Contacts of the helix formed by residues 837 - 849 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71G TYR* 2.6 38.2 + - - -
72G GLU* 5.2 4.9 - - - +
785G ARG* 3.0 36.8 + - + +
836G GLY* 1.3 74.2 - - - +
838G PRO* 1.3 74.2 - - - +
839G GLY 3.3 1.9 + - - -
840G ILE* 2.9 33.5 + - + +
841G ALA* 3.2 20.6 + - - +
864G TYR* 3.8 1.2 + - - -
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Residues in contact with PRO 838 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
786G PHE* 5.4 2.9 - - + -
836G GLY 4.4 1.1 - - - +
837G ASP* 1.3 86.5 - - - +
839G GLY* 1.3 57.9 + - - +
841G ALA* 3.3 8.2 + - + +
842G GLY* 2.8 27.2 + - - -
858G LYS* 5.9 2.0 - - - +
861G ARG* 3.7 21.5 - - + -
864G TYR* 3.5 39.2 - - + +
865G VAL* 4.8 12.1 - - + -
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Residues in contact with GLY 839 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71G TYR* 3.5 17.4 + - - -
77G THR* 4.3 19.8 - - - +
80G LEU* 5.3 1.3 - - - -
837G ASP* 3.2 4.0 + - - -
838G PRO* 1.3 80.8 - - - +
840G ILE* 1.3 57.4 + - - +
842G GLY* 3.3 2.9 + - - -
843G LEU* 2.9 24.6 + - - +
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Residues in contact with ILE 840 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71G TYR* 4.0 11.2 - - + +
72G GLU* 4.8 0.2 - - - +
80G LEU* 4.2 9.2 - - + -
784G THR 4.2 0.2 - - - -
785G ARG* 3.4 34.1 - - + +
837G ASP* 2.9 25.8 + - + +
838G PRO 3.3 0.2 - - - -
839G GLY* 1.3 73.4 - - - +
841G ALA* 1.3 66.6 + - - +
843G LEU* 3.1 22.4 + - + +
844G TYR* 3.1 31.5 + - + -
899G THR* 3.6 28.5 - - + +
902G ASN* 3.6 27.8 - - + -
903G VAL* 5.2 1.3 - - + +
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Residues in contact with ALA 841 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
784G THR* 3.6 21.1 + - - +
786G PHE* 3.7 35.9 - - + -
837G ASP 3.2 11.6 + - - +
838G PRO* 3.6 9.0 - - + +
840G ILE* 1.3 77.2 - - - +
842G GLY* 1.3 59.4 + - - +
844G TYR* 3.4 9.5 + - - +
845G ASP* 3.2 24.1 + - - +
861G ARG* 4.2 5.6 + - - +
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Residues in contact with GLY 842 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
838G PRO 2.8 15.3 + - - -
839G GLY* 3.3 4.5 + - - -
840G ILE 3.2 0.2 - - - -
841G ALA* 1.3 73.2 - - - +
843G LEU* 1.3 60.5 + - - +
845G ASP* 3.3 3.2 + - - +
846G GLU* 3.0 32.6 + - - +
861G ARG* 3.8 25.5 + - - +
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Residues in contact with LEU 843 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77G THR* 5.0 17.0 - - + +
80G LEU* 4.1 27.1 - - + -
81G GLY* 5.0 8.7 - - - +
839G GLY 2.9 13.2 + - - +
840G ILE* 3.1 16.3 + - + +
842G GLY* 1.3 72.7 - - - +
844G TYR* 1.3 67.1 + - + +
846G GLU* 2.8 20.6 + - + +
847G LEU* 3.0 41.1 - - + +
903G VAL* 4.2 23.3 - - + -
906G ALA* 4.9 6.1 - - + -
907G TYR* 4.6 17.0 - - + +
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Residues in contact with TYR 844 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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745G ALA 3.7 26.9 - - - +
747G PRO* 5.0 1.1 - - + -
784G THR* 3.9 23.8 - - + -
840G ILE* 3.1 39.9 + - + -
841G ALA* 3.5 8.3 - - - +
843G LEU* 1.3 73.4 - - + +
845G ASP* 1.3 63.1 + - - +
848G LEU* 3.1 43.6 + - + +
849G VAL* 4.6 1.5 - - - +
902G ASN* 3.0 46.1 + - - -
905G GLN* 2.3 38.6 + - - +
906G ALA* 4.2 20.9 - - + -
909G LEU* 4.2 11.7 - - + -
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Residues in contact with ASP 845 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741G TYR* 2.8 42.0 + - - -
745G ALA* 3.7 12.1 - - - +
841G ALA 3.2 8.5 + - - +
842G GLY* 3.5 9.4 - - - +
843G LEU 3.1 0.8 - - - -
844G TYR* 1.3 76.6 - - - +
846G GLU* 1.3 65.9 + - - +
849G VAL* 3.1 34.0 + - + +
854G LYS* 3.8 15.6 - - + +
857G GLY* 3.5 7.1 - - - -
861G ARG* 2.9 29.7 + - - +
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Residues in contact with GLU 846 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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842G GLY 3.0 15.1 + - - +
843G LEU* 2.8 23.0 + - + +
845G ASP* 1.3 74.0 - - - +
847G LEU* 1.3 69.6 + - + +
849G VAL 4.8 0.7 - - - +
851G GLU* 5.2 1.4 - - - +
854G LYS* 2.8 45.7 + - - +
861G ARG* 5.6 2.9 + - - -
910G LYS* 5.6 0.2 + - - -
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Residues in contact with LEU 847 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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843G LEU* 3.0 58.4 + - + +
846G GLU* 1.3 87.5 - - + +
848G LEU* 1.3 72.2 + - + +
849G VAL 3.8 0.9 - - - -
906G ALA* 4.5 9.4 - - + +
907G TYR* 4.3 37.2 - - + +
910G LYS* 3.0 48.9 + - + +
917G PHE* 6.4 2.0 - - + -
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Residues in contact with LEU 848 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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744G SER* 3.2 33.0 - - - +
844G TYR* 3.1 40.7 + - + +
847G LEU* 1.3 93.8 - - + +
849G VAL* 1.3 62.4 + - - +
850G ALA 3.9 1.0 + - - -
906G ALA* 3.8 19.1 - - + +
909G LEU* 4.0 10.3 - - + +
910G LYS* 3.5 36.1 - - + +
913G ARG* 3.6 24.5 + - - +
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Residues in contact with VAL 849 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741G TYR* 3.9 21.1 - - + -
744G SER* 3.8 15.9 - - - +
745G ALA* 3.8 30.3 - - + +
845G ASP* 3.1 25.3 + - - +
846G GLU 4.8 0.9 - - - +
847G LEU 5.3 0.3 - - - -
848G LEU* 1.3 79.5 - - - +
850G ALA* 1.3 79.4 + - - +
851G GLU 3.6 0.2 + - - -
853G LEU* 4.0 11.0 - - + -
854G LYS* 3.3 36.5 + - + +
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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