Contacts of the helix formed by residues 887 - 896 (chain E) in PDB entry 2BT4
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 SER 887 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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859E GLU* 2.4 31.3 + - - -
883E TYR* 2.9 33.7 + - - +
885E HIS 3.9 0.6 - - - -
886E THR* 1.3 73.7 + - - +
888E VAL* 1.3 62.5 + - - +
889E ALA 3.5 0.2 + - - -
890E ILE* 3.0 29.1 + - - +
891E LEU 3.4 12.1 + - - -
921E TYR* 3.9 13.9 - - - +
922E VAL* 5.2 1.4 - - - +
2406F TRS 3.9 0.9 - - - -
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Residues in contact with VAL 888 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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682D ALA* 3.6 19.7 - - + +
685D HIS* 4.3 8.3 - - + -
686D THR* 3.5 27.3 - - + +
716D PHE* 3.8 26.7 - - + -
717D ARG* 3.9 15.7 - - - +
886E THR 3.4 2.4 + - - -
887E SER* 1.3 74.0 - - - +
889E ALA* 1.3 55.6 + - - +
891E LEU* 3.2 8.2 + - + +
892E ASP* 2.8 29.6 + - - +
921E TYR* 3.7 35.0 - - + +
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Residues in contact with ALA 889 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615D PRO* 3.9 19.1 - - + -
616D ASN* 3.3 10.5 + - - +
682D ALA* 3.4 12.3 - - + +
683D TYR* 3.7 34.0 - - + +
686D THR* 5.5 0.4 - - - +
859E GLU* 3.8 7.8 + - - +
863E VAL* 3.9 9.9 - - + +
887E SER* 3.1 0.8 - - - +
888E VAL* 1.3 78.3 - - - +
890E ILE* 1.3 58.1 + - - +
892E ASP 3.3 0.3 + - - -
893E ALA* 3.0 24.8 + - - +
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Residues in contact with ILE 890 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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859E GLU* 4.2 8.5 - - + +
862E LEU* 4.0 29.8 - - + -
863E VAL* 3.9 16.8 - - + -
866E ILE* 3.9 15.5 - - + -
878E ILE* 4.3 9.4 - - + -
880E PRO* 5.1 3.8 - - + -
883E TYR* 3.9 22.7 - - + -
887E SER* 3.0 25.2 + - - +
889E ALA* 1.3 73.6 - - - +
891E LEU* 1.3 67.6 + - - +
893E ALA* 3.2 6.2 + - - +
894E LEU* 2.9 29.9 + - + +
922E VAL* 3.8 23.8 - - + -
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Residues in contact with LEU 891 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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716D PHE* 4.0 18.6 - - + -
717D ARG* 4.7 4.5 - - - +
887E SER 3.4 10.3 + - - +
888E VAL* 3.2 9.4 + - - +
890E ILE* 1.3 81.6 - - - +
892E ASP* 1.3 58.0 + - - +
894E LEU* 3.3 6.8 + - - +
895E ASN* 2.9 38.1 + - - +
921E TYR* 3.4 39.9 - - + +
922E VAL* 4.9 3.8 - - - +
924E GLN* 3.8 25.1 - - + +
925E ARG* 3.6 28.7 - - + +
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Residues in contact with ASP 892 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616D ASN* 3.3 21.1 + - + +
682D ALA* 3.4 14.3 + - - +
717D ARG* 2.7 34.0 + - - -
760D CA2 2.5 41.2 + - + +
888E VAL* 2.8 13.9 + - - +
889E ALA 3.6 3.1 - - - +
891E LEU* 1.3 76.3 - - - +
893E ALA* 1.3 63.2 + - - +
895E ASN* 3.3 16.2 + - - +
896E THR* 3.4 17.5 + - - +
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Residues in contact with ALA 893 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616D ASN* 3.2 21.5 - - - +
863E VAL* 4.0 13.7 - - + -
866E ILE* 3.5 34.2 - - + +
867E HIS* 4.4 2.2 - - - +
889E ALA 3.0 12.6 + - - +
890E ILE* 3.2 10.3 + - - +
892E ASP* 1.3 75.2 - - - +
894E LEU* 1.3 62.5 + - - +
896E THR* 2.6 25.8 + - - -
897E CYS* 3.6 1.7 - - - -
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Residues in contact with LEU 894 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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866E ILE* 3.9 18.4 - - + -
876E ILE* 3.7 33.4 - - + -
878E ILE* 4.7 6.3 - - + -
890E ILE* 2.9 31.4 + - + +
891E LEU* 3.7 5.6 - - - +
893E ALA* 1.3 74.1 - - - +
895E ASN* 1.3 66.5 + - - +
897E CYS* 3.0 17.3 + - - +
902E VAL* 4.0 23.8 - - + -
922E VAL* 3.8 31.9 - - + +
925E ARG* 3.3 30.3 + - + -
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Residues in contact with ASN 895 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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623D ARG* 3.2 29.8 + - - +
713D ARG* 6.2 0.2 - - - +
717D ARG* 3.9 20.8 - - - +
891E LEU* 2.9 29.5 + - - +
892E ASP* 3.5 11.7 + - - +
893E ALA 3.2 0.8 - - - -
894E LEU* 1.3 76.9 - - - +
896E THR* 1.3 58.8 + - - +
897E CYS 3.1 1.8 + - - -
898E ASP* 4.3 3.8 + - - +
924E GLN 5.1 1.2 - - - +
925E ARG* 3.4 32.1 + - - +
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Residues in contact with THR 896 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616D ASN* 4.6 6.3 - - + +
619D LEU* 3.7 20.3 - - + +
623D ARG* 3.3 23.1 - - - +
760D CA2 4.4 18.6 - - + -
867E HIS* 4.3 3.1 - - - -
870E ARG* 2.9 40.2 + - - -
892E ASP 3.5 14.8 - - - +
893E ALA* 2.6 21.1 + - - +
894E LEU 3.1 0.2 - - - -
895E ASN* 1.3 74.5 - - - +
897E CYS* 1.3 57.3 + - - +
898E ASP* 3.0 19.3 + - - +
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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