Contacts of the helix formed by residues 745 - 762 (chain A) in PDB entry 6J8H
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 745 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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742A MET* 3.1 3.2 + - + -
744A PRO* 1.3 105.1 - - + +
746A VAL* 1.3 59.9 + - + +
747A ASP 3.4 2.0 - - - -
748A LEU* 3.3 13.2 + - + +
749A ALA* 2.7 39.1 + - - +
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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
----------------------------------------------------------
740A ILE* 3.8 20.2 - - + +
741A VAL 3.7 2.9 - - - +
742A MET* 2.8 41.6 + - + +
745A PHE* 1.3 74.5 - - + +
747A ASP* 1.3 61.9 + - - +
749A ALA* 3.4 6.9 + - - +
750A ILE* 3.4 25.6 + - + +
794A LYS* 5.6 5.6 - - - +
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Residues in contact with ASP 747 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741A VAL 3.8 6.2 + - - +
742A MET 3.1 6.6 + - - +
743A ASP* 3.9 33.9 - - - +
746A VAL* 1.3 78.6 - - - +
748A LEU* 1.3 61.4 + - - +
750A ILE* 3.4 16.6 + - - +
751A THR* 3.5 13.5 - - - +
794A LYS* 4.9 14.1 + - - +
847A LYS* 3.7 24.6 + - - -
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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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743A ASP 4.1 4.5 + - - +
744A PRO 3.7 17.5 - - - +
745A PHE* 3.3 22.0 + - + +
746A VAL 3.3 0.2 - - - -
747A ASP* 1.3 76.8 - - - +
749A ALA* 1.3 76.7 + - + +
751A THR* 3.2 28.1 + - + +
752A ILE* 3.6 16.9 + - + +
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Residues in contact with ALA 749 (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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745A PHE* 2.7 23.1 + - + +
746A VAL* 3.6 9.0 - - - +
747A ASP 3.3 0.4 - - - -
748A LEU* 1.3 83.2 - - + +
750A ILE* 1.3 61.8 + - + +
752A ILE* 3.3 17.4 + - - +
753A CYS* 3.3 9.7 + - - +
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Residues in contact with ILE 750 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
746A VAL* 3.4 13.9 + - + +
747A ASP* 3.8 13.2 - - - +
748A LEU 3.2 0.8 - - - -
749A ALA* 1.3 76.7 - - + +
751A THR* 1.3 64.4 + - + +
753A CYS* 2.8 25.4 + - + +
754A ILE* 2.9 28.1 + - + +
786A ILE* 4.4 20.0 - - + -
787A PHE* 4.6 11.7 - - + -
790A GLU* 4.1 44.9 - - + +
844A LYS* 4.9 6.1 - - + +
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Residues in contact with THR 751 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747A ASP* 3.5 21.8 - - - +
748A LEU* 3.2 20.8 + - + +
750A ILE* 1.3 75.1 - - + +
752A ILE* 1.3 72.7 + - - +
754A ILE* 3.1 13.0 + - + +
755A VAL* 3.0 23.7 + - - +
844A LYS* 6.0 7.9 - - + -
845A LEU* 4.6 20.9 - - - +
847A LYS* 5.3 11.2 - - - -
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Residues in contact with ILE 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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748A LEU* 3.6 23.7 + - + +
749A ALA* 3.3 11.4 + - - +
750A ILE 3.2 0.6 - - - -
751A THR* 1.3 85.8 + - - +
753A CYS* 1.3 62.8 + - - +
755A VAL* 3.2 15.9 - - + +
756A LEU* 3.1 28.5 + - + +
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Residues in contact with CYS 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 ALA 3.3 6.2 + - - +
750A ILE* 2.8 20.7 + - + +
752A ILE* 1.3 81.9 - - - +
754A ILE* 1.3 54.3 + - - -
756A LEU* 3.4 9.0 + - - +
757A ASN* 3.0 25.5 + - - +
783A PHE* 3.9 19.9 - - + -
786A ILE* 4.5 17.0 - - + -
787A PHE* 3.5 30.1 - - - -
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Residues in contact with ILE 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 ILE* 2.9 19.6 + - + +
751A THR* 3.1 11.4 + - - +
753A CYS* 1.3 73.5 - - - +
755A VAL* 1.3 66.8 + - - +
757A ASN* 3.2 4.7 + - + +
758A THR* 3.2 20.8 + - - +
787A PHE* 3.1 31.4 - - + -
841A ARG* 3.6 37.5 - - + +
842A VAL* 4.0 17.3 - - + +
844A LYS* 3.4 38.4 - - + +
845A LEU* 5.1 6.7 - - + -
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Residues in contact with VAL 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 THR 3.0 11.5 + - - +
752A ILE* 3.2 27.8 - - + +
754A ILE* 1.3 78.0 - - - +
756A LEU* 1.3 65.3 + - + +
758A THR* 2.7 32.1 - - + +
759A LEU* 3.3 7.4 + - - +
842A VAL* 5.7 3.6 - - + -
845A LEU* 4.6 20.2 - - + +
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Residues in contact with LEU 756 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
752A ILE* 3.1 20.5 + - + +
753A CYS* 3.6 8.5 - - - +
755A VAL* 1.3 85.2 - - + +
757A ASN* 1.3 62.9 + - - +
759A LEU* 3.3 12.6 + - + +
760A PHE* 3.0 24.2 + - + +
783A PHE* 4.3 15.7 - - + -
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Residues in contact with ASN 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 CYS 3.0 13.9 + - - +
754A ILE* 3.2 13.1 + - - +
756A LEU* 1.3 74.9 - - - +
758A THR* 1.3 65.7 + - - +
760A PHE* 3.1 12.0 + - - +
761A MET* 3.1 24.8 + - - +
780A ASN* 4.7 5.3 - - - +
783A PHE* 3.5 39.6 - - + +
787A PHE* 3.9 10.3 - - + -
838A ARG* 3.0 31.4 + - - +
841A ARG* 4.9 2.8 + - - +
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Residues in contact with THR 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 ILE 3.2 5.9 + - - +
755A VAL* 2.7 38.6 - - + +
757A ASN* 1.3 78.0 - - - +
759A LEU* 1.3 74.5 + - + +
761A MET* 3.0 25.5 + - - +
762A ALA* 3.0 13.7 + - - +
839A LEU* 5.1 0.5 - - - +
842A VAL* 3.8 34.3 - - + +
1333A LEU* 4.5 11.9 - - + +
1334A ILE* 5.7 1.2 - - - +
1337A ILE* 3.8 18.5 - - - +
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Residues in contact with LEU 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 VAL 3.7 7.0 - - - +
756A LEU* 3.3 19.7 + - + +
757A ASN 3.2 0.4 - - - -
758A THR* 1.3 88.9 - - + +
760A PHE* 1.3 62.4 + - - +
762A ALA* 3.3 18.5 + - + +
763A MET* 3.3 39.9 - - + +
1333A LEU* 5.5 8.7 - - + -
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Residues in contact with PHE 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 LEU* 3.0 16.7 + - + +
757A ASN* 3.1 12.1 + - - +
759A LEU* 1.3 78.0 - - - +
761A MET* 1.3 60.0 + - - +
762A ALA 3.4 0.5 + - - -
763A MET* 3.4 25.5 + - - +
775A VAL* 4.3 16.4 - - + -
776A LEU* 3.8 44.5 - - + +
779A GLY* 3.6 33.2 - - - -
780A ASN* 4.5 11.7 - - - -
783A PHE* 4.2 17.3 - + + -
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Residues in contact with MET 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 ASN* 3.1 14.5 + - - +
758A THR* 3.0 22.2 + - - +
760A PHE* 1.3 75.3 - - - +
762A ALA* 1.3 61.7 + - - +
763A MET 3.1 2.7 - - - -
764A GLU* 2.8 27.9 - - - +
776A LEU* 4.9 3.6 - - + -
780A ASN* 4.0 21.3 - - - +
836A SER* 4.7 8.3 - - - +
838A ARG* 4.0 26.5 - - + -
839A LEU* 3.3 44.4 - - + +
1337A ILE* 4.3 19.1 - - + +
1341A ASN* 5.8 2.7 - - - +
1392A VAL* 5.3 0.2 - - - +
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Residues in contact with ALA 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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758A THR 3.0 10.2 + - - +
759A LEU* 3.5 22.4 - - + +
760A PHE 3.2 0.6 - - - -
761A MET* 1.3 76.1 - - - +
763A MET* 1.3 62.1 + - + +
764A GLU* 3.3 4.9 + - - +
1333A LEU* 5.1 6.5 - - + -
1337A ILE* 4.5 13.7 - - + +
1392A VAL* 2.6 43.8 - - + +
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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
------------------------------------------------------------
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