Contacts of the helix formed by residues 852 - 864 (chain A) in PDB entry 3BWT
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 ASN 852 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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813A GLU* 3.2 29.3 + - + +
848A SER* 2.8 21.2 + - - +
849A HIS 4.6 0.4 - - - -
850A LYS 3.7 0.8 - - - -
851A GLN* 1.3 82.7 + - + +
853A ASP* 1.3 59.0 + - - +
854A TYR* 3.0 26.1 + - - +
855A LEU* 3.0 30.2 + - + +
856A TYR 2.9 20.1 + - - -
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Residues in contact with ASP 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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848A SER 4.6 0.2 - - - -
849A HIS* 4.2 15.6 + - - +
851A GLN 6.0 0.2 - - - -
852A ASN* 1.3 72.8 + - - +
854A TYR* 1.3 62.6 + - - +
856A TYR* 4.3 8.2 - - - +
857A LYS* 3.0 37.8 + - + +
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Residues in contact with TYR 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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817A LEU* 5.4 3.2 - - + +
852A ASN* 3.0 11.7 + - - +
853A ASP* 1.3 79.1 - - - +
855A LEU* 1.3 89.6 + - + +
857A LYS* 4.3 3.1 - - - +
858A ARG* 3.1 57.2 + - + +
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Residues in contact with LEU 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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813A GLU* 3.9 30.1 - - + +
816A ILE* 4.2 18.4 - - + -
817A LEU* 4.2 18.8 - - + -
820A LEU* 3.5 24.4 - - + +
848A SER* 4.2 11.2 - - - -
852A ASN* 3.0 38.9 + - + +
854A TYR* 1.3 98.3 - - + +
856A TYR* 1.3 59.2 + - - +
858A ARG* 3.2 3.6 + - - +
859A LEU* 2.8 34.0 + - - +
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Residues in contact with TYR 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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845A LEU* 3.5 19.5 - - + -
848A SER* 3.4 21.7 - - - +
849A HIS* 3.4 42.8 - + + +
852A ASN 2.9 15.2 + - - +
853A ASP* 3.9 7.9 - - - +
855A LEU* 1.3 73.6 - - - +
857A LYS* 1.3 88.3 + - + +
859A LEU* 3.3 3.3 + - - +
860A SER* 2.7 49.2 + - - -
883A MET 2.9 18.0 + - - -
884A LEU 2.7 32.7 + - - -
885A HIS 3.2 12.5 + - - -
886A LEU* 3.6 3.9 + - + +
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Residues in contact with LYS 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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853A ASP* 3.0 25.6 + - + +
854A TYR* 4.3 3.4 - - - +
856A TYR* 1.3 101.8 - - + +
858A ARG* 1.3 63.5 + - - +
860A SER* 3.6 6.3 + - - +
861A GLU* 3.1 33.6 + - - +
884A LEU 5.2 2.6 + - - -
885A HIS* 4.4 11.5 + - - +
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Residues in contact with ARG 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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817A LEU* 4.2 14.1 - - - +
820A LEU* 3.4 38.8 + - + +
821A ASN* 2.3 35.1 + - - +
854A TYR* 3.1 52.3 + - + +
855A LEU 3.2 6.0 + - - +
856A TYR 3.2 0.6 - - - -
857A LYS* 1.3 77.3 - - - +
859A LEU* 1.3 61.4 + - - +
861A GLU* 3.3 29.5 + - - +
862A ILE* 3.6 14.9 + - + +
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Residues in contact with LEU 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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816A ILE* 4.1 13.2 - - + +
819A ILE* 5.0 8.7 - - + -
820A LEU* 3.4 32.1 - - + -
828A ILE* 4.6 12.6 - - + -
841A LEU* 5.5 4.5 - - + -
844A ALA* 3.6 28.0 - - + +
845A LEU* 3.9 14.4 - - + +
848A SER* 3.2 30.7 - - - +
855A LEU 2.8 19.4 + - - +
856A TYR 3.6 3.4 - - - +
858A ARG* 1.3 71.0 - - - +
860A SER* 1.3 66.7 + - - +
862A ILE* 3.1 6.4 + - - +
863A VAL* 3.0 29.5 + - + +
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Residues in contact with SER 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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845A LEU* 4.2 2.2 - - - +
856A TYR* 2.7 39.6 + - - -
857A LYS* 3.6 12.1 - - - -
859A LEU* 1.3 73.3 - - - +
861A GLU* 1.3 58.6 + - - +
863A VAL* 3.8 0.8 - - - +
864A ALA* 2.9 35.5 + - - +
884A LEU* 3.5 37.5 + - - +
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Residues in contact with GLU 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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857A LYS* 3.1 22.6 + - - +
858A ARG* 3.3 23.2 - - - +
859A LEU 3.2 0.2 + - - -
860A SER* 1.3 77.5 - - - +
862A ILE* 1.3 61.5 + - + +
864A ALA* 5.1 2.0 - - - -
865A PRO* 3.1 22.8 - - - +
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Residues in contact with ILE 862 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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820A LEU* 4.2 18.6 - - + +
824A GLY* 4.6 5.4 - - - -
825A GLU* 3.4 51.0 - - + +
828A ILE* 3.8 35.0 - - + -
858A ARG* 3.6 11.4 + - + +
859A LEU 3.1 6.8 + - - +
861A GLU* 1.3 83.0 - - + +
863A VAL* 1.3 63.0 + - - +
864A ALA 3.5 0.2 - - - -
865A PRO* 3.3 7.2 - - - +
866A LEU* 3.4 13.2 - - - +
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Residues in contact with VAL 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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828A ILE* 3.9 21.3 - - + -
832A LEU* 5.4 3.8 - - + -
841A LEU* 4.4 20.4 - - + -
845A LEU* 4.7 8.1 - - + -
859A LEU* 3.0 24.0 + - + +
860A SER 3.8 2.2 - - - +
862A ILE* 1.3 77.4 - - - +
864A ALA* 1.3 60.6 + - - +
866A LEU* 2.9 30.3 + - - +
867A LEU* 3.4 17.9 + - + +
880A ILE* 3.5 29.6 - - + -
884A LEU* 4.2 11.0 - - + -
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Residues in contact with ALA 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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860A SER* 2.9 18.6 + - - +
861A GLU* 5.1 2.2 - - - -
863A VAL* 1.3 72.9 - - - +
865A PRO* 1.3 69.4 - - + +
866A LEU 3.2 0.3 + - - -
867A LEU* 3.3 17.4 + - - +
868A VAL* 4.6 3.8 - - - +
872A ARG* 5.7 0.2 + - - -
884A LEU* 3.9 24.4 - - + +
885A HIS* 5.7 6.7 - - + -
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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