Contacts of the helix formed by residues 753 - 762 (chain A) in PDB entry 5A7R
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 VAL 753 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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752A LEU* 1.3 82.9 - - - +
754A GLN* 1.3 65.9 + - - +
755A GLU 3.4 1.3 - - - -
756A ASN* 3.0 15.7 + - - +
757A ILE* 2.9 21.8 + - - +
795A TYR* 3.3 35.4 - - + +
796A ALA* 4.1 2.2 - - + -
874A ALA* 4.7 0.2 - - + -
1964A AR6 3.2 37.0 - - - +
1965A AR6 3.8 28.5 - - + +
1977A GOL 4.0 19.7 - - - +
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Residues in contact with GLN 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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726A ILE* 3.8 19.0 - - - +
736A VAL 3.0 26.5 + - - -
737A ASP* 3.8 2.5 - - - +
738A PHE* 2.8 41.6 + - + +
753A VAL* 1.3 71.4 - - - +
755A GLU* 1.3 71.8 + - - +
757A ILE* 3.9 5.0 - - - +
758A ARG* 3.0 28.4 + - - +
795A TYR* 3.6 3.9 + - - -
1964A AR6 2.9 68.4 + - + +
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Residues in contact with GLU 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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737A ASP* 2.6 41.0 - - - +
738A PHE 3.5 14.5 + - - +
739A ALA* 3.3 14.6 - - - +
740A ASN 3.0 13.5 + - - -
743A VAL* 4.0 0.9 - - - +
744A GLY* 2.9 42.5 + - - -
745A GLY 3.3 0.2 + - - -
753A VAL* 3.4 0.6 - - - +
754A GLN* 1.3 80.1 + - - +
756A ASN* 1.3 62.7 + - - +
758A ARG* 3.3 1.3 + - - -
759A PHE* 3.0 33.5 + - + -
1964A AR6 2.8 29.2 + - - +
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Residues in contact with ASN 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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744A GLY 3.1 22.6 + - - -
746A GLY 3.5 10.5 - - - +
747A VAL* 3.7 16.0 - - - +
751A GLY* 3.4 31.5 - - - +
752A LEU* 3.2 5.2 + - - +
753A VAL* 3.0 33.8 + - - +
755A GLU* 1.3 74.4 - - - +
757A ILE* 1.3 64.1 + - - +
759A PHE* 3.4 3.6 + - - +
760A LEU* 3.1 28.8 + - - +
1964A AR6 3.2 22.5 + - - +
1965A AR6 3.7 2.2 + - - -
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Residues in contact with ILE 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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727A GLU* 6.2 0.4 - - - -
752A LEU* 3.6 26.5 - - + +
753A VAL 2.9 17.9 + - - +
754A GLN* 3.9 4.0 - - - +
756A ASN* 1.3 76.3 - - - +
758A ARG* 1.3 64.9 + - - +
760A LEU* 3.0 18.6 + - - +
761A ILE* 3.0 16.5 + - + +
792A TYR* 3.7 44.2 - - + +
795A TYR* 3.7 30.3 - - + -
799A TYR* 3.8 30.3 - - + -
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Residues in contact with ARG 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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726A ILE* 4.4 4.9 - - - +
727A GLU* 3.5 31.6 - - - +
735A GLN* 2.8 38.4 + - - +
736A VAL 5.5 2.0 + - - -
737A ASP* 4.7 8.3 - - + +
754A GLN* 3.0 23.7 + - - +
755A GLU* 3.3 6.9 + - - +
757A ILE* 1.3 77.4 - - - +
759A PHE* 1.3 56.8 + - - +
761A ILE* 3.7 11.3 - - - +
762A ASN* 2.9 44.6 + - - +
765A LEU* 3.7 15.4 - - + +
788A GLN* 5.3 0.6 + - - -
819A THR* 4.2 0.4 - - - +
821A ILE* 3.7 29.3 - - + +
1974A GOL 3.2 32.1 + - - -
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Residues in contact with PHE 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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737A ASP* 3.8 15.9 - - - -
743A VAL* 4.3 6.3 - - + -
744A GLY* 3.5 32.5 - - - -
747A VAL* 3.7 22.9 - - + -
755A GLU* 3.0 41.2 + - + +
756A ASN 3.8 0.4 - - - +
757A ILE 3.3 0.2 - - - -
758A ARG* 1.3 76.1 - - + +
760A LEU* 1.3 57.5 + - - +
762A ASN 4.2 0.4 - - - -
763A PRO* 3.2 25.6 - - - +
765A LEU* 3.3 53.8 - - + -
766A ILE* 3.4 26.5 - - + +
768A SER* 3.8 11.4 - - - -
769A ARG* 4.5 2.0 - - - -
781A LEU* 6.0 0.4 - - + -
783A ILE* 5.8 3.8 - - + -
821A ILE* 6.2 0.4 - - + -
823A ALA* 5.7 2.5 - - + -
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Residues in contact with LEU 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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664A LEU* 5.8 0.2 - - + -
675A LYS* 3.9 28.3 - - + +
678A THR* 3.4 25.8 - - + +
679A LEU* 4.1 34.7 - - + +
747A VAL* 3.8 23.3 - - + +
752A LEU* 3.6 30.7 - - + -
756A ASN 3.1 14.9 + - - +
757A ILE* 3.0 8.7 + - - +
759A PHE* 1.3 75.4 - - - +
761A ILE* 1.3 63.3 + - - +
763A PRO* 3.3 17.2 - - - +
766A ILE* 5.0 0.2 - - + -
789A TYR* 6.0 0.2 - - - +
790A SER* 5.0 0.7 + - - -
799A TYR* 4.4 12.8 - - + +
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Residues in contact with ILE 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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678A THR* 4.4 2.2 - - + -
727A GLU* 4.3 15.7 - - + -
757A ILE* 3.0 19.3 + - + +
758A ARG* 3.7 15.7 - - - +
760A LEU* 1.3 78.2 - - - +
762A ASN* 1.4 69.7 + - - +
763A PRO* 3.4 3.9 - - - +
788A GLN* 3.6 21.0 - - + +
789A TYR* 2.9 30.7 + - - +
790A SER* 3.6 30.4 + - - +
792A TYR* 4.0 37.5 - - + -
799A TYR* 4.1 15.0 - - - +
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Residues in contact with ASN 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 ARG* 2.9 31.3 + - - +
759A PHE 3.5 4.8 - - - +
761A ILE* 1.4 80.9 - - - +
763A PRO* 1.3 59.4 - - - +
764A GLU* 3.2 2.7 - - - -
765A LEU* 3.0 37.6 + - + +
786A THR* 3.1 24.9 + - - +
787A GLU 3.5 20.2 + - - +
788A GLN* 3.2 23.0 - - - +
819A THR* 4.8 0.2 - - - +
821A ILE* 4.4 1.4 - - - +
1974A GOL 3.3 20.8 + - - -
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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