Contacts of the helix formed by residues 836 - 852 (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 TYR 836 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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793A SER 3.7 9.0 - - - +
794A ILE 3.8 15.0 - - - -
795A HIS 4.2 2.2 - - - +
796A LYS* 2.7 66.7 - - + +
799A SER* 4.1 12.4 + - - +
834A ASP* 2.7 24.5 + - - +
835A SER* 1.3 92.4 - - - +
837A GLY* 1.3 63.8 + - - +
838A ASN 3.1 3.2 + - - -
839A TYR* 3.1 21.6 + + - +
840A VAL* 3.5 10.6 + - - +
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Residues in contact with GLY 837 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
793A SER 3.0 21.3 + - - -
794A ILE* 4.6 0.2 - - - -
831A LEU* 3.3 23.6 - - - +
834A ASP* 3.0 12.2 + - - -
836A TYR* 1.3 72.3 - - - +
838A ASN* 1.3 54.3 + - - +
839A TYR 3.3 0.2 - - - -
840A VAL* 3.4 7.8 - - - +
841A LEU* 2.7 36.4 + - - +
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Residues in contact with ASN 838 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
831A LEU 2.9 15.2 + - - +
832A LEU* 3.0 19.6 - - - +
834A ASP 3.2 18.4 + - - +
835A SER 4.9 1.1 - - - +
836A TYR 3.1 1.3 - - - +
837A GLY* 1.3 75.2 - - - +
839A TYR* 1.3 61.8 + - + +
841A LEU* 3.0 7.9 + - - +
842A GLN* 2.8 25.3 + - - +
876A HIS* 3.4 34.2 + - + +
879A ARG* 2.9 37.5 - - - +
880A ILE* 3.7 14.0 - - - +
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Residues in contact with TYR 839 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
803A GLU* 3.5 13.0 - - - +
835A SER 3.4 26.0 - - - -
836A TYR* 3.1 11.7 + + - +
838A ASN* 1.3 80.3 - - + +
840A VAL* 1.3 57.6 + - + +
842A GLN* 3.2 10.2 + - - +
843A THR* 2.8 31.0 + - - -
879A ARG* 3.5 45.6 + - - -
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Residues in contact with VAL 840 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
793A SER* 3.4 37.9 - - - +
799A SER* 3.9 19.3 - - - +
802A ILE* 4.0 7.2 - - + -
803A GLU* 4.1 19.1 - - + +
806A LEU* 3.7 18.6 - - + +
819A ILE* 4.6 7.0 - - + -
831A LEU* 4.8 2.2 - - + -
836A TYR 3.8 13.2 - - - +
837A GLY* 3.2 9.2 + - - +
839A TYR* 1.3 72.7 - - + +
841A LEU* 1.3 61.8 + - - +
843A THR* 3.2 5.8 + - - -
844A ALA* 2.9 27.0 + - - +
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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
----------------------------------------------------------
819A ILE* 5.6 1.1 - - + -
828A ILE* 3.9 16.4 - - + +
831A LEU* 4.0 18.8 - - + +
832A LEU* 3.6 39.3 - - + +
837A GLY 2.7 17.8 + - - +
838A ASN* 3.0 11.4 + - - +
840A VAL* 1.3 72.7 - - - +
842A GLN* 1.3 62.9 + - - +
844A ALA* 3.1 11.7 + - + +
845A LEU* 3.1 28.1 + - + +
859A LEU* 5.5 6.3 - - + -
863A VAL* 4.4 26.5 - - + -
880A ILE* 4.1 15.0 - - + -
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Residues in contact with GLN 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 ASN 2.8 11.9 + - - +
839A TYR* 3.5 12.6 - - - +
841A LEU* 1.3 74.4 - - - +
843A THR* 1.3 65.9 + - - +
845A LEU* 3.5 3.2 + - - +
846A ASP* 3.0 23.2 + - + +
879A ARG* 2.1 51.1 + - - +
880A ILE* 3.8 12.5 - - + +
883A MET* 3.2 40.3 - - + +
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Residues in contact with THR 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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803A GLU* 3.1 29.0 + - + -
806A LEU* 3.6 31.6 - - + -
807A LYS* 4.2 21.7 + - + -
839A TYR 2.8 9.4 + - - -
840A VAL* 3.2 9.6 + - - -
842A GLN* 1.3 78.2 - - - +
844A ALA* 1.3 56.4 + - - +
846A ASP* 3.1 6.2 + - - +
847A ILE* 2.8 39.8 + - + +
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Residues in contact with ALA 844 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
806A LEU* 4.3 13.5 - - + -
816A ILE* 4.0 15.9 - - + +
819A ILE* 5.1 12.1 - - + -
840A VAL 2.9 13.0 + - - +
841A LEU* 3.1 18.8 + - + +
843A THR* 1.3 75.9 - - - +
845A LEU* 1.3 57.9 + - - +
847A ILE* 4.9 0.4 - - - -
848A SER* 2.9 33.1 + - - -
859A LEU* 3.6 17.5 - - + +
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Residues in contact with LEU 845 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
841A LEU* 3.1 30.9 + - + +
842A GLN 3.9 1.3 - - - +
844A ALA* 1.3 74.9 - - - +
846A ASP* 1.3 59.0 + - - +
848A SER* 3.1 5.1 + - - -
849A HIS* 2.9 32.1 + - - +
856A TYR* 3.5 12.0 - - + -
859A LEU* 3.9 26.7 - - + -
860A SER* 4.2 20.2 - - - +
863A VAL* 4.7 5.2 - - + -
880A ILE* 3.7 27.6 - - + +
883A MET* 3.7 34.8 - - + +
884A LEU* 4.3 10.1 - - + -
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Residues in contact with ASP 846 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
807A LYS* 6.0 2.4 - - - -
842A GLN* 3.0 19.9 + - + +
843A THR* 3.1 7.6 + - - +
845A LEU* 1.3 79.0 - - - +
847A ILE* 1.3 73.5 + - - +
849A HIS* 3.5 7.1 + - - +
850A LYS* 3.4 55.4 + - - +
883A MET* 3.7 21.3 - - + +
886A LEU* 5.6 1.5 - - - +
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Residues in contact with ILE 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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806A LEU* 3.2 26.9 - - + +
807A LYS* 4.5 15.9 - - + -
812A SER* 3.9 8.1 - - - -
816A ILE* 3.9 11.0 - - + -
843A THR* 2.8 33.3 + - + +
844A ALA* 4.1 2.0 - - - +
846A ASP* 1.3 82.6 - - - +
848A SER* 1.3 58.0 + - - +
850A LYS* 2.9 30.1 + - + +
851A GLN* 2.9 48.4 + - + +
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Residues in contact with SER 848 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
816A ILE* 4.1 14.4 - - - -
844A ALA 2.9 23.0 + - - -
845A LEU* 3.1 6.2 + - - -
847A ILE* 1.3 77.4 - - - +
849A HIS* 1.3 60.4 + - - +
851A GLN* 5.0 1.3 - - - -
852A ASN* 2.8 40.1 + - - +
855A LEU* 4.2 7.4 - - - -
856A TYR* 3.4 24.2 - - - -
859A LEU* 3.2 20.8 - - - +
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Residues in contact with HIS 849 (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 2.9 20.2 + - - +
846A ASP* 3.6 6.5 - - - +
848A SER* 1.3 76.6 + - - +
850A LYS* 1.3 70.9 + - + +
852A ASN 4.7 0.2 + - - -
853A ASP* 4.2 15.9 + - - +
856A TYR* 3.4 33.2 - + + -
886A LEU* 3.5 55.2 + - + +
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Residues in contact with LYS 850 (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 ASP* 3.4 43.7 + - - +
847A ILE* 2.9 15.9 + - + +
849A HIS* 1.3 90.0 - - + +
851A GLN* 1.3 66.1 + - + +
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Residues in contact with GLN 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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807A LYS 6.0 0.8 - - - -
809A ALA* 3.9 22.2 - - - +
812A SER* 3.3 30.6 + - - -
813A GLU* 3.4 22.2 - - + +
847A ILE* 2.9 39.7 + - + +
848A SER* 5.0 0.9 - - - -
850A LYS* 1.3 85.0 - - + +
852A ASN* 1.3 64.9 + - + +
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Residues in contact with ASN 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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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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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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