Contacts of the strand formed by residues 740 - 746 (chain A) in PDB entry 6CKX
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 GLN 740 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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732A ILE* 4.2 24.6 - - + +
734A GLY 3.6 12.8 - - - +
735A GLU* 3.2 23.8 + - - +
736A GLY 4.2 0.9 - - - +
739A GLY* 1.3 73.9 - - - +
741A VAL* 1.3 66.0 + - - +
742A TYR* 3.0 34.8 + - + -
757A LYS* 3.0 34.8 + - - +
759A ARG* 4.0 14.7 + - - -
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Residues in contact with VAL 741 (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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732A ILE* 3.6 4.5 - - - -
733A ILE* 3.1 27.2 + - + -
734A GLY* 3.2 25.0 + - - +
735A GLU 4.6 1.1 - - - -
736A GLY* 4.2 18.8 - - - +
740A GLN* 1.3 79.8 - - - +
742A TYR* 1.3 68.2 + - - +
754A ALA* 4.1 13.2 - - + -
755A LEU 3.3 16.4 - - - +
756A LYS* 4.0 19.3 - - + +
1102A 8M1 3.7 31.0 - - + -
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Residues in contact with TYR 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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729A ILE* 4.1 30.5 - - + -
731A GLY 3.4 14.6 - - - +
732A ILE* 3.8 20.8 - - + +
733A ILE* 3.9 5.4 - - - -
740A GLN* 3.0 52.5 + - + -
741A VAL* 1.3 76.2 - - - +
743A LYS* 1.3 65.6 + - - +
754A ALA* 3.2 7.4 - - - +
755A LEU* 2.7 53.7 + - + +
757A LYS* 4.1 27.3 + - + -
810A TYR* 4.6 9.2 - + - -
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Residues in contact with LYS 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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729A ILE* 3.8 3.5 - - - +
730A ILE* 3.0 53.2 + - + +
731A GLY* 2.9 12.1 + - - +
733A ILE* 3.8 26.1 - - + +
742A TYR* 1.3 72.5 - - - +
744A ALA* 1.3 68.2 + - - +
752A LEU* 4.2 18.2 - - + +
753A VAL 3.5 4.0 - - - +
815A TYR* 3.2 50.0 + - + +
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Residues in contact with ALA 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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727A PHE* 4.3 6.5 - - + -
728A ASP 3.1 20.4 - - - +
729A ILE* 4.1 3.4 - - + -
730A ILE* 3.9 9.0 - - - -
743A LYS* 1.3 80.3 - - - +
745A LYS* 1.3 59.2 + - - +
752A LEU* 3.3 6.8 - - - +
753A VAL* 2.8 51.8 + - + +
755A LEU* 4.2 19.7 - - + -
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Residues in contact with LYS 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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727A PHE* 3.4 4.4 - - - -
728A ASP* 2.8 51.9 + - + +
730A ILE* 4.2 12.5 - - + +
744A ALA* 1.3 72.2 - - - +
746A ASP* 1.3 65.3 + - - +
747A LYS* 3.4 2.1 + - + -
750A GLY* 3.8 15.3 - - - +
751A GLU 3.5 2.2 - - - -
752A LEU* 3.6 28.0 - - + -
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Residues in contact with ASP 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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722A ARG* 3.1 31.2 + - - -
727A PHE* 3.7 25.5 - - + -
744A ALA 4.2 0.4 - - - -
745A LYS* 1.3 70.8 - - - +
747A LYS* 1.3 62.5 + - - +
748A ASP* 3.0 12.7 + - - +
749A THR* 3.5 31.2 + - - +
750A GLY* 2.7 31.5 + - - -
751A GLU* 2.9 17.4 + - + +
753A VAL* 5.1 3.8 - - + +
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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