Contacts of the strand formed by residues 741 - 748 (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 ILE 741 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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698A ILE* 3.5 2.8 - - + +
699A THR* 3.3 5.0 - - - -
700A ALA* 2.8 37.9 + - + +
711A PHE* 3.7 29.6 - - + -
728A PRO* 4.2 7.9 - - + -
729A SER* 3.4 8.3 - - - +
730A GLY* 3.6 25.4 - - - +
731A ASN 3.5 7.9 - - - -
732A THR 3.4 31.2 - - - +
733A VAL* 3.3 26.6 - - + +
740A PRO* 1.3 73.4 - - - +
742A THR* 1.3 71.4 + - - +
743A GLN* 4.9 2.0 - - + +
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Residues in contact with THR 742 (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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697A THR* 4.3 12.8 - - + -
698A ILE 3.2 5.4 - - - -
699A THR* 4.2 19.7 - - + +
727A ALA 4.7 0.2 - - - +
728A PRO* 3.5 0.9 - - - +
729A SER* 2.9 43.1 + - - +
740A PRO* 4.7 11.4 - - + +
741A ILE* 1.3 81.0 - - - +
743A GLN* 1.3 61.7 + - - +
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Residues in contact with GLN 743 (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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696A ILE 3.7 0.5 - - - +
697A THR* 3.4 5.3 - - - +
698A ILE* 2.9 55.4 + - + +
711A PHE* 5.9 0.3 - - - -
713A CYS* 3.6 21.5 + - - +
725A LEU* 3.9 17.6 - - - +
726A GLN* 2.8 29.2 + - - +
727A ALA* 4.4 0.9 - - - +
728A PRO* 3.6 33.4 - - + +
741A ILE* 5.3 1.8 - - + -
742A THR* 1.3 77.0 - - - +
744A LEU* 1.3 66.3 + - - +
745A PHE* 3.8 14.1 - - + -
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Residues in contact with LEU 744 (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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695A LEU* 4.0 29.6 - - + -
696A ILE 3.5 10.1 - - - +
697A THR* 3.7 16.6 - - + +
725A LEU* 3.9 0.7 - - - -
726A GLN* 3.1 65.8 + - + +
743A GLN* 1.3 76.5 - - - +
745A PHE* 1.3 76.7 + - - +
746A ARG* 4.1 21.2 + - + +
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Residues in contact with PHE 745 (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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694A LEU 3.5 4.0 - - - +
695A LEU* 3.8 1.7 - - - -
696A ILE* 2.7 52.9 + - + +
698A ILE* 3.4 48.7 - - + -
713A CYS* 4.2 12.1 - - - -
715A ALA* 3.8 19.5 - - + -
723A LEU* 3.7 14.1 - - + -
724A GLN 3.9 2.2 - - - -
725A LEU* 3.2 47.8 - - + -
743A GLN* 3.8 17.9 - - + -
744A LEU* 1.3 77.8 - - - +
746A ARG* 1.3 63.3 + - - +
747A ILE* 3.6 5.4 + - + +
757A LEU* 6.4 1.3 - - + -
759A LEU* 5.5 1.3 - - + -
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Residues in contact with ARG 746 (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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693A LEU* 3.4 37.2 - - + +
694A LEU 4.0 2.2 - - - -
695A LEU* 3.6 19.7 - - + +
722A GLN 3.9 0.5 - - - +
723A LEU* 3.5 5.5 - - - +
724A GLN* 2.9 48.0 + - + +
725A LEU 6.1 0.2 - - - -
726A GLN* 6.0 3.1 - - + +
744A LEU* 4.4 16.8 - - + +
745A PHE* 1.3 71.5 - - - +
747A ILE* 1.3 59.8 + - - +
748A LEU* 4.2 9.5 + - + +
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Residues in contact with ILE 747 (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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692A ALA 3.6 0.7 - - - +
693A LEU* 3.4 7.0 - - - +
694A LEU* 2.8 60.3 + - + +
696A ILE* 3.9 29.2 - - + -
717A VAL* 4.5 10.3 - - + -
721A LEU* 4.0 20.0 - - + -
722A GLN 3.5 3.4 - - - +
723A LEU* 3.8 19.7 - - + -
745A PHE* 4.2 6.1 - - + +
746A ARG* 1.3 78.6 - - - +
748A LEU* 1.3 69.7 + - - +
749A ASN* 4.4 8.7 - - + +
755A LEU* 4.0 21.1 - - + -
757A LEU* 5.3 2.5 - - + -
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Residues in contact with LEU 748 (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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690A ASN* 4.8 7.9 - - - +
692A ALA* 3.5 27.8 - - + +
693A LEU* 4.3 17.7 - - + -
721A LEU* 3.5 3.6 - - - +
722A GLN* 3.0 44.4 + - + +
746A ARG* 4.2 8.9 + - + +
747A ILE* 1.3 73.0 - - - +
749A ASN* 1.3 60.6 + - - +
750A PRO* 3.4 11.3 - - + +
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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