Contacts of the strand formed by residues 809 - 813 (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 ILE 809 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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804E LEU* 4.2 19.3 - - + -
808E PRO* 1.3 71.9 - - - +
810E MET* 1.3 74.2 + - - +
811E ILE* 3.5 11.2 + - + -
844E ALA* 4.6 4.9 - - + -
850E THR 2.9 17.1 + - - +
851E VAL* 3.3 8.0 - - + +
852E ASP 2.9 22.1 + - - -
873E HIS* 4.1 0.4 - - - -
874E CYS* 3.6 19.7 - - - -
875E GLY 3.7 14.1 - - - +
877E VAL* 4.1 15.9 - - + -
942E VAL* 4.0 28.7 - - + +
945E ILE* 4.0 20.6 - - + -
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Residues in contact with MET 810 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
808E PRO 3.7 3.2 + - - -
809E ILE* 1.3 72.0 - - - +
811E ILE* 1.3 60.8 + - - +
812E LEU* 3.5 28.7 - - + -
852E ASP* 3.5 15.3 - - - +
854E ARG* 3.7 31.2 - - - +
865E TRP 3.6 22.9 - - - +
868E GLU* 4.5 2.0 - - - -
869E ALA* 3.9 15.9 - - + +
873E HIS* 3.3 45.8 - - + +
875E GLY 2.9 13.6 + - - +
876E ILE* 3.2 5.5 - - + +
877E VAL 2.8 26.2 + - - +
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Residues in contact with ILE 811 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
809E ILE* 3.8 14.8 - - + +
810E MET* 1.3 74.6 - - - +
812E LEU* 1.3 63.8 + - - +
813E ASN* 3.9 3.7 + - - +
840E CYS* 3.6 31.0 - - + -
851E VAL* 3.8 22.2 - - + -
852E ASP 2.9 10.2 + - - +
853E PHE* 3.4 29.8 - - + -
854E ARG 2.8 29.3 + - - +
877E VAL* 3.1 15.3 - - + +
938E TYR* 4.2 19.3 - - + -
942E VAL* 4.0 15.0 - - + -
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Residues in contact with LEU 812 (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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810E MET* 3.5 35.7 - - + -
811E ILE* 1.3 74.9 - - - +
813E ASN* 1.3 64.7 + - - +
854E ARG* 3.6 5.4 - - + -
862E LEU* 4.4 13.9 - - + +
865E TRP* 4.0 26.9 - - + -
866E ILE* 3.5 42.0 - - + +
876E ILE* 4.4 13.5 - - + -
877E VAL 2.8 8.9 + - - +
878E ILE* 3.3 19.6 - - + +
879E ASN 2.8 27.6 + - - +
938E TYR* 5.3 0.2 - - - -
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Residues in contact with ASN 813 (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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811E ILE* 3.9 5.9 + - - +
812E LEU* 1.3 79.6 - - - +
814E GLY* 1.3 61.0 + - - +
817E LEU* 3.7 13.5 - - + +
833E LEU* 3.9 7.9 - - + +
853E PHE* 3.4 33.0 - - - -
854E ARG 2.9 20.4 + - - +
855E GLN* 3.2 13.7 - - + -
856E SER 2.9 27.0 + - - +
862E LEU* 3.9 7.4 - - - +
879E ASN* 3.4 3.5 - - - +
938E TYR* 2.6 36.1 + - - -
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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
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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