Contacts of the helix formed by residues 751 - 765 (chain A) in PDB entry 2KFZ
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 SER 751 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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750A THR* 1.3 75.4 - - - +
752A GLU* 1.3 57.8 + - - +
754A ARG* 3.8 8.1 - - - +
755A ARG* 3.0 47.1 + - - +
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Residues in contact with GLU 752 (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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750A THR* 3.2 6.8 + - - +
751A SER* 1.3 76.2 - - - +
753A GLN* 1.3 69.8 + - - +
755A ARG* 3.4 24.5 + - - +
756A SER* 3.0 37.6 + - - +
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Residues in contact with GLN 753 (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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738A ALA* 3.7 9.2 - - + +
742A PHE* 3.7 33.6 - - + +
744A LEU* 3.2 38.3 - - - +
749A VAL* 3.4 9.8 - - + +
750A THR* 3.0 42.0 + - - +
752A GLU* 1.3 83.3 - - - +
754A ARG* 1.3 59.4 + - - +
756A SER* 3.1 5.7 + - - -
757A ALA* 3.0 24.4 + - - +
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Residues in contact with ARG 754 (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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682A ARG* 5.2 4.9 - - - +
732A ASP* 2.7 39.4 + - - -
734A HIS* 3.7 30.2 + - + +
735A ARG* 3.8 23.9 - - + +
738A ALA* 4.2 9.6 - - - -
749A VAL* 4.0 7.8 - - + +
750A THR 3.0 17.7 + - - +
751A SER* 3.8 8.3 - - - +
753A GLN* 1.3 76.0 - - - +
755A ARG* 1.3 58.0 + - - +
757A ALA* 3.5 1.7 + - - +
758A LYS* 3.0 52.6 + - - +
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Residues in contact with ARG 755 (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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751A SER* 3.0 33.1 + - - +
752A GLU* 3.6 34.9 + - - +
753A GLN 3.2 0.2 - - - -
754A ARG* 1.3 78.0 - - - +
756A SER* 1.3 60.3 + - - +
758A LYS* 3.9 9.9 - - - +
759A ALA* 3.3 22.3 + - - +
777A LEU* 3.8 11.2 - - + +
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Residues in contact with SER 756 (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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742A PHE* 3.9 20.9 - - - -
752A GLU* 3.0 23.4 + - - +
753A GLN* 3.1 10.6 + - - -
755A ARG* 1.3 77.8 - - - +
757A ALA* 1.3 62.1 + - - +
759A ALA* 3.6 4.2 + - - +
760A ILE* 3.2 27.7 + - - +
777A LEU* 3.6 31.7 - - - +
779A ILE* 5.9 0.5 - - - +
787A TYR* 4.2 7.4 + - - -
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Residues in contact with ALA 757 (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 3.3 25.1 - - - +
737A THR* 3.8 13.5 - - + +
738A ALA* 3.7 18.4 - - + +
741A VAL* 5.5 1.6 - - + -
742A PHE* 4.7 3.1 - - + -
753A GLN 3.0 14.1 + - - +
754A ARG 3.9 0.9 - - - +
756A SER* 1.3 73.5 - - - +
758A LYS* 1.3 59.5 + - - +
760A ILE* 3.2 14.3 + - - +
761A ASN* 2.9 33.4 + - - -
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Residues in contact with LYS 758 (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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682A ARG* 3.1 33.6 - - - +
734A HIS* 3.3 34.9 - - + +
754A ARG* 3.0 44.0 + - - +
755A ARG* 3.9 9.4 - - - +
757A ALA* 1.3 77.1 - - - +
759A ALA* 1.3 59.6 + - - +
761A ASN* 3.4 1.2 + - - +
762A PHE* 3.1 48.2 + - + -
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Residues in contact with ALA 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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755A ARG 3.3 15.6 + - - +
756A SER 3.8 3.8 - - - +
757A ALA 3.3 0.4 - - - -
758A LYS* 1.3 79.9 - - - +
760A ILE* 1.3 58.2 + - - +
762A PHE* 4.1 2.9 - - - +
763A GLY* 3.1 23.9 + - - -
773A LEU* 3.7 25.3 - - + +
776A GLN* 5.1 9.9 - - + -
777A LEU* 3.9 13.0 - - + -
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Residues in contact with ILE 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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741A VAL* 5.0 8.3 - - + -
742A PHE* 5.8 1.3 - - + -
756A SER 3.2 18.4 - - - +
757A ALA* 3.2 13.2 + - - +
759A ALA* 1.3 76.0 - - - +
761A ASN* 1.3 65.9 + - - +
763A GLY* 3.0 2.2 + - - -
764A LEU* 2.9 38.6 + - + +
773A LEU* 4.4 23.3 - - + -
787A TYR* 3.7 39.5 - - + +
788A MET* 4.8 11.5 - - + +
791A TYR* 3.5 37.2 - - + -
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Residues in contact with ASN 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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321A MG 2.3 28.4 - - - -
711A LEU* 3.8 22.0 - - + +
714A MET* 4.7 1.0 - - - +
733A ILE* 4.1 8.5 + - - +
734A HIS* 3.3 29.9 + - + +
737A THR* 3.3 21.9 + - - -
757A ALA 2.9 15.1 + - - +
758A LYS 3.4 5.6 + - - +
760A ILE* 1.3 77.7 - - - +
762A PHE* 1.3 61.4 + - - +
764A LEU* 3.5 17.9 + - - +
765A ILE* 3.7 12.5 - - - +
791A TYR* 3.1 12.6 + - - -
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Residues in contact with PHE 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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708A GLN* 4.9 9.6 - - + -
710A GLU* 5.3 6.5 - - - -
711A LEU* 3.5 21.5 - - + -
734A HIS* 3.6 28.0 - + - -
758A LYS* 3.1 43.1 + - + +
759A ALA* 4.7 2.5 - - - +
761A ASN* 1.3 75.2 - - - +
763A GLY* 1.3 64.3 + - - +
765A ILE* 3.6 23.4 + - + +
766A TYR* 3.1 36.4 - + + -
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Residues in contact with GLY 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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759A ALA 3.1 14.7 + - - -
760A ILE* 3.0 8.4 + - - -
762A PHE* 1.3 77.8 - - - +
764A LEU* 1.3 59.4 + - - +
766A TYR 3.2 3.8 + - - -
767A GLY 3.0 4.0 + - - -
768A MET* 2.8 52.5 + - - +
773A LEU* 6.4 1.3 - - - -
788A MET* 5.8 2.5 - - - -
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Residues in contact with LEU 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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714A MET* 4.1 15.5 - - + -
760A ILE* 2.9 24.2 + - + +
761A ASN* 3.7 8.1 - - - +
762A PHE 3.3 0.4 - - - -
763A GLY* 1.3 76.5 - - - +
765A ILE* 1.3 58.2 + - - +
767A GLY* 3.0 18.5 + - - +
768A MET 4.8 0.9 - - - +
788A MET* 4.3 17.3 - - + -
791A TYR* 3.4 44.4 - - + +
792A PHE* 3.7 31.0 - - + -
798A VAL* 4.0 9.9 - - + -
802A MET* 3.9 18.1 - - + +
844A ILE* 3.5 14.4 - - - +
848A MET* 4.5 1.1 - - - +
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Residues in contact with ILE 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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710A GLU* 3.9 30.3 - - + +
711A LEU* 3.4 32.5 - - + +
714A MET* 4.4 4.3 - - - -
761A ASN 3.7 7.0 - - - +
762A PHE* 3.6 25.5 + - + +
763A GLY 3.3 0.4 - - - -
764A LEU* 1.3 76.5 - - - +
766A TYR* 1.3 70.2 + - + +
767A GLY 3.5 0.9 + - - -
845A ASN* 3.1 46.3 + - - +
848A MET* 3.7 31.3 - - + +
849A GLN* 5.8 1.6 - - + +
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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