Contacts of the strand formed by residues 708 - 716 (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 VAL 708 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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678A VAL* 3.4 37.2 - - + -
702A ASN* 3.8 14.4 - - + +
707A ASP* 1.3 74.3 - - - +
709A THR* 1.3 62.8 + - - +
711A PHE* 4.1 20.2 - - + -
732A THR* 3.2 9.0 - - - +
733A VAL* 2.9 46.2 + - + +
763A TYR* 3.7 30.7 - - + -
764A ASP 3.4 3.4 - - - -
765A HIS* 4.0 10.5 - - + -
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Residues in contact with THR 709 (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* 4.6 12.0 + - + +
708A VAL* 1.3 78.6 - - - +
710A HIS* 1.3 74.7 - - - +
711A PHE 3.1 4.6 + - - -
731A ASN 3.6 3.8 - - - -
732A THR* 4.1 19.3 - - + +
763A TYR* 3.4 2.1 - - - +
764A ASP* 2.8 50.9 + - - +
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Residues in contact with HIS 710 (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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709A THR* 1.3 85.5 - - - +
711A PHE* 1.3 63.1 + - - +
712A ILE* 3.3 13.7 + - + +
731A ASN* 3.0 15.3 + - - +
732A THR* 4.8 0.6 + - - -
762A THR* 3.1 13.7 + - - +
763A TYR* 3.6 2.6 - - - -
764A ASP* 3.2 28.0 - - - +
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Residues in contact with PHE 711 (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* 6.3 0.2 - + - -
678A VAL* 5.1 7.4 - - + -
680A LEU* 3.9 24.7 - - + -
698A ILE* 5.1 4.5 - - + -
700A ALA* 4.0 17.9 - - + -
708A VAL* 4.1 13.9 - - + -
709A THR 3.1 1.0 - - - -
710A HIS* 1.3 74.6 - - - +
712A ILE* 1.3 63.1 + - - +
713A CYS* 4.1 17.9 - - + -
728A PRO* 5.5 1.4 - - - +
730A GLY 4.4 1.0 - - - +
731A ASN* 2.9 39.9 + - - +
733A VAL* 5.3 0.2 - - + -
741A ILE* 3.7 32.1 - - + -
743A GLN* 5.9 0.4 - - - -
761A LEU* 4.2 22.2 - - + -
762A THR 3.4 2.9 - - - -
763A TYR* 3.6 37.5 - + + -
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Residues in contact with ILE 712 (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* 3.9 11.2 - - + +
711A PHE* 1.3 83.5 - - - +
713A CYS* 1.3 66.5 + - - +
714A GLN* 4.1 29.2 - - + +
731A ASN* 4.4 9.6 - - - +
760A ARG* 3.6 1.4 - - - +
761A LEU* 3.5 5.5 - - - +
762A THR* 2.9 43.9 + - - +
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Residues in contact with CYS 713 (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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680A LEU* 4.7 1.1 - - - -
698A ILE* 3.4 34.8 - - + -
711A PHE* 4.1 10.6 - - + -
712A ILE* 1.3 76.7 - - - +
714A GLN* 1.3 71.4 + - - +
725A LEU* 4.1 12.3 - - - +
743A GLN* 3.6 17.7 + - - +
745A PHE* 4.2 9.4 - - - -
759A LEU* 4.3 16.6 - - - -
760A ARG 3.6 2.9 - - - -
761A LEU* 3.5 24.2 - - + -
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Residues in contact with GLN 714 (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* 4.1 19.7 - - + +
713A CYS* 1.3 77.5 - - - +
715A ALA* 1.3 61.8 + - - +
725A LEU* 5.0 5.2 - - + -
759A LEU* 3.4 6.8 - - - +
760A ARG* 3.0 76.3 + - + +
1787A PDO 3.7 20.6 - - - -
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Residues in contact with ALA 715 (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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714A GLN* 1.3 76.9 - - - +
716A ALA* 1.3 60.1 + - - +
723A LEU* 3.9 21.7 - - + +
725A LEU* 4.9 5.3 - - + +
745A PHE* 3.8 27.2 - - + -
757A LEU* 4.3 9.4 - - + -
758A LYS 3.4 5.4 - - - +
759A LEU* 3.8 18.2 - - + -
1787A PDO 3.9 11.5 + - - -
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Residues in contact with ALA 716 (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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715A ALA* 1.3 74.3 - - - +
717A VAL* 1.3 72.2 + - - +
723A LEU* 4.9 0.7 - - - -
757A LEU* 3.6 2.1 - - - +
758A LYS* 2.9 39.8 + - + +
1786A IMD 3.5 8.2 - - + +
1787A PDO 4.0 21.3 - - + +
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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