Contacts of the strand formed by residues 864 - 869 (chain A) in PDB entry 3L4U
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 TYR 864 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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796A LEU 4.6 0.4 - - - -
797A GLU* 3.6 4.3 - - - +
798A VAL* 3.0 40.0 + - + +
829A VAL* 4.0 6.3 - - + -
830A LYS 3.2 17.0 - - - +
831A HIS* 3.6 30.2 + + + -
832A ASN 5.0 0.7 - - - +
836A SER* 4.5 5.6 - - - -
837A GLN* 5.9 1.1 - - + -
857A ASP 3.9 5.1 + - - -
858A LEU* 3.6 43.8 - - + -
859A LEU* 2.9 52.8 + - - +
862A GLU* 3.4 32.1 + - + +
863A ALA* 1.3 71.6 - - - +
865A THR* 1.3 69.5 + - - +
866A VAL* 4.3 2.0 - - + -
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Residues in contact with THR 865 (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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795A ARG* 3.5 37.8 + - + +
796A LEU 3.4 3.6 - - - -
797A GLU* 2.7 20.2 + - - +
828A THR 3.8 0.9 - - - +
829A VAL* 3.5 1.9 - - - +
830A LYS* 2.8 49.3 + - - +
833A GLY* 5.6 3.1 + - - -
864A TYR* 1.3 73.8 - - - +
866A VAL* 1.3 64.7 + - - +
867A GLU* 3.7 24.3 - - + +
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Residues in contact with VAL 866 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
795A ARG* 3.4 2.9 - - - -
796A LEU* 2.7 60.5 + - + +
798A VAL* 5.9 0.4 - - + -
816A ILE* 4.8 2.2 - - + -
827A VAL* 3.8 21.3 - - + -
828A THR 3.3 9.2 - - - +
829A VAL* 4.4 19.3 - - + -
853A ILE* 4.8 7.6 - - + -
856A ILE* 4.5 7.9 - - + -
858A LEU* 4.2 20.0 - - + -
864A TYR* 4.8 2.9 - - + -
865A THR* 1.3 79.2 - - - +
867A GLU* 1.3 64.3 + - - +
868A TRP* 3.5 13.2 - - + -
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Residues in contact with GLU 867 (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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794A ASN 3.3 12.2 - - - +
795A ARG* 4.1 23.0 + - + -
826A ASN 3.7 1.7 - - - +
827A VAL* 3.3 5.2 - - - +
828A THR* 2.9 43.4 + - - +
830A LYS* 3.8 29.7 + - - +
865A THR* 3.7 25.8 - - + +
866A VAL* 1.3 78.8 - - - +
868A TRP* 1.3 63.2 + - - +
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Residues in contact with TRP 868 (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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756A ILE* 5.5 0.9 - - + -
758A LEU* 6.1 2.9 - - + -
791A VAL* 4.2 14.8 - - + -
792A THR 4.3 5.2 - - - -
794A ASN* 2.9 43.6 + - - +
795A ARG 3.8 23.8 - - - -
796A LEU* 3.7 13.2 - - + -
818A ILE* 4.3 28.3 - - + -
821A THR* 5.0 2.9 + - - -
824A PRO* 3.6 30.2 - - + +
825A SER 3.5 12.3 - - - +
826A ASN 4.1 3.4 - - - -
827A VAL* 3.8 8.5 - - + -
853A ILE* 5.1 5.4 - - + -
866A VAL* 3.5 29.6 - - + -
867A GLU* 1.3 82.9 - - - +
869A ALA* 1.3 59.9 - - - +
870A HIS* 3.4 31.7 + + - -
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Residues in contact with ALA 869 (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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794A ASN* 3.7 6.1 - - - +
824A PRO* 3.4 7.3 - - - +
825A SER* 2.8 42.6 + - - +
826A ASN* 4.0 17.0 + - + +
868A TRP* 1.3 74.2 - - - +
870A HIS* 1.3 69.2 + - - +
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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