Contacts of the helix formed by residues 743 - 761 (chain A) in PDB entry 4B9N
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 PHE 743 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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668A ASP* 3.0 30.7 - - - +
670A ASN* 3.3 20.4 - - - -
671A LEU* 4.0 29.8 - - + -
681A ILE* 5.5 1.1 - - + -
684A LYS* 5.3 5.2 - - + -
685A THR* 4.2 23.8 - - + -
688A ASP* 3.5 18.6 - - + -
689A ILE* 5.4 0.4 - - + -
739A TYR* 2.7 61.3 + + + +
740A PHE* 3.3 8.6 - - - +
742A SER* 1.3 88.0 - - - +
744A PRO* 1.3 61.8 - - - +
746A VAL* 3.1 15.2 + - + +
747A LYS 3.3 8.1 + - - -
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Residues in contact with PRO 744 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668A ASP* 3.9 3.1 - - - +
670A ASN* 5.7 1.3 - - + -
740A PHE 3.1 11.6 - - - +
741A GLU* 3.6 11.4 - - - +
742A SER 3.4 10.1 - - - +
743A PHE* 1.3 88.3 - - - +
745A GLY* 1.3 57.0 + - - +
747A LYS* 3.4 7.8 + - + +
748A ARG* 2.9 48.2 + - - +
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Residues in contact with GLY 745 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
666A ALA* 3.7 14.9 - - - +
668A ASP* 2.7 29.3 + - - -
744A PRO* 1.3 74.3 - - - +
746A VAL* 1.3 57.8 + - - -
748A ARG* 3.3 24.5 - - - +
749A TYR* 2.8 28.4 + - - +
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Residues in contact with VAL 746 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662A LEU* 3.9 22.4 - - + -
666A ALA* 4.0 8.1 - - + -
668A ASP* 3.2 21.3 + - + +
671A LEU* 4.0 20.4 - - + -
712A ILE* 4.6 0.7 - - + -
739A TYR* 4.0 17.7 - - + +
740A PHE* 4.5 2.5 - - + -
743A PHE* 3.1 20.7 + - + +
745A GLY* 1.3 74.3 - - - +
747A LYS* 1.3 59.5 + - - +
749A TYR* 3.2 2.3 + - - +
750A MET* 2.8 57.0 + - + +
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Residues in contact with LYS 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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740A PHE* 3.5 57.0 - - + +
743A PHE 3.3 5.6 + - - +
744A PRO* 3.6 10.8 - - + +
746A VAL* 1.3 77.6 - - - +
748A ARG* 1.3 62.5 + - - +
750A MET* 3.2 4.7 + - + +
751A GLU* 3.0 49.6 + - + +
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Residues in contact with ARG 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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666A ALA 5.4 2.9 + - - -
667A GLU 5.4 3.8 + - - -
744A PRO* 2.9 37.4 + - - +
745A GLY* 3.3 27.0 - - - +
747A LYS* 1.3 76.3 - - - +
749A TYR* 1.3 57.0 + - - +
751A GLU* 3.4 12.1 + - - +
752A ASN* 2.9 50.3 + - - +
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Residues in contact with TYR 749 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662A LEU* 3.9 23.3 - - + -
665A ILE* 3.6 33.3 - - + +
666A ALA* 3.6 18.4 - - + -
745A GLY 2.8 19.7 + - - +
746A VAL 3.2 4.0 + - - +
748A ARG* 1.3 73.0 - - - +
750A MET* 1.3 86.2 + - - +
752A ASN* 4.5 6.1 - - + +
753A ILE* 2.9 50.5 + - + +
791A ALA 4.0 0.7 + - - -
792A MET 2.9 28.7 + - - -
795A PRO* 3.3 25.4 - - + +
796A ILE* 4.3 1.6 - - + -
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Residues in contact with MET 750 (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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662A LEU* 4.8 2.7 - - + -
712A ILE* 3.9 35.4 - - + +
740A PHE* 4.3 18.6 - - + -
746A VAL* 2.8 41.8 + - + +
747A LYS* 3.2 7.8 + - + +
749A TYR* 1.3 87.2 - - + +
751A GLU* 1.3 64.0 + - + +
753A ILE* 3.3 3.9 - - - +
754A VAL* 3.2 29.1 + - - +
792A MET* 3.5 45.8 - - + +
796A ILE* 4.8 2.5 - - + -
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Residues in contact with GLU 751 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747A LYS* 3.0 50.9 + - + +
748A ARG* 3.7 13.3 - - - +
750A MET* 1.3 77.7 - - + +
752A ASN* 1.3 65.5 + - - +
754A VAL* 3.4 5.6 + - - +
755A GLN* 3.2 21.8 + - - +
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Residues in contact with ASN 752 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
748A ARG* 2.9 44.9 + - - +
749A TYR* 3.3 6.3 + - + +
751A GLU* 1.3 75.6 - - - +
753A ILE* 1.3 57.7 + - - +
755A GLN* 3.3 8.0 + - - +
756A GLU* 2.9 30.3 + - - +
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Residues in contact with ILE 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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749A TYR* 2.9 44.2 + - + +
750A MET* 3.3 10.3 - - - +
752A ASN* 1.3 74.6 - - - +
754A VAL* 1.3 63.7 + - - +
756A GLU* 3.6 23.7 - - - +
757A ALA* 2.9 28.4 + - - +
763A VAL* 3.9 17.0 - - + +
764A THR 5.6 2.2 - - - +
791A ALA* 3.4 28.0 - - - +
792A MET* 3.9 17.0 - - + +
795A PRO* 4.2 11.0 - - + -
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Residues in contact with VAL 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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750A MET 3.2 19.2 + - - +
751A GLU* 3.7 5.8 - - - +
752A ASN 3.3 0.2 - - - -
753A ILE* 1.3 76.4 - - + +
755A GLN* 1.3 58.5 + - - +
757A ALA* 3.2 4.2 + - - +
758A LYS* 3.0 45.9 + - - +
776A ILE* 4.4 3.3 - - + +
788A GLU* 3.9 48.7 - - + +
791A ALA* 4.4 6.1 - - + -
792A MET* 4.0 18.2 - - + -
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Residues in contact with GLN 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 GLU 3.2 11.0 + - - +
752A ASN* 3.5 11.2 - - - +
754A VAL* 1.3 80.2 - - - +
756A GLU* 1.3 55.7 + - - +
758A LYS* 3.2 28.0 + - - +
759A GLN* 2.9 35.8 + - + +
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Residues in contact with GLU 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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752A ASN* 2.9 18.6 + - - +
753A ILE* 3.6 25.5 - - + +
755A GLN* 1.3 75.4 - - - +
757A ALA* 1.3 57.1 + - - +
759A GLN* 4.5 6.7 - - - +
760A LYS* 2.8 63.7 + - + +
762A TYR 4.5 4.7 - - - +
763A VAL* 5.8 2.0 - - + -
764A THR* 5.7 1.6 + - - -
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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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753A ILE 2.9 17.2 + - - +
754A VAL* 3.5 5.8 - - - +
756A GLU* 1.3 75.6 - - - +
758A LYS* 1.3 59.1 + - - +
761A GLY* 2.8 30.1 + - - -
762A TYR 3.8 12.8 - - - +
763A VAL* 3.7 18.3 - - + +
773A LEU* 4.3 10.0 - - + +
776A ILE* 4.1 15.0 - - + +
791A ALA* 3.9 13.2 - - + -
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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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754A VAL* 3.0 36.1 + - - +
755A GLN* 3.2 29.0 + - - +
757A ALA* 1.3 78.7 - - - +
759A GLN* 1.3 61.9 + - - +
761A GLY* 3.9 4.7 + - - -
776A ILE* 3.8 37.3 - - + +
777A THR* 5.3 10.2 - - + +
784A ARG* 5.6 4.1 - - - +
788A GLU* 4.6 9.1 + - - -
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Residues in contact with GLN 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 GLN* 2.9 25.5 + - + +
756A GLU* 4.0 7.5 - - - +
758A LYS* 1.3 80.2 - - - +
760A LYS* 1.3 96.1 + - - +
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Residues in contact with LYS 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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756A GLU* 2.8 44.4 + - + +
759A GLN* 1.3 104.7 + - - +
761A GLY* 1.3 58.5 + - - +
762A TYR* 3.3 54.6 - - + +
772A TYR* 5.5 0.3 - - - -
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Residues in contact with GLY 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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757A ALA* 2.8 18.0 + - - -
758A LYS 3.9 3.7 + - - -
759A GLN 3.5 1.8 + - - -
760A LYS* 1.3 77.0 - - - +
762A TYR* 1.3 61.3 + - - +
772A TYR* 3.4 10.9 - - - +
773A LEU* 3.0 28.1 + - - -
774A PRO* 5.1 1.1 - - - +
776A ILE* 5.8 1.1 - - - -
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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
------------------------------------------------------------
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