Contacts of the helix formed by residues 854 - 864 (chain A) in PDB entry 3B7B
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 HIS 854 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A SO4 3.5 12.0 + - - +
816A ALA 3.6 8.1 - - - -
817A LYS 3.5 8.5 + - - -
818A LYS* 3.6 13.5 - - - -
819A GLY* 3.5 27.5 + - - +
849A ALA* 2.8 19.4 + - + +
852A TYR* 3.4 38.4 + - + +
853A LYS* 1.3 69.4 + - - +
855A VAL* 1.3 65.3 + - - +
856A ASP 3.5 2.0 - - - -
857A LEU* 2.9 30.3 + - + +
858A VAL* 3.2 8.3 + - - +
890A ILE* 4.2 2.0 - - - +
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Residues in contact with VAL 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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7A SO4 2.9 23.9 + - - +
853A LYS 3.1 6.4 + - - +
854A HIS* 1.3 70.5 - - - +
856A ASP* 1.3 63.3 + - - +
858A VAL* 2.9 22.7 + - - +
859A LYS* 3.1 18.2 + - - +
887A CYS* 4.1 11.9 - - - -
889A ASP* 4.5 17.7 - - + +
890A ILE* 4.0 23.1 - - + -
893A ILE* 4.2 21.3 - - + +
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Residues in contact with ASP 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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7A SO4 2.7 32.7 + - - +
821A TYR* 3.4 26.6 - - + -
855A VAL* 1.3 81.5 - - - +
857A LEU* 1.3 57.0 + - - +
858A VAL 3.3 0.2 - - - -
859A LYS* 3.4 25.0 + - + +
860A LEU 2.9 22.2 + - - -
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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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7A SO4 4.4 1.2 + - - -
816A ALA* 3.2 47.3 - - + +
819A GLY* 3.7 12.6 - - - +
820A HIS 4.2 0.7 - - - -
821A TYR* 3.8 39.4 - - + +
824A VAL* 4.2 15.7 - - + -
849A ALA* 3.6 14.1 - - + -
854A HIS* 2.9 20.2 + - + +
856A ASP* 1.3 75.9 - - - +
858A VAL* 1.3 59.5 + - - +
860A LEU* 3.4 4.5 + - + +
861A LEU* 2.8 42.5 + - + +
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Residues in contact with VAL 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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846A MET* 3.8 24.7 - - + -
849A ALA* 4.2 14.8 - - + -
850A THR* 3.6 20.4 - - - +
854A HIS 3.2 11.1 + - - +
855A VAL* 2.9 8.5 + - - +
857A LEU* 1.3 73.7 - - - +
859A LYS* 1.3 60.3 + - - +
861A LEU* 3.8 6.3 - - - +
862A LEU* 2.9 28.6 + - + +
890A ILE* 4.0 21.3 - - + -
893A ILE* 4.2 13.5 - - + -
894A LEU* 3.9 18.4 - - + -
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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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821A TYR* 6.0 0.2 - - - +
855A VAL* 3.1 20.3 + - - +
856A ASP* 3.4 26.5 - - + +
857A LEU 3.2 0.2 - - - -
858A VAL* 1.3 77.5 - - - +
860A LEU* 1.3 52.4 + - - +
862A LEU* 3.0 6.9 + - - +
863A SER* 2.7 37.8 + - - -
893A ILE* 3.3 37.9 - - + +
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Residues in contact with LEU 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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821A TYR* 3.5 37.9 + - + +
824A VAL* 3.8 28.0 - - + -
825A GLN* 3.7 34.8 - - + +
828A LEU* 4.6 7.0 - - + -
856A ASP 2.9 18.5 + - - +
857A LEU* 3.6 6.5 - - + +
859A LYS* 1.3 77.3 - - - +
861A LEU* 1.3 63.3 + - - +
863A SER* 2.9 25.6 + - - +
864A LYS* 3.1 23.6 + - + +
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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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812A LEU* 5.1 3.6 - - + -
816A ALA* 4.9 4.0 - - + -
824A VAL* 3.9 26.2 - - + -
828A LEU* 4.1 15.5 - - + -
835A VAL* 4.5 11.3 - - + +
845A PRO* 3.5 22.4 - - + +
846A MET* 3.4 38.4 - - + +
849A ALA* 4.5 7.6 - - + -
857A LEU* 2.8 30.8 + - + +
858A VAL* 3.9 4.5 - - - +
860A LEU* 1.3 73.3 - - - +
862A LEU* 1.3 60.0 + - - +
864A LYS 3.5 1.9 + - - -
865A GLY 3.4 5.0 + - - -
866A SER* 2.8 38.6 + - - +
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Residues in contact with LEU 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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846A MET* 3.7 15.3 - - - -
858A VAL 2.9 18.1 + - - +
859A LYS* 3.0 5.1 + - - +
861A LEU* 1.3 73.2 - - - +
863A SER* 1.3 54.4 + - - +
864A LYS 2.7 15.3 + - - -
865A GLY* 3.0 12.5 + - - -
866A SER* 3.7 15.8 + - - +
868A ILE* 3.6 26.9 - - + -
893A ILE* 3.6 38.8 - - + +
894A LEU* 4.3 6.7 - - + -
897A ALA* 4.1 15.0 - - + -
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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 2.7 17.2 + - - -
860A LEU* 2.9 24.5 + - - +
862A LEU* 1.3 71.2 - - - +
864A LYS* 1.3 67.9 + - - +
865A GLY 3.7 0.4 - - - -
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Residues in contact with LYS 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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825A GLN* 5.6 8.3 - - - +
828A LEU* 3.9 34.1 - - + -
829A SER* 4.9 18.2 - - - +
835A VAL* 3.9 15.3 - - - +
860A LEU* 3.1 22.0 + - + +
861A LEU 3.7 3.8 - - - +
862A LEU 2.7 6.3 + - - -
863A SER* 1.3 88.0 + - - +
865A GLY* 1.3 55.7 + - - -
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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