP* 3.9 29.4 - - - +
818B MET* 3.8 20.4 - - + -
846B PRO* 4.2 4.5 - - + -
849B CYS* 3.8 28.9 - - - -
853B LEU* 3.2 13.8 + - + +
854B HIS* 3.0 25.6 + - + +
856B LEU* 1.4 73.5 - - - +
858B LEU* 1.4 56.6 + - - +
860B CYS* 3.2 7.4 + - - +
861B TRP* 3.1 49.8 + - + -
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Residues in contact with LEU 858 (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 ARG* 3.8 32.6 + - + +
843B LEU 4.7 0.2 - - - +
854B HIS* 2.9 50.0 + - + +
855B GLN* 3.2 31.6 + - - +
857B MET* 1.4 73.1 - - - +
859B ASP* 1.4 59.9 + - - +
861B TRP* 3.2 19.5 + - + +
862B GLN* 3.4 15.7 + - - +
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Residues in contact with ASP 859 (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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855B GLN* 2.9 45.4 + - - +
856B LEU* 3.4 19.2 - - + +
858B LEU* 1.4 75.7 - - - +
860B CYS* 1.4 60.2 + - - +
861B TRP 3.4 0.5 + - - -
862B GLN* 2.8 37.0 + - - +
868B ARG* 3.6 3.3 - - - -
869B PRO* 3.3 25.6 - - + +
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Residues in contact with CYS 860 (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 VAL* 3.5 38.8 - - - +
808B TRP* 3.4 13.5 + - - -
810B TYR* 4.2 7.6 - - - -
811B GLY* 3.7 19.1 - - - -
814B MET* 4.5 3.4 - - - -
856B LEU* 3.1 21.1 + - - -
857B MET 3.2 9.2 + - - +
859B ASP* 1.4 74.5 - - - +
861B TRP* 1.4 59.4 + - - +
862B GLN 3.4 0.2 - - - -
868B ARG* 3.3 22.6 + - - -
869B PRO* 4.2 4.9 - - - -
874B ILE* 3.9 19.1 - - - -
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Residues in contact with TRP 861 (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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808B TRP* 3.1 41.3 + + + -
811B GLY* 3.2 24.7 - - - -
812B ILE* 3.3 40.0 - - + +
815B TRP* 4.2 7.0 - + + -
825B TYR* 5.6 0.9 - - - -
842B ARG* 2.8 50.5 + - + +
843B LEU* 3.7 42.8 - - + -
854B HIS* 4.5 1.1 - - - -
857B MET* 3.1 41.8 + - + +
858B LEU* 3.2 24.6 + - + +
859B ASP 3.2 0.6 - - - -
860B CYS* 1.4 79.6 - - - +
862B GLN* 1.3 60.4 + - - +
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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