Contacts of the helix formed by residues 751 - 761 (chain A) in PDB entry 3F2B
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 ASP 751 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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274A TYR* 5.1 8.1 - - - -
357A VAL* 4.3 6.2 - - + +
358A THR* 4.1 3.7 + - - -
746A TYR* 3.7 21.8 - - + -
747A LEU* 3.5 12.1 + - - +
748A ASN* 2.7 45.9 + - - +
750A GLU* 1.3 78.7 + - - +
752A LYS* 1.3 64.6 + - - +
753A ILE 3.1 1.5 + - - -
754A TYR* 3.2 46.0 + - + +
755A ARG 3.9 2.3 + - - -
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Residues in contact with LYS 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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746A TYR* 3.5 30.2 - - + +
749A PRO 3.4 16.6 + - - +
750A GLU* 2.9 1.5 - - - +
751A ASP* 1.3 77.7 - - - +
753A ILE* 1.3 64.0 + - - +
755A ARG* 3.1 15.6 + - - +
756A LYS* 3.1 33.5 + - - +
772A GLU* 4.7 3.3 + - - +
773A LEU* 2.6 42.4 + - + +
774A PRO 4.0 3.5 - - - -
775A ASP* 3.2 28.4 + - - +
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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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274A TYR 5.7 1.1 - - - +
750A GLU 3.3 17.3 + - - +
752A LYS* 1.3 79.1 - - - +
754A TYR* 1.3 70.7 + - + +
756A LYS* 3.2 13.7 + - + +
757A ILE* 3.0 25.0 + - + +
1020A TYR* 3.9 31.6 - - + +
1035A ARG* 4.2 25.1 - - - +
1036A LEU* 4.0 22.2 - - + -
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Residues in contact with TYR 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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274A TYR* 3.4 18.7 - + - -
357A VAL* 3.8 20.9 - - + -
750A GLU 4.8 0.4 - - - -
751A ASP* 3.2 47.4 + - - +
753A ILE* 1.3 77.5 - - + +
755A ARG* 1.3 63.2 + - - +
757A ILE* 3.2 10.3 + - + +
758A LEU* 3.1 23.9 + - - +
1035A ARG* 2.7 47.8 + - - -
1036A LEU* 3.8 20.2 - - + -
1039A GLY* 3.4 46.9 - - - +
1040A CYS* 4.1 4.1 - - - -
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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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354A MET 5.5 0.2 - - - +
355A ASP* 2.7 58.2 + - - -
356A ALA* 4.8 0.4 - - - +
357A VAL* 3.8 17.0 - - + +
745A HIS* 3.6 17.7 + - - -
746A TYR* 4.1 21.8 + - + -
751A ASP 3.9 1.2 + - - -
752A LYS 3.1 9.8 + - - +
754A TYR* 1.3 75.1 - - - +
756A LYS* 1.3 66.6 + - - +
758A LEU* 3.1 5.8 + - + +
759A ILE* 2.9 45.6 + - + +
768A LEU* 4.5 9.3 - - - +
773A LEU* 4.3 16.0 - - + +
774A PRO* 4.4 18.2 + - - +
776A VAL* 3.7 22.8 - - - +
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Residues in contact with LYS 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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2A PO4 3.7 23.1 - - - +
752A LYS* 3.1 31.6 + - - +
753A ILE* 3.4 18.2 - - + +
755A ARG* 1.3 76.4 - - - +
757A ILE* 1.3 62.3 + - - +
759A ILE* 3.5 2.0 + - - +
760A HIS* 3.0 25.3 + - - +
769A ASN* 5.0 0.7 - - - +
772A GLU* 3.2 35.0 + - - -
773A LEU* 3.8 29.4 - - + +
1020A TYR* 3.3 24.2 - - - +
1024A HIS* 5.8 0.2 - - + -
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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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753A ILE* 3.0 23.9 + - + +
754A TYR* 3.4 10.8 - - - +
756A LYS* 1.3 76.8 - - - +
758A LEU* 1.3 63.2 - - - +
760A HIS* 3.4 10.7 + - - +
761A SER* 3.4 11.8 + - - -
1016A PHE* 4.1 34.5 - - + +
1017A VAL* 4.3 8.5 - - + -
1020A TYR* 3.9 38.8 - - + -
1036A LEU* 4.1 40.2 - - + -
1040A CYS* 4.2 13.0 - - - -
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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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354A MET* 3.8 34.9 - - + +
355A ASP 5.9 0.2 - - - -
356A ALA 4.6 0.4 - - - +
357A VAL* 4.2 17.5 - - + -
754A TYR 3.1 11.2 + - - +
755A ARG* 3.1 8.2 + - - +
757A ILE* 1.3 72.5 - - - +
759A ILE* 1.3 67.7 + - - +
761A SER* 2.6 26.4 + - - -
762A GLN* 4.1 5.2 + - - +
1008A VAL* 4.3 4.7 - - + -
1016A PHE* 3.6 33.7 - - + -
1040A CYS* 4.5 17.7 - - + +
1043A VAL* 3.6 40.4 - - + -
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Residues in contact with ILE 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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354A MET 4.0 15.5 - - - +
355A ASP* 3.8 6.5 - - - +
755A ARG* 2.9 57.0 + - + +
756A LYS* 4.0 3.6 - - - +
758A LEU* 1.3 74.8 - - - +
760A HIS* 1.3 62.7 + - - +
762A GLN* 3.0 24.3 + - - +
766A ASN* 4.2 20.4 - - - +
768A LEU* 4.5 11.0 - - + -
769A ASN* 3.2 37.2 + - - +
773A LEU* 4.3 18.6 - - + -
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Residues in contact with HIS 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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2A PO4 2.7 28.5 + - - +
756A LYS 3.0 19.4 + - - +
757A ILE 3.7 4.9 - - - +
758A LEU 3.1 0.4 - - - -
759A ILE* 1.3 77.0 - - - +
761A SER* 1.3 62.2 + - - +
762A GLN 3.0 5.9 + - - -
763A GLY* 3.4 11.3 + - - -
769A ASN* 3.6 15.2 + - - +
1016A PHE 5.7 0.9 - - - -
1019A ALA* 5.1 2.5 - - + -
1020A TYR* 3.9 30.3 - + + -
1023A ASP* 2.6 41.4 + - + +
1024A HIS* 4.6 4.9 - + - -
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Residues in contact with SER 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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354A MET* 4.9 2.8 - - - -
757A ILE 3.4 7.6 + - - -
758A LEU 2.6 20.5 + - - -
760A HIS* 1.3 82.7 - - - +
762A GLN* 1.3 64.3 + - - +
763A GLY 3.5 1.0 + - - -
1016A PHE* 3.7 46.4 - - - -
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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