Contacts of the helix formed by residues 850 - 867 (chain A) in PDB entry 3F2B
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 PRO 850 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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845A TYR* 3.4 31.9 - - + +
848A PRO 4.2 1.6 - - - +
849A LEU* 1.3 88.6 - - + +
851A LYS* 1.3 66.6 + - - +
852A LEU* 3.2 4.5 - - + +
853A VAL* 2.9 27.5 + - + -
854A GLU* 3.0 9.0 + - - +
925A SER* 3.7 22.9 - - - +
927A PHE* 4.7 8.1 - - + -
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Residues in contact with LYS 851 (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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849A LEU 3.6 2.1 + - - -
850A PRO* 1.3 72.4 - - - +
852A LEU* 1.3 64.5 + - - +
854A GLU* 3.2 7.1 + - + +
855A GLU* 2.9 52.7 + - + +
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Residues in contact with LEU 852 (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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850A PRO* 4.8 3.1 - - + -
851A LYS* 1.3 80.2 - - - +
853A VAL* 1.3 68.2 + - + +
855A GLU* 3.5 9.4 + - - +
856A ARG* 3.2 22.1 + - + +
913A LEU* 4.9 8.3 - - + -
914A PRO* 4.1 22.0 - - + -
927A PHE* 4.3 30.5 - - + -
929A ASN* 3.8 27.4 - - - +
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Residues in contact with VAL 853 (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 ALA* 4.3 2.5 - - + -
845A TYR* 4.2 18.4 - - + -
849A LEU* 4.2 23.1 - - + -
850A PRO* 2.9 18.4 + - + +
852A LEU* 1.3 73.0 - - - +
854A GLU* 1.3 67.8 + - - +
856A ARG* 3.1 6.5 + - - +
857A LEU* 2.9 28.5 + - + +
900A PHE* 3.7 30.7 - - + -
913A LEU* 4.2 10.1 - - + -
927A PHE* 4.1 26.0 - - + -
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Residues in contact with GLU 854 (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 TYR* 3.4 28.6 + - - -
842A LYS* 6.1 0.3 - - - -
848A PRO* 5.3 4.0 - - - +
849A LEU* 4.0 32.7 + - + +
850A PRO 3.0 11.5 + - - +
851A LYS* 3.6 13.2 - - + +
853A VAL* 1.3 77.5 - - - +
855A GLU* 1.3 59.8 + - + +
857A LEU* 3.4 3.9 + - - +
858A GLU* 3.0 44.5 + - - +
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Residues in contact with GLU 855 (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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851A LYS* 2.9 45.0 + - + +
852A LEU* 4.0 7.3 + - - +
854A GLU* 1.3 77.4 - - + +
856A ARG* 1.3 64.1 + - - +
858A GLU* 4.1 7.7 - - - +
859A LYS* 3.0 29.2 + - - +
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Residues in contact with ARG 856 (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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852A LEU* 3.2 20.1 + - + +
853A VAL* 3.1 4.9 + - - +
855A GLU* 1.3 76.8 - - - +
857A LEU* 1.3 58.7 + - - +
859A LYS* 3.9 15.1 - - - +
860A GLU* 2.8 51.8 + - - +
898A SER 2.8 24.5 + - - -
900A PHE* 3.8 22.2 - - + -
912A PRO* 3.6 24.4 + - - +
913A LEU* 3.8 19.0 - - + +
914A PRO* 5.4 3.2 - - - +
958A ILE 2.7 31.1 + - - -
959A PRO* 4.7 1.4 - - - +
960A PHE* 3.2 16.3 - - - +
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Residues in contact with LEU 857 (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 SER* 4.0 21.8 - - - +
838A TYR* 3.8 26.7 - - + +
841A ALA* 3.8 18.6 - - + -
849A LEU* 3.8 28.7 - - + -
853A VAL* 2.9 17.5 + - + +
854A GLU 3.7 4.3 - - - +
856A ARG* 1.3 77.7 - - - +
858A GLU* 1.3 58.6 + - - +
860A GLU* 4.5 2.0 - - - -
861A LEU* 2.8 40.3 + - + +
900A PHE* 3.8 23.3 - - + -
901A VAL* 4.0 19.1 - - + -
904A MET* 4.7 0.7 - - + -
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Residues in contact with GLU 858 (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 TYR* 3.2 20.4 - - - +
854A GLU* 3.0 36.2 + - - +
855A GLU* 4.2 6.6 - - - +
857A LEU* 1.3 76.4 - - - +
859A LYS* 1.3 62.0 - - - +
861A LEU* 4.4 3.2 - - - +
862A LYS* 3.4 34.6 + - - +
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Residues in contact with LYS 859 (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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855A GLU 3.0 19.1 + - - +
856A ARG* 4.1 18.3 - - - +
858A GLU* 1.3 76.0 - - - +
860A GLU* 1.3 68.4 + - - +
862A LYS* 3.7 10.6 - - - +
863A SER* 3.5 18.5 + - - -
960A PHE* 3.8 31.6 - - + +
961A GLU* 3.3 26.3 + - - -
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Residues in contact with GLU 860 (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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856A ARG* 2.8 48.6 + - - +
859A LYS* 1.3 80.8 - - - +
861A LEU* 1.3 57.4 + - - +
863A SER* 3.2 4.5 + - - -
864A ILE* 3.0 34.4 + - + +
899A SER* 2.6 9.1 + - - -
900A PHE* 2.7 12.5 + - - -
901A VAL* 2.5 44.2 + - + +
960A PHE* 3.0 46.1 - - + -
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Residues in contact with LEU 861 (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 ILE* 3.9 22.7 - - + -
834A ARG* 3.7 25.4 - - + +
837A SER* 3.8 17.5 - - - +
838A TYR* 3.5 34.3 - - + +
857A LEU* 2.8 24.8 + - + +
858A GLU* 4.4 2.7 - - - +
860A GLU* 1.3 74.1 - - - +
862A LYS* 1.3 62.7 + - - +
864A ILE* 4.6 4.3 - - + +
865A ILE* 3.0 42.9 + - + +
901A VAL* 3.9 18.2 - - + -
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Residues in contact with LYS 862 (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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858A GLU* 3.4 25.2 + - - +
859A LYS* 3.7 9.8 - - - +
860A GLU 3.3 0.2 - - - -
861A LEU* 1.3 80.0 - - - +
863A SER* 1.3 60.2 + - - +
865A ILE* 4.8 4.0 - - - -
866A GLY* 3.1 23.6 + - - -
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Residues in contact with SER 863 (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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859A LYS 3.5 6.5 + - - -
860A GLU 3.2 7.9 + - - -
861A LEU 3.2 0.6 - - - -
862A LYS* 1.3 82.1 - - - +
864A ILE* 1.3 65.8 + - - +
867A HIS* 3.1 50.9 + - - +
960A PHE* 3.8 18.8 - - - -
964A LEU* 3.7 14.3 - - - +
965A GLY 5.3 2.4 + - - -
968A GLY* 5.2 0.7 - - - -
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Residues in contact with ILE 864 (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 ILE* 5.1 4.7 - - + -
860A GLU 3.0 18.8 + - - +
861A LEU* 4.1 4.9 - - + +
863A SER* 1.3 75.5 - - - +
865A ILE* 1.3 63.5 + - + +
867A HIS 3.9 0.3 - - - -
868A GLY 3.3 1.7 + - - -
869A PHE* 2.8 31.6 + - + +
870A ALA* 3.8 18.2 - - + +
873A TYR* 3.4 55.0 - - + +
899A SER* 4.1 3.6 - - - +
901A VAL* 3.8 31.2 - - + -
960A PHE* 3.9 13.0 - - + -
964A LEU* 4.2 10.8 - - + -
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Residues in contact with ILE 865 (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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830A ASP* 3.7 53.5 - - + +
833A ILE* 5.5 1.1 - - + -
834A ARG* 5.0 7.2 - - + -
861A LEU* 3.0 41.2 + - + +
862A LYS* 4.5 2.9 - - - +
864A ILE* 1.3 78.7 - - + +
866A GLY* 1.3 61.3 + - - +
868A GLY* 2.9 20.1 + - - -
870A ALA* 4.2 15.9 - - + -
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Residues in contact with GLY 866 (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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862A LYS 3.1 21.4 + - - -
863A SER* 5.1 0.2 - - - -
865A ILE* 1.3 81.3 - - - +
867A HIS* 1.3 65.8 + - - +
868A GLY 3.2 0.9 + - - -
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Residues in contact with HIS 867 (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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821A LEU* 4.6 5.0 - - - +
823A THR* 3.6 8.0 + - - -
863A SER* 3.1 43.6 + - - +
866A GLY* 1.3 79.3 + - - +
868A GLY* 1.3 61.4 + - - +
869A PHE* 3.3 27.2 - - + -
964A LEU* 4.5 5.2 - - + -
966A PHE 5.2 1.4 + - - -
967A LYS 3.2 23.5 + - - -
968A GLY* 3.3 32.2 + - - +
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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