Contacts of the helix formed by residues 840 - 853 (chain B) in PDB entry 5MQF
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 ALA 840 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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839B PRO* 1.3 75.9 - - - +
841B ASP* 1.3 59.0 + - - +
843B VAL* 3.1 7.5 + - - +
844B SER* 2.9 29.1 + - - -
869B TYR* 4.5 4.8 - - + +
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Residues in contact with ASP 841 (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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839B PRO* 3.4 6.1 - - + +
840B ALA* 1.3 77.9 - - - +
842B CYS* 1.3 56.9 + - - +
844B SER* 3.2 7.5 + - - -
845B ALA* 2.9 27.7 + - - +
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Residues in contact with CYS 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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838B ALA* 3.6 24.4 - - + +
839B PRO* 3.5 17.8 + - + +
840B ALA 3.4 0.4 - - - -
841B ASP* 1.3 77.7 - - - +
843B VAL* 1.3 58.0 + - - +
845B ALA* 3.8 9.2 - - - +
846B VAL* 2.9 27.5 + - - +
891B THR* 4.3 24.0 - - - +
894B GLN* 4.8 3.8 - - + -
895B ALA* 4.6 2.6 - - + +
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Residues in contact with VAL 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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838B ALA* 4.8 4.9 - - + +
839B PRO 2.8 19.7 + - - +
840B ALA* 3.1 9.6 + - - +
842B CYS* 1.3 75.2 - - - +
844B SER* 1.3 60.1 + - - +
846B VAL* 3.2 7.6 + - - +
847B TYR* 2.9 26.7 + - - +
869B TYR* 4.4 13.0 - - + +
871B ILE* 5.7 9.9 - - + -
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Residues in contact with SER 844 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
840B ALA 2.9 12.6 + - - -
841B ASP* 3.7 9.2 - - - -
843B VAL* 1.3 75.5 - - - +
845B ALA* 1.3 58.5 + - - +
847B TYR* 3.2 8.9 + - - +
848B THR* 2.9 26.5 + - - -
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Residues in contact with ALA 845 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
841B ASP 2.9 16.5 + - - +
842B CYS* 3.9 9.6 - - - +
844B SER* 1.3 76.7 - - - +
846B VAL* 1.3 57.2 + - - +
848B THR* 3.2 9.1 + - - -
849B VAL* 2.9 26.7 + - - +
890B HIS* 5.0 19.4 - - + +
891B THR* 5.8 2.0 - - - -
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Residues in contact with VAL 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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836B VAL* 5.4 10.8 - - + -
842B CYS 2.9 19.0 + - - +
843B VAL* 3.2 9.6 + - - +
845B ALA* 1.3 73.6 - - - +
847B TYR* 1.3 60.5 + - - +
849B VAL* 3.2 8.7 + - - +
850B LEU* 2.9 28.6 + - - +
871B ILE* 6.5 0.9 - - + -
887B LEU* 6.0 6.7 - - + +
895B ALA* 5.4 8.7 - - + -
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Residues in contact with TYR 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 VAL 2.9 13.1 + - - +
844B SER* 3.2 11.2 + - - +
846B VAL* 1.3 77.4 - - - +
848B THR* 1.3 55.9 + - - +
850B LEU* 3.5 6.8 + - - +
851B ALA* 2.9 28.1 + - - +
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Residues in contact with THR 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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844B SER 2.9 12.7 + - - -
845B ALA* 3.2 13.4 + - - -
847B TYR* 1.3 73.7 - - - +
849B VAL* 1.3 61.2 + - - +
851B ALA* 3.4 8.0 + - - +
852B ARG* 2.9 26.9 + - - +
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Residues in contact with VAL 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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845B ALA 2.9 13.6 + - - +
846B VAL* 3.2 11.4 + - - +
848B THR* 1.3 74.6 - - - +
850B LEU* 1.3 60.5 + - - +
852B ARG* 3.1 8.7 + - - +
853B ARG* 2.9 28.1 + - - +
886B ASP* 5.6 6.7 - - + +
887B LEU* 5.5 13.7 - - + +
890B HIS* 5.7 6.1 - - + -
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Residues in contact with LEU 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 VAL 2.9 17.1 + - - +
847B TYR* 3.8 7.2 - - - +
849B VAL* 1.3 75.1 - - - +
851B ALA* 1.3 57.2 + - - +
853B ARG* 3.3 5.4 + - - +
854B ARG 2.8 6.6 + - - -
855B GLY* 2.6 47.5 + - - +
857B VAL* 5.5 10.3 - - + -
873B ALA* 5.9 5.2 - - + -
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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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847B TYR 2.9 18.7 + - - +
848B THR* 3.6 8.7 - - - +
850B LEU* 1.3 75.0 - - - +
852B ARG* 1.3 65.1 + - - +
854B ARG* 3.1 14.3 + - - +
855B GLY 5.0 2.0 - - - -
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Residues in contact with ARG 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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848B THR 2.9 14.9 + - - +
849B VAL* 3.1 11.6 + - - +
851B ALA* 1.3 77.6 - - - +
853B ARG* 1.3 58.8 + - - +
854B ARG* 3.5 1.6 + - - +
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Residues in contact with ARG 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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849B VAL 2.9 14.7 + - - +
850B LEU* 3.9 6.7 - - - +
852B ARG* 1.3 74.8 - - - +
854B ARG* 1.3 68.9 + - - +
855B GLY* 3.1 3.8 + - - +
876B PRO* 4.7 0.7 - - - +
879B ASP* 3.4 43.9 - - + +
883B PHE* 6.6 0.4 - - + -
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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