Contacts of the strand formed by residues 876 - 879 (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 876 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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810E MET* 3.2 9.0 - - + +
812E LEU* 4.4 12.8 - - + -
866E ILE* 4.1 14.4 - - + -
869E ALA* 3.8 24.7 - - + -
875E GLY* 1.3 77.2 - - - +
877E VAL* 1.3 75.5 + - - +
878E ILE* 3.9 20.4 - - + -
894E LEU* 3.7 23.6 - - + -
897E CYS* 4.3 2.7 - - - -
900E LEU* 3.7 20.9 - - + -
901E PRO 3.0 10.3 + - - +
902E VAL* 3.3 10.3 - - + -
903E VAL 3.0 24.8 + - - +
945E ILE* 3.8 3.5 - - - +
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Residues in contact with VAL 877 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
809E ILE* 4.1 11.2 - - + +
810E MET 2.8 6.7 + - - +
811E ILE* 3.1 22.5 - - + +
812E LEU 2.8 26.2 + - - +
876E ILE* 1.3 73.7 - - - +
878E ILE* 1.3 63.4 + - - +
879E ASN 4.3 0.2 - - - -
903E VAL* 3.3 6.1 - - + +
905E VAL* 3.8 26.5 - - + -
938E TYR* 4.6 14.8 - - + +
941E GLY* 3.7 31.9 - - - -
942E VAL* 3.9 7.6 - - + +
945E ILE* 3.8 17.3 - - + -
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Residues in contact with ILE 878 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
812E LEU* 3.3 24.0 - - + +
813E ASN 6.1 0.2 - - - -
862E LEU* 5.7 5.2 - - + -
866E ILE* 4.5 13.0 - - + -
876E ILE* 3.9 17.3 - - + -
877E VAL* 1.3 76.6 - - - +
879E ASN* 1.3 63.7 + - - +
880E PRO* 3.4 29.7 - - + +
890E ILE* 4.3 22.4 - - + -
894E LEU* 4.7 4.3 - - + -
902E VAL* 4.1 13.7 - - + -
903E VAL 2.9 18.6 + - - +
904E GLU* 3.3 7.8 - - - -
905E VAL* 3.0 24.2 + - - -
922E VAL* 4.5 11.7 - - + -
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Residues in contact with ASN 879 (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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812E LEU 2.8 7.9 + - - -
813E ASN* 3.4 5.0 - - - +
814E GLY 2.8 24.1 + - - -
817E LEU* 3.6 15.2 - - + +
878E ILE* 1.3 72.3 - - - +
880E PRO* 1.3 61.5 - - - +
881E ALA* 3.1 5.2 + - - -
905E VAL* 3.1 19.2 + - + +
907E ILE* 4.1 9.7 - - - +
938E TYR* 3.1 37.2 + - + +
960E CA2 2.6 44.0 + - - -
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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