Contacts of the helix formed by residues 733 - 741 (chain A) in PDB entry 2KFN
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 733 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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708A GLN* 3.4 30.5 - - - +
711A LEU* 3.7 11.4 - - + -
723A LEU* 4.6 13.5 - - + +
726A ALA* 3.7 24.5 - - + -
727A PHE* 3.4 50.0 - - + -
731A LYS 3.1 6.0 + - - +
732A ASP* 1.3 72.6 - - - +
734A HIS* 1.3 86.3 + - + +
736A ALA* 3.7 4.8 - - + +
737A THR* 2.6 40.6 + - - +
761A ASN* 4.4 2.5 - - - +
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Residues in contact with HIS 734 (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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708A GLN* 3.7 13.9 + - - -
711A LEU* 3.7 4.4 - - - +
732A ASP* 3.1 11.0 + - - +
733A ILE* 1.3 98.2 - - + +
735A ARG* 1.3 57.0 + - - +
738A ALA* 3.1 22.9 + - - +
754A ARG* 3.7 39.1 + - + +
757A ALA* 3.3 13.3 - - - +
758A LYS* 3.3 29.6 - - + +
761A ASN* 3.3 25.0 + - + +
762A PHE* 3.6 32.6 - + - -
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Residues in contact with ARG 735 (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 ASP* 2.9 32.7 + - + +
734A HIS* 1.3 73.5 - - - +
736A ALA* 1.3 60.6 + - - +
738A ALA* 3.3 5.1 + - - +
739A ALA* 2.8 31.0 + - - +
746A LEU* 2.9 54.4 + - + +
747A GLU* 3.2 21.4 + - - +
749A VAL* 3.4 35.8 + - + +
754A ARG* 3.8 24.4 - - + +
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Residues in contact with ALA 736 (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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726A ALA* 4.0 21.3 - - + -
731A LYS* 4.6 13.0 - - + +
732A ASP 2.9 16.1 + - - +
733A ILE* 3.7 10.3 - - + +
735A ARG* 1.3 77.4 - - - +
737A THR* 1.3 60.6 + - - +
739A ALA* 3.4 4.8 + - - +
740A GLU* 3.3 26.9 + - - +
746A LEU* 3.6 14.6 - - + +
795A TYR* 3.6 3.5 + - - +
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Residues in contact with THR 737 (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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321A MG 3.6 8.1 - - - -
723A LEU* 4.4 7.8 - - - +
733A ILE* 2.6 25.5 + - - +
734A HIS 3.7 4.9 - - - -
736A ALA* 1.3 74.9 - - - +
738A ALA* 1.3 59.3 + - - +
740A GLU* 3.2 2.1 + - - +
741A VAL* 2.8 44.6 + - + +
757A ALA* 3.8 12.8 - - + -
761A ASN* 3.3 17.2 + - - +
791A TYR* 3.5 31.4 - - + -
795A TYR* 3.7 13.0 + - + -
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Residues in contact with ALA 738 (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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734A HIS 3.1 15.8 + - - +
735A ARG 3.7 0.9 - - - +
737A THR* 1.3 76.0 - - - +
739A ALA* 1.3 60.9 + - - +
741A VAL* 4.5 0.4 - - - -
742A PHE* 2.9 45.9 + - + +
744A LEU* 3.7 2.4 - - - +
749A VAL* 3.7 23.6 - - + -
753A GLN 3.7 24.9 - - - +
754A ARG 4.2 0.2 - - - +
757A ALA* 3.7 6.3 - - + -
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Residues in contact with ALA 739 (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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735A ARG 2.8 17.5 + - - +
736A ALA* 3.6 8.7 - - - +
737A THR 3.3 0.2 - - - -
738A ALA* 1.3 76.5 - - - +
740A GLU* 1.3 58.7 + - + +
743A GLY* 3.1 6.4 + - - -
744A LEU* 3.1 47.4 + - - +
745A PRO 4.4 0.9 - - - +
746A LEU* 4.1 21.3 - - + +
749A VAL* 4.9 2.8 - - + +
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Residues in contact with GLU 740 (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 GLY* 5.4 4.0 - - - -
736A ALA 3.3 6.9 + - - +
737A THR 3.2 4.1 + - - +
738A ALA 3.1 0.2 - - - -
739A ALA* 1.3 79.9 - - + +
741A VAL* 1.3 67.2 + - - +
742A PHE 3.4 0.2 - - - -
743A GLY* 3.5 8.2 + - - -
794A ARG* 3.2 52.6 + - + +
795A TYR* 3.0 33.6 + - + +
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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
----------------------------------------------------------
737A THR* 2.8 41.9 + - + +
738A ALA* 4.2 2.2 - - - +
740A GLU* 1.3 75.3 - - - +
742A PHE* 1.3 81.5 + - + +
757A ALA* 5.5 0.7 - - + -
760A ILE* 5.0 7.6 - - + -
787A TYR* 4.0 13.0 - - - +
790A LEU* 3.6 54.1 - - + +
791A TYR* 3.9 23.8 - - + -
794A ARG* 5.5 0.2 - - + -
795A TYR* 4.6 4.7 - - + -
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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