Contacts of the helix formed by residues 882 - 887 (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 ALA 882 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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815E PRO* 4.0 4.6 - - + +
881E ALA* 1.3 80.4 - - - +
883E TYR* 1.3 61.0 + - - +
884E SER 3.1 1.4 + - - -
885E HIS* 3.2 20.3 + - - -
886E THR* 3.8 13.0 + - - +
960E CA2 3.4 10.1 + - - -
1088F VAL* 3.6 6.4 - - + +
1089F ALA* 3.2 42.8 - - + +
1092F ASP* 3.4 15.5 + - - +
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Residues in contact with TYR 883 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
815E PRO* 3.2 31.2 - - + -
857E ASN 2.6 23.1 + - - -
858E HIS* 3.9 2.5 - - - -
859E GLU* 3.5 35.2 + - + -
862E LEU* 3.7 14.6 - - + -
880E PRO* 3.1 10.7 + - + +
881E ALA 3.0 0.4 + - - -
882E ALA* 1.3 73.3 - - - +
884E SER* 1.3 64.5 + - - +
885E HIS 3.1 2.0 - - - -
886E THR* 3.7 16.2 - - - -
887E SER* 2.9 36.2 + - - +
890E ILE* 3.9 10.1 - - + -
922E VAL* 4.8 3.1 - - - +
1059F GLU* 3.4 42.4 + - - +
1060F GLY* 4.3 2.3 + - - -
1063F VAL* 5.2 0.2 - - - +
1089F ALA* 3.8 13.0 - - + +
2406F TRS 4.0 5.8 - - - -
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Residues in contact with SER 884 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
880E PRO* 3.2 22.3 - - - +
881E ALA 2.7 19.7 + - - -
883E TYR* 1.3 78.6 - - - +
885E HIS* 1.3 65.2 + - - +
886E THR 3.8 0.2 + - - -
904E GLU* 4.2 0.4 - - - -
906E HIS* 3.0 31.6 - - - -
920E SER* 3.1 17.1 - - - -
921E TYR* 2.8 33.1 + - - +
922E VAL* 4.0 5.3 + - - -
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Residues in contact with HIS 885 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
881E ALA 4.2 5.5 + - - -
882E ALA* 3.2 17.6 + - - +
883E TYR 3.1 0.6 - - - -
884E SER* 1.3 86.8 - - - +
886E THR* 1.3 65.9 + - + +
887E SER 3.9 0.2 - - - -
906E HIS* 5.2 0.7 - + - -
910E ILE* 4.4 11.9 - - + -
916E PHE* 3.7 15.0 + + - +
917E ARG* 2.9 39.0 + - + -
919E HIS* 2.7 31.1 + - - +
920E SER* 5.2 0.2 - - - -
921E TYR* 3.5 17.1 - - - -
960E CA2 2.9 29.8 + - - -
1088F VAL* 4.4 15.7 - - + -
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Residues in contact with THR 886 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
686D THR* 3.5 13.0 - - - +
882E ALA 3.8 6.1 - - - +
883E TYR* 3.4 18.8 + - - -
885E HIS* 1.3 85.0 - - - +
887E SER* 1.3 59.3 + - - +
888E VAL 3.4 5.9 + - - -
921E TYR* 3.9 8.4 - - - -
1086F THR 3.6 13.9 - - - +
1088F VAL* 3.5 34.5 - - + +
1089F ALA 5.7 0.3 + - - -
1121F TYR* 5.5 2.5 - - + +
2406F TRS 2.8 41.0 + - - -
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Residues in contact with SER 887 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
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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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
------------------------------------------------------------
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