Contacts of the helix formed by residues 837 - 849 (chain B) in PDB entry 6V3O
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 ASP 837 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71B TYR* 2.5 41.2 + - - -
72B GLU* 4.8 6.8 - - - +
785B ARG* 3.0 28.7 + - + +
836B GLY* 1.3 75.0 - - - +
838B PRO* 1.3 69.7 - - - +
839B GLY 3.0 7.3 + - - -
840B ILE* 3.0 40.5 + - + +
841B ALA* 3.1 20.7 + - - +
864B TYR* 3.8 1.2 + - - -
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Residues in contact with PRO 838 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
786B PHE* 5.4 2.9 - - + -
836B GLY 4.4 0.7 - - - +
837B ASP* 1.3 87.4 - - - +
839B GLY* 1.3 58.0 + - - +
841B ALA* 3.4 7.2 + - + -
842B GLY* 2.8 24.8 + - - -
861B ARG* 3.6 25.4 - - + -
864B TYR* 3.4 39.7 - - + +
865B VAL* 4.6 14.1 - - + -
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Residues in contact with GLY 839 (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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71B TYR* 3.5 11.0 + - - -
77B THR* 4.0 22.3 - - - +
80B LEU* 5.5 0.4 - - - -
837B ASP* 3.0 8.9 + - - -
838B PRO* 1.3 79.0 - - - +
840B ILE* 1.3 57.5 + - - +
842B GLY* 3.3 3.0 + - - -
843B LEU* 3.0 24.3 + - - +
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Residues in contact with ILE 840 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B TYR* 4.1 3.6 - - + +
80B LEU* 4.1 19.1 - - + -
784B THR 3.9 7.0 - - - +
785B ARG* 3.5 28.5 - - + +
837B ASP* 3.0 33.4 + - + +
839B GLY* 1.3 73.3 - - - +
841B ALA* 1.3 66.9 + - - +
843B LEU* 2.9 21.7 + - + +
844B TYR* 3.1 27.0 + - + -
899B THR* 3.6 24.9 - - + +
902B ASN* 3.8 28.3 - - + +
903B VAL* 5.9 1.1 - - + -
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Residues in contact with ALA 841 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
784B THR* 3.6 19.9 + - - +
786B PHE* 3.7 37.9 - - + -
837B ASP 3.1 12.2 + - - +
838B PRO* 3.8 7.9 - - + +
840B ILE* 1.3 77.6 - - - +
842B GLY* 1.3 60.7 + - - +
844B TYR* 3.5 8.3 + - - +
845B ASP* 3.3 24.6 + - - +
861B ARG* 4.2 5.6 + - + +
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Residues in contact with GLY 842 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B THR* 6.0 0.4 - - - -
838B PRO 2.8 15.3 + - - -
839B GLY 3.7 4.5 - - - -
840B ILE 3.1 0.4 - - - -
841B ALA* 1.3 75.2 - - - +
843B LEU* 1.3 58.8 + - - +
845B ASP* 3.2 3.4 + - - +
846B GLU* 2.8 29.4 + - - +
861B ARG* 3.9 24.5 + - - +
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Residues in contact with LEU 843 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B THR* 4.8 14.6 - - + +
80B LEU* 4.2 14.1 - - + -
81B GLY* 5.0 9.4 - - - +
839B GLY 3.0 12.6 + - - +
840B ILE* 2.9 15.5 + - + +
842B GLY* 1.3 74.7 - - - +
844B TYR* 1.3 66.5 + - + +
846B GLU* 3.3 23.0 + - - +
847B LEU* 3.1 38.2 + - + +
902B ASN 5.5 0.9 - - - +
903B VAL* 4.1 30.5 - - + -
906B ALA* 4.8 8.3 - - + -
907B TYR* 4.5 20.2 - - + +
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Residues in contact with TYR 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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745B ALA* 3.7 27.1 - - + +
747B PRO* 4.9 1.1 - - + -
783B GLN 3.6 0.2 + - - -
784B THR* 3.8 30.3 - - + -
840B ILE* 3.1 42.1 + - + -
841B ALA* 3.6 7.9 - - - +
842B GLY 3.3 0.2 - - - -
843B LEU* 1.3 77.6 - - + +
845B ASP* 1.3 57.8 + - - +
848B LEU* 2.9 54.5 + - + +
849B VAL* 4.1 1.4 + - - +
902B ASN* 3.2 36.7 + - - -
905B GLN* 2.7 30.9 + - - +
906B ALA* 4.1 14.4 - - + -
909B LEU* 4.1 15.7 - - + -
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Residues in contact with ASP 845 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741B TYR* 2.8 41.0 + - - -
745B ALA* 3.5 14.7 - - - +
841B ALA 3.3 9.6 + - - +
842B GLY* 3.2 9.5 + - - +
844B TYR* 1.3 74.5 - - - +
846B GLU* 1.3 66.7 + - - +
849B VAL* 3.0 37.6 + - + +
854B LYS* 3.8 12.6 - - + +
857B GLY* 3.5 7.6 - - - -
861B ARG* 3.1 26.8 + - - +
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Residues in contact with GLU 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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77B THR* 5.2 5.9 - - - +
842B GLY 2.8 19.4 + - - +
843B LEU* 3.3 25.7 + - - +
845B ASP* 1.3 73.4 - - - +
847B LEU* 1.3 69.4 + - + +
849B VAL 4.9 0.7 - - - +
854B LYS* 3.0 30.2 + - - +
907B TYR* 5.4 1.2 + - - -
910B LYS* 5.5 0.3 - - - -
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Residues in contact with LEU 847 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
843B LEU* 3.1 28.5 + - + +
844B TYR* 5.0 0.7 - - - -
846B GLU* 1.3 92.8 - - - +
848B LEU* 1.3 71.9 + - + +
849B VAL 3.8 0.7 - - - -
906B ALA* 3.7 21.3 - - + +
907B TYR* 3.6 61.0 - - + +
910B LYS* 2.9 44.1 + - + +
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Residues in contact with LEU 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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744B SER* 3.2 35.9 - - - +
745B ALA 5.1 0.7 - - - -
844B TYR* 2.9 45.9 + - + +
847B LEU* 1.3 84.1 - - + +
849B VAL* 1.3 62.0 + - - +
850B ALA 3.9 1.0 + - - -
906B ALA* 3.5 22.0 - - - +
909B LEU* 3.8 22.7 - - + +
910B LYS* 3.6 26.9 - - + +
913B ARG* 3.7 13.1 + - - +
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Residues in contact with VAL 849 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741B TYR* 3.8 26.9 - - + -
744B SER* 4.0 13.9 - - - -
745B ALA* 3.8 16.8 - - + +
845B ASP* 3.0 27.9 + - - +
846B GLU 4.9 0.9 - - - +
847B LEU 5.2 0.5 - - - +
848B LEU* 1.3 79.7 - - - +
850B ALA* 1.3 79.4 + - - +
853B LEU* 3.9 29.8 - - + +
854B LYS* 3.3 23.8 - - + +
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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
------------------------------------------------------------
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