Contacts of the helix formed by residues 835 - 848 (chain A) in PDB entry 6FF7
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 835 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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829A PRO 5.7 0.2 - - - +
830A LEU 5.5 3.4 - - - +
832A TYR* 3.3 37.0 - - + +
833A LYS 3.1 4.6 + - - +
834A HIS* 1.3 73.3 - - - +
836A THR* 1.3 65.7 + - - +
837A LYS 3.3 1.1 - - - -
838A LEU* 3.7 5.5 + - - +
839A LEU* 3.7 17.5 + - - +
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Residues in contact with THR 836 (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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833A LYS 5.0 0.2 + - - -
835A ASP* 1.3 77.7 - - - +
837A LYS* 1.3 59.0 + - - +
838A LEU 3.1 0.4 - - - -
839A LEU* 3.1 7.3 + - - +
840A ILE* 3.0 34.4 + - - +
874A PRO* 5.4 12.1 - - - -
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Residues in contact with LYS 837 (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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834A HIS* 4.4 22.2 - - + +
835A ASP 3.3 1.2 - - - +
836A THR* 1.3 78.3 - - - +
838A LEU* 1.3 56.4 + - - +
840A ILE* 4.5 4.6 - - - +
841A LEU* 4.0 14.1 + - - +
1428A HIS 5.1 3.8 - - - +
1429A THR* 4.3 32.0 - - - +
1432A TYR* 4.7 10.7 - - + +
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Residues in contact with LEU 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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834A HIS 4.2 9.3 + - - +
835A ASP 3.7 7.4 + - - +
836A THR 3.1 0.4 - - - -
837A LYS* 1.3 77.7 - - - +
839A LEU* 1.3 59.5 + - - +
840A ILE 3.3 2.0 - - - -
841A LEU* 3.3 7.6 + - - +
842A ALA* 3.0 27.4 + - - +
921A TYR* 5.4 4.5 - - + +
924A GLN* 4.0 30.8 - - + +
925A TYR* 4.9 4.7 - - + +
1432A TYR* 5.6 8.1 - - + +
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Residues in contact with LEU 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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835A ASP 3.7 10.6 + - - +
836A THR* 3.1 11.1 + - - +
838A LEU* 1.3 77.4 - - - +
840A ILE* 1.3 58.6 + - - +
842A ALA* 3.3 8.2 + - - +
843A LEU* 2.9 29.3 + - - +
874A PRO* 6.0 3.4 - - + +
878A LEU* 6.0 7.2 - - + -
921A TYR* 5.1 12.3 - - + +
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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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836A THR 3.0 16.5 + - - +
837A LYS* 5.1 3.6 - - - +
839A LEU* 1.3 73.4 - - - +
841A LEU* 1.3 59.5 + - - +
843A LEU* 3.4 6.0 + - - +
844A GLU* 2.9 31.4 + - - +
418C MET* 5.8 0.8 - - - +
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Residues in contact with LEU 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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837A LYS 4.0 14.1 + - - +
838A LEU* 3.3 13.2 + - - +
840A ILE* 1.3 78.7 - - - +
842A ALA* 1.3 56.9 + - - +
844A GLU* 3.4 5.1 + - - +
845A ARG* 2.9 29.8 + - - +
924A GLN* 5.3 5.2 - - + -
1429A THR* 5.3 5.4 - - - +
1432A TYR 5.6 2.0 - - - +
1433A ASP* 5.1 17.5 - - + -
418C MET* 6.0 3.8 - - - -
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Residues in contact with ALA 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 LEU 3.0 16.0 + - - +
839A LEU* 3.7 6.1 - - - +
841A LEU* 1.3 75.3 - - - +
843A LEU* 1.3 57.2 + - - +
845A ARG* 3.3 7.8 + - - +
846A LEU* 3.0 27.5 + - - +
917A ILE* 5.2 1.1 - - - +
920A ALA* 3.7 43.8 - - + +
921A TYR* 3.9 6.5 - - + +
924A GLN* 4.5 3.8 - - + +
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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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839A LEU 2.9 17.6 + - - +
840A ILE* 3.9 6.7 - - - +
841A LEU 3.3 0.2 - - - -
842A ALA* 1.3 78.3 - - - +
844A GLU* 1.3 56.9 + - - +
846A LEU* 3.3 7.7 + - - +
847A LYS* 2.9 28.0 + - - +
867A ILE* 5.3 19.4 - - + +
870A ALA* 5.8 6.3 - - + -
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Residues in contact with GLU 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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840A ILE 2.9 17.8 + - - +
841A LEU* 4.0 3.4 - - - +
843A LEU* 1.3 74.3 - - - +
845A ARG* 1.3 60.7 + - - +
847A LYS* 3.8 7.5 - - - +
848A GLU* 2.9 30.5 + - - +
418C MET* 3.8 35.8 - - + +
419C ASP* 5.5 2.3 - - - -
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Residues in contact with ARG 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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841A LEU 2.9 19.0 + - - +
842A ALA* 3.4 9.9 - - - +
844A GLU* 1.3 77.7 - - - +
846A LEU* 1.3 58.0 + - - +
848A GLU* 3.9 13.3 + - - +
849A ALA* 4.4 5.0 + - - +
920A ALA* 6.4 0.2 - - + -
418C MET 5.2 0.6 + - - -
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Residues in contact with LEU 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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842A ALA 3.0 13.3 + - - +
843A LEU* 3.7 9.2 - - - +
844A GLU 3.3 0.2 - - - -
845A ARG* 1.3 76.4 - - - +
847A LYS* 1.3 62.4 + - - +
848A GLU 3.5 0.2 + - - -
849A ALA* 3.6 16.0 + - - +
850A TYR* 4.5 3.6 + - - +
867A ILE* 5.8 7.0 - - + -
920A ALA* 6.1 2.9 - - + -
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Residues in contact with LYS 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 2.9 16.9 + - - +
844A GLU* 3.2 10.4 + - - +
846A LEU* 1.3 74.9 - - - +
848A GLU* 1.3 64.5 + - - +
849A ALA 3.2 0.2 - - - -
850A TYR* 3.2 25.2 + - - +
867A ILE* 5.9 6.3 - - + -
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Residues in contact with GLU 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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844A GLU 2.9 15.9 + - - +
845A ARG* 4.0 10.1 - - - +
846A LEU 3.3 0.4 - - - -
847A LYS* 1.3 76.9 - - - +
849A ALA* 1.3 56.3 + - - +
850A TYR 3.1 9.0 + - - -
851A SER* 4.4 2.3 + - - -
419C ASP* 5.3 14.6 - - + -
420C SER* 5.4 5.6 - - - +
423C ALA* 4.0 15.3 - - - +
424C GLY* 3.9 23.7 + - - +
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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