Contacts of the helix formed by residues 752 - 763 (chain A) in PDB entry 4B87
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 752 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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730A LEU 4.8 0.8 + - - -
751A CYS* 1.3 82.4 - - - +
753A GLU* 1.3 60.7 + - - +
754A ILE 3.5 1.4 + - - -
755A THR* 3.0 17.6 + - - -
756A GLY* 3.0 22.2 + - - -
772A PRO* 3.9 2.8 - - - +
773A LEU 4.0 8.1 - - - -
775A LEU* 4.8 7.0 - - - -
788A LEU* 4.0 4.4 - - - +
796A GLY* 2.8 35.7 + - - -
798A VAL* 3.8 17.3 - - - +
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Residues in contact with GLU 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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752A SER* 1.3 72.9 - - - +
754A ILE* 1.3 68.4 + - + +
756A GLY* 3.1 1.6 + - - -
757A ASN* 2.9 35.8 + - - +
772A PRO* 3.8 22.9 - - + +
773A LEU 4.3 7.5 + - - +
774A PRO* 6.4 0.7 - - + -
912A ASN* 4.5 15.4 + - - +
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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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752A SER* 3.4 1.0 + - - -
753A GLU* 1.3 77.3 - - + +
755A THR* 1.3 64.2 + - - +
757A ASN* 3.2 11.8 + - - +
758A LEU* 3.1 24.8 + - + +
795A PRO* 3.6 26.9 - - + +
796A GLY* 3.7 20.6 - - - +
910A CYS 3.9 8.5 - - - +
911A LEU* 3.3 44.0 - - + +
912A ASN* 3.7 24.5 - - + +
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Residues in contact with THR 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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730A LEU* 3.5 36.3 - - + +
731A THR 4.4 0.9 + - - -
732A HIS* 4.0 8.8 - - - -
733A PHE* 4.2 14.9 + - + +
751A CYS* 3.8 17.7 - - + -
752A SER* 3.0 21.7 + - - -
754A ILE* 1.3 77.2 - - - +
756A GLY* 1.3 52.4 + - - +
758A LEU* 3.1 10.9 + - - +
759A LEU* 2.7 39.7 + - + +
795A PRO 4.9 0.9 + - - -
796A GLY* 3.1 15.9 + - - -
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Residues in contact with GLY 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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751A CYS* 3.6 5.5 - - - -
752A SER 3.0 16.4 + - - -
753A GLU* 3.1 4.2 + - - -
755A THR* 1.3 74.5 - - - +
757A ASN* 1.3 57.0 + - - +
759A LEU* 3.3 3.6 + - - +
760A LYS* 2.9 30.9 + - - +
770A ILE* 3.6 29.1 - - - +
772A PRO* 5.3 2.5 - - - -
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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
----------------------------------------------------------
753A GLU* 2.9 31.1 + - - +
754A ILE* 3.4 9.2 - - - +
756A GLY* 1.3 74.1 - - - +
758A LEU* 1.3 58.7 + - - +
760A LYS* 3.4 4.6 + - - +
761A ASN* 2.9 45.6 + - - +
910A CYS* 3.2 36.2 + - + +
912A ASN* 4.3 14.5 + - - +
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Residues in contact with LEU 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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733A PHE* 3.6 46.2 - - + -
754A ILE* 3.1 19.4 + - + +
755A THR* 3.5 5.6 - - - +
757A ASN* 1.3 77.2 - - - +
759A LEU* 1.3 64.4 + - - +
762A LYS* 2.9 39.6 + - + +
763A LEU 3.5 1.0 + - - -
881A ILE* 3.8 17.3 - - + -
907A THR* 3.9 26.9 - - + +
910A CYS* 3.7 27.4 - - + -
911A LEU* 3.8 11.0 - - + -
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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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730A LEU* 3.5 27.8 - - + -
733A PHE* 3.9 19.1 - - + -
738A TYR* 4.8 0.2 - - + -
741A LEU* 3.8 17.0 - - + -
749A VAL* 3.7 32.1 - - + -
751A CYS* 4.3 13.2 - - - -
755A THR 2.7 22.7 + - - +
756A GLY* 3.3 6.3 + - - +
758A LEU* 1.3 72.5 - - - +
760A LYS* 1.3 56.8 + - - +
763A LEU* 3.2 14.4 + - + +
764A HIS 3.0 24.4 + - - -
765A VAL* 3.0 21.9 + - + -
770A ILE* 4.0 12.8 - - + -
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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 GLY 2.9 17.2 + - - +
757A ASN* 3.7 5.8 - - - +
759A LEU* 1.3 77.2 - - - +
761A ASN* 1.3 75.6 + - - +
764A HIS* 3.2 27.2 - - - -
765A VAL 3.9 15.9 - - - +
767A GLU* 3.3 32.1 - - + +
770A ILE* 3.8 9.8 - - + +
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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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757A ASN* 2.9 31.5 + - - +
760A LYS* 1.3 94.1 - - - +
762A LYS* 1.3 61.3 + - + +
764A HIS* 3.5 18.9 + - - -
910A CYS* 4.2 20.4 - - - -
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Residues in contact with LYS 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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733A PHE* 4.0 21.3 - - + -
758A LEU* 2.9 32.6 + - + +
761A ASN* 1.3 81.6 - - + +
763A LEU* 1.3 68.1 + - + +
764A HIS* 3.5 13.5 - - - -
903A GLU* 4.3 22.6 + - - +
906A LYS* 6.0 0.9 - - + -
907A THR* 3.1 36.8 + - - +
910A CYS* 5.2 3.1 - - - -
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Residues in contact with LEU 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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733A PHE* 3.7 26.2 - - + -
738A TYR* 3.6 39.7 - - + +
741A LEU* 3.9 32.1 - - + +
742A SER* 3.7 4.2 - - - -
743A LYS* 3.6 13.3 + - - +
758A LEU 3.5 0.4 + - - -
759A LEU* 3.2 19.0 + - + +
762A LYS* 1.3 83.5 - - + +
764A HIS* 1.3 76.0 + - - +
765A VAL* 3.1 8.3 + - + -
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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