Contacts of the helix formed by residues 837 - 849 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A TYR* 2.3 39.6 + - - -
72A GLU* 4.5 5.2 - - - +
785A ARG* 3.0 34.5 + - + +
836A GLY* 1.3 75.4 - - - +
838A PRO* 1.3 71.5 - - - +
839A GLY 3.1 3.7 + - - -
840A ILE* 2.8 33.9 + - + +
841A ALA* 3.1 18.4 + - - +
864A TYR* 3.7 1.6 + - - -
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Residues in contact with PRO 838 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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786A PHE* 5.2 2.9 - - + -
836A GLY 4.4 0.9 - - - +
837A ASP* 1.3 84.7 - - - +
839A GLY* 1.3 56.7 + - - +
841A ALA* 3.4 8.2 + - + -
842A GLY* 2.9 26.9 + - - -
861A ARG* 3.7 26.6 - - + -
864A TYR* 3.5 39.2 - - + +
865A VAL* 5.1 9.9 - - + -
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Residues in contact with GLY 839 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A TYR* 3.8 9.2 + - - -
77A THR* 5.0 15.9 - - - +
80A LEU* 4.4 6.4 - - - +
837A ASP* 3.1 8.9 + - - -
838A PRO* 1.3 80.0 - - - +
840A ILE* 1.3 61.0 + - - +
842A GLY* 3.2 3.5 + - - -
843A LEU* 3.2 19.8 + - - +
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Residues in contact with ILE 840 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A TYR* 3.6 14.1 - - + +
80A LEU* 4.1 14.6 - - + -
785A ARG* 3.6 20.9 - - + +
837A ASP* 2.8 31.4 + - + +
839A GLY* 1.3 70.2 - - - +
841A ALA* 1.3 65.3 + - - +
843A LEU* 3.1 15.1 + - + +
844A TYR* 3.2 27.3 + - + -
899A THR* 3.6 40.6 - - + +
902A ASN* 3.6 31.9 - - + +
903A VAL* 5.4 2.2 - - + +
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Residues in contact with ALA 841 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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784A THR* 3.5 21.3 + - - +
786A PHE* 3.6 37.0 - - + -
837A ASP 3.1 11.8 + - - +
838A PRO* 3.8 8.1 - - + +
840A ILE* 1.3 77.2 - - - +
842A GLY* 1.3 60.2 + - - +
844A TYR* 3.5 9.1 + - - +
845A ASP* 3.3 23.0 + - - +
861A ARG* 4.3 4.7 + - - +
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Residues in contact with GLY 842 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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838A PRO 2.9 15.2 + - - -
839A GLY* 3.2 5.1 + - - -
840A ILE 3.1 0.4 - - - -
841A ALA* 1.3 74.2 - - - +
843A LEU* 1.3 60.3 + - - +
845A ASP* 3.3 4.6 + - - +
846A GLU* 2.9 26.0 + - - +
861A ARG* 3.9 24.9 + - - +
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Residues in contact with LEU 843 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A THR* 5.6 8.3 - - + -
80A LEU* 4.2 34.3 - - + -
81A GLY* 5.3 3.8 - - - -
839A GLY 3.2 10.7 + - - +
840A ILE* 3.1 12.1 + - + +
842A GLY* 1.3 77.4 - - - +
844A TYR* 1.3 64.9 + - + +
845A ASP 3.1 0.2 - - - -
846A GLU* 4.1 20.6 - - - +
847A LEU* 3.1 44.5 + - + +
902A ASN 5.8 0.2 - - - -
903A VAL* 4.3 19.7 - - + -
906A ALA* 4.6 4.5 - - + -
907A TYR* 4.2 25.1 - - + +
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Residues in contact with TYR 844 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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745A ALA* 3.8 20.8 - - - +
746A THR* 5.4 0.2 - - - -
747A PRO* 5.1 0.7 - - + -
783A GLN 3.6 0.3 + - - -
784A THR* 3.7 33.0 - - + -
840A ILE* 3.2 33.6 + - + -
841A ALA* 3.5 8.7 - - - +
843A LEU* 1.3 77.8 - - + +
845A ASP* 1.3 62.3 + - - +
848A LEU* 3.1 42.1 + - + +
849A VAL* 4.1 1.9 + - - +
902A ASN* 3.0 47.9 + - - -
905A GLN* 2.6 30.6 + - - +
906A ALA* 4.0 26.7 - - + -
909A LEU* 4.1 9.9 - - + -
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Residues in contact with ASP 845 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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741A TYR* 2.8 34.0 + - - -
745A ALA* 3.5 17.3 - - - +
841A ALA 3.3 6.9 + - - +
842A GLY* 3.3 12.5 + - - +
843A LEU 3.1 0.4 - - - -
844A TYR* 1.3 80.0 - - - +
846A GLU* 1.3 62.3 + - - +
849A VAL* 3.0 43.4 + - + +
854A LYS* 3.9 14.2 - - + +
857A GLY* 3.6 6.9 - - - -
861A ARG* 3.0 26.4 + - - +
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Residues in contact with GLU 846 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A THR* 5.4 7.4 - - - +
842A GLY 2.9 15.7 + - - +
843A LEU* 3.2 24.1 + - + +
845A ASP* 1.3 76.5 - - - +
847A LEU* 1.3 65.3 + - + +
849A VAL 5.0 0.3 - - - +
854A LYS* 4.2 25.3 + - - +
907A TYR* 5.6 0.5 + - - -
910A LYS* 5.4 0.3 + - - -
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Residues in contact with LEU 847 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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843A LEU* 3.1 27.0 + - + +
846A GLU* 1.3 87.9 - - - +
848A LEU* 1.3 71.2 + - + +
849A VAL 3.8 1.2 - - - +
906A ALA* 3.5 36.1 - - + +
907A TYR* 3.7 48.5 - - + +
910A LYS* 3.1 44.8 + - + +
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Residues in contact with LEU 848 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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744A SER* 3.5 30.8 + - - +
745A ALA 5.5 0.7 - - - -
844A TYR* 3.1 30.4 + - + +
847A LEU* 1.3 82.2 - - + +
849A VAL* 1.3 64.9 + - - +
850A ALA 3.9 0.9 + - - -
906A ALA* 4.1 6.5 - - - +
909A LEU* 3.9 29.4 - - + -
910A LYS* 3.4 46.7 - - + +
913A ARG* 3.6 22.5 + - - +
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Residues in contact with VAL 849 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741A TYR* 4.0 21.1 - - + -
744A SER* 4.1 9.9 - - - -
745A ALA* 4.0 15.7 - - + -
844A TYR 4.3 0.2 - - - +
845A ASP* 3.0 43.5 + - - +
846A GLU 5.0 0.5 - - - +
847A LEU 5.1 0.9 - - - +
848A LEU* 1.3 79.7 + - - +
850A ALA* 1.3 76.7 + - - +
851A GLU 3.6 0.3 + - - -
853A LEU* 3.7 22.0 - - + -
854A LYS* 3.2 26.8 - - + -
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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
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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