Contacts of the strand formed by residues 758 - 765 (chain A) in PDB entry 4BCX
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 LYS 758 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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715A ALA* 3.4 3.8 - - - -
716A ALA* 2.9 38.8 + - + +
757A LEU* 1.3 73.0 - - - +
759A LEU* 1.3 64.6 + - - +
773A ILE* 3.5 26.6 - - + +
774A PHE* 3.6 15.9 - - - +
775A GLU* 4.0 8.7 - - + +
1786A IMD 3.5 29.3 + - + +
1787A PDO 3.9 17.2 - - - +
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Residues in contact with LEU 759 (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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672A VAL* 4.5 4.3 - - + -
680A LEU* 3.7 29.2 - - + -
682A LEU* 4.9 7.9 - - + -
698A ILE* 5.4 3.8 - - + -
713A CYS* 4.3 9.4 - - - -
714A GLN 3.4 5.4 - - - +
715A ALA* 3.8 21.3 - - + -
745A PHE* 5.5 2.0 - - + -
757A LEU* 4.0 16.4 - - + -
758A LYS* 1.3 82.1 - - - +
760A ARG* 1.3 59.2 + - - +
761A LEU* 4.1 8.1 - - + -
772A GLU 3.9 0.3 - - - +
773A ILE* 3.3 6.4 - - - +
774A PHE* 3.0 56.8 + - + +
776A VAL* 4.2 17.7 - - + -
1787A PDO 4.5 2.7 - - - -
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Residues in contact with ARG 760 (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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712A ILE* 3.6 2.2 - - - +
713A CYS* 3.6 3.6 - - - -
714A GLN* 3.0 67.2 + - - +
759A LEU* 1.3 73.8 - - - +
761A LEU* 1.3 66.9 + - - +
762A THR* 3.7 24.4 + - + +
771A GLN* 3.8 31.8 + - + +
772A GLU 3.4 4.0 - - - +
773A ILE* 3.7 24.8 - - + +
1787A PDO 3.8 20.6 - - - -
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Residues in contact with LEU 761 (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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673A PHE* 3.9 32.5 - - + -
680A LEU* 4.0 23.1 - - + -
711A PHE* 4.2 15.7 - - + -
712A ILE 3.5 2.0 - - - +
713A CYS* 3.5 38.1 - - + -
759A LEU* 4.5 4.3 - - + -
760A ARG* 1.3 75.9 - - - +
762A THR* 1.3 65.8 + - - +
763A TYR* 4.6 13.2 - - + -
770A VAL* 3.8 0.5 - - - +
771A GLN* 3.4 1.7 - - - +
772A GLU* 2.7 42.4 + - + +
774A PHE* 4.0 19.7 - - + -
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Residues in contact with THR 762 (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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710A HIS 3.1 3.1 + - - +
712A ILE* 2.9 55.6 + - - +
760A ARG* 3.7 32.9 + - - +
761A LEU* 1.3 80.9 - - - +
763A TYR* 1.3 64.6 + - - +
770A VAL 3.2 7.6 - - - +
771A GLN* 3.7 23.3 - - + +
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Residues in contact with TYR 763 (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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673A PHE* 3.9 25.2 - + - -
675A ARG* 4.2 10.2 + - - +
678A VAL* 4.0 16.8 - - + +
708A VAL* 3.7 24.0 - - + -
709A THR 3.4 12.8 - - - +
710A HIS* 3.6 6.3 - - - -
711A PHE* 3.6 34.8 - + + -
761A LEU* 4.6 9.6 - - + -
762A THR* 1.3 83.2 - - - +
764A ASP* 1.3 68.8 + - - +
765A HIS* 3.7 18.2 + + + -
769A SER* 3.8 0.7 + - - -
770A VAL* 2.7 71.5 + - + +
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Residues in contact with ASP 764 (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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707A ASP 3.7 1.2 - - - +
708A VAL* 3.4 4.7 - - - -
709A THR* 2.8 48.1 + - - +
710A HIS* 3.2 28.6 - - - -
763A TYR* 1.3 79.7 - - - +
765A HIS* 1.3 63.6 + - - +
767A HIS* 5.2 4.5 - - - -
768A GLN 3.4 5.6 - - - +
769A SER* 3.6 20.8 + - - -
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Residues in contact with HIS 765 (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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675A ARG* 4.8 1.8 + - - +
676A GLU* 3.4 29.3 + - + +
678A VAL* 3.8 16.1 - - + +
704A SER* 2.8 21.3 + - - -
706A GLY 3.2 17.8 + - - -
707A ASP 3.4 10.8 - - - -
708A VAL* 4.0 9.4 - - + -
763A TYR* 3.7 19.0 + + + -
764A ASP* 1.3 76.4 - - - +
766A PHE* 1.3 106.9 + + - +
767A HIS 3.1 0.6 - - - +
768A GLN* 3.1 24.2 + - - +
770A VAL* 4.4 7.8 - - + +
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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