Contacts of the strand formed by residues 901 - 905 (chain A) in PDB entry 3B8R
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 LEU 901 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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827A TRP* 3.4 37.6 - - + -
886A LEU* 3.9 11.7 - - + -
889A LEU* 4.0 29.3 - - + +
890A ILE* 3.5 34.5 - - + +
899A VAL 3.8 3.2 + - - -
900A ASN* 1.3 71.6 - - - +
902A LEU* 1.3 61.6 + - - +
903A GLY 3.4 18.2 - - - +
914A VAL* 4.0 19.3 - - + -
915A ILE 3.2 20.0 - - - +
916A THR* 4.3 3.4 - - - -
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Residues in contact with LEU 902 (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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826A LYS 5.6 0.7 - - - +
827A TRP* 4.1 10.2 - - - +
856A ILE* 3.7 33.7 - - + +
857A ASP* 5.8 4.0 - - + -
863A ARG* 3.6 40.6 - - - +
865A VAL* 3.7 17.5 - - + -
900A ASN* 4.3 9.2 - - + +
901A LEU* 1.3 79.9 - - - +
903A GLY* 1.3 55.0 + - - +
915A ILE* 2.7 15.8 + - + +
916A THR 3.7 3.8 - - - -
917A GLU* 3.5 34.1 - - + +
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Residues in contact with GLY 903 (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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827A TRP* 3.2 22.7 - - - -
829A PHE* 4.8 1.3 - - - -
856A ILE* 4.4 8.5 - - - -
901A LEU* 3.4 10.1 - - - +
902A LEU* 1.3 82.0 - - - +
904A ALA* 1.3 63.4 + - - +
915A ILE* 2.8 31.6 + - - +
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Residues in contact with ALA 904 (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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822A TYR* 4.3 7.0 - - + +
827A TRP* 2.9 7.6 + - + +
828A GLU* 3.3 8.0 - - - -
829A PHE* 2.9 27.6 + - - +
886A LEU* 3.9 25.8 - - + -
903A GLY* 1.3 76.8 - - - +
905A CYS* 1.3 65.4 + - - +
906A THR* 3.9 17.0 - - + -
913A MET 3.1 14.4 - - - +
914A VAL* 4.4 1.8 - - - -
915A ILE* 4.4 2.7 - - - -
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Residues in contact with CYS 905 (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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828A GLU* 3.5 5.2 - - - -
829A PHE* 3.3 22.2 - - - +
831A ARG* 3.6 26.8 + - + +
834A LEU* 4.2 16.4 - - - -
904A ALA* 1.3 74.2 - - - +
906A THR* 1.3 60.2 + - - +
912A LEU* 3.1 9.9 - - - +
913A MET* 2.8 65.2 + - + -
915A ILE* 4.4 5.2 - - - -
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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