Contacts of the helix formed by residues 748 - 759 (chain S) in PDB entry 1I84
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 748 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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747S MET* 1.3 74.0 - - - +
749S GLY* 1.3 67.4 + - - +
750S LYS 3.0 2.4 + - - -
751S GLN* 3.4 7.0 + - + +
752S ALA* 2.6 24.8 + - - +
368V LYS* 5.5 3.8 - - - -
371V ARG* 0.5 182.4 + - - +
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Residues in contact with GLY 749 (chain S).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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727S PHE* 4.0 3.2 - - - +
731S ARG* 5.0 6.8 + - - -
747S MET 3.2 6.4 + - - -
748S ASP* 1.3 75.1 + - - +
750S LYS* 1.3 66.2 + - - +
752S ALA* 3.8 3.7 - - - +
753S CYS* 3.0 22.5 + - - +
368V LYS* 5.4 0.6 - - - +
369V LYS 4.3 11.6 + - - -
370V GLU* 4.4 16.4 - - - -
371V ARG* 4.0 0.9 - - - +
372V ASN* 3.5 11.1 + - - -
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Residues in contact with LYS 750 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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727S PHE* 3.2 18.6 - - + -
748S ASP* 3.0 15.2 + - - +
749S GLY* 1.3 71.7 - - - +
751S GLN* 1.3 63.2 + - + +
753S CYS* 2.6 29.3 + - - +
754S ILE* 3.0 26.8 + - + +
769S ILE* 4.2 10.0 - - + +
770S GLY 4.1 18.7 + - - -
771S GLN* 4.9 4.5 - - - +
371V ARG* 3.7 9.8 - - + +
372V ASN* 2.7 26.2 + - - +
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Residues in contact with GLN 751 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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747S MET* 2.8 42.9 - - - +
748S ASP* 3.3 6.0 + - - +
750S LYS* 1.3 83.1 - - + +
752S ALA* 1.3 60.5 + - - +
754S ILE* 3.0 24.8 + - + +
755S LEU* 3.2 34.1 + - + +
371V ARG* 3.5 18.1 - - - +
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Residues in contact with ALA 752 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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731S ARG* 3.8 17.3 - - - +
742S ILE* 2.9 30.6 - - + +
747S MET* 3.3 44.6 - - + +
748S ASP 2.6 26.6 + - - +
749S GLY 3.8 2.2 - - - +
751S GLN* 1.3 73.4 - - - +
753S CYS* 1.3 58.4 + - - +
755S LEU* 3.6 5.0 - - - +
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Residues in contact with CYS 753 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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727S PHE* 4.2 4.5 - - - +
730S PHE* 4.2 9.1 - - + -
731S ARG* 3.9 23.1 - - + -
749S GLY 3.0 12.4 + - - +
750S LYS 2.6 16.7 + - - -
752S ALA* 1.3 72.2 - - - +
754S ILE* 1.3 66.5 + - - -
755S LEU 3.0 5.4 - - - -
756S MET* 2.9 27.6 + - + +
757S ILE* 3.3 13.4 + - - +
774S ILE* 3.7 30.1 - - - -
372V ASN* 4.1 12.8 - - - -
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Residues in contact with ILE 754 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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750S LYS* 3.0 34.7 + - + +
751S GLN* 3.0 17.8 + - + +
753S CYS* 1.3 80.4 - - - +
755S LEU* 1.3 72.5 + - + +
757S ILE* 3.3 17.3 + - + +
758S LYS* 3.4 22.1 + - + +
769S ILE* 3.4 42.4 - - + -
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Residues in contact with LEU 755 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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741S ALA* 3.1 32.4 - - + +
742S ILE* 4.0 0.7 - - - -
743S PRO* 3.7 7.6 - - + -
747S MET* 3.1 36.3 - - + -
751S GLN* 3.2 29.9 + - + +
752S ALA 3.6 9.0 - - - +
754S ILE* 1.3 82.5 - - + +
756S MET* 1.3 58.3 + - - +
757S ILE 3.0 0.2 - - - -
758S LYS* 2.8 26.6 + - + +
759S ALA* 3.0 9.5 + - - +
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Residues in contact with MET 756 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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730S PHE* 3.9 20.9 - - + -
731S ARG* 3.8 29.2 - - - -
734S TYR 4.0 9.0 - - - +
735S GLU* 3.5 37.0 - - + -
738S ALA* 4.0 9.4 - - + +
741S ALA* 3.7 6.7 - - + +
742S ILE* 3.2 30.7 - - + -
753S CYS* 2.9 21.3 - - - +
755S LEU* 1.3 74.7 - - - +
757S ILE* 1.3 57.6 + - - +
758S LYS 3.3 0.2 - - - -
759S ALA* 3.5 12.7 - - - +
760S LEU* 3.1 30.5 + - + +
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Residues in contact with ILE 757 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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730S PHE* 4.4 14.1 - - + -
753S CYS 3.4 14.6 - - - +
754S ILE* 3.3 14.3 + - + +
755S LEU 3.0 1.2 - - - -
756S MET* 1.3 76.9 - - - +
758S LYS* 1.3 70.6 + - - +
759S ALA 3.1 0.4 - - - -
760S LEU* 3.3 6.6 + - - -
761S GLU 3.2 14.9 + - - -
762S LEU* 3.3 17.9 + - + +
767S TYR* 3.2 49.1 - - + +
769S ILE* 4.3 14.6 - - + -
774S ILE* 4.0 26.0 - - + -
776S PHE* 4.8 6.5 - - + -
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Residues in contact with LYS 758 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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754S ILE* 3.6 20.2 - - + +
755S LEU* 2.8 10.0 + - - +
757S ILE* 1.3 84.8 + - - +
759S ALA* 1.3 59.3 + - - +
760S LEU 3.1 0.4 - - - -
761S GLU* 2.9 30.2 + - - +
762S LEU 4.0 16.6 + - - +
764S PRO* 5.4 5.5 - - - +
767S TYR* 3.4 25.3 + - - -
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Residues in contact with ALA 759 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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738S ALA* 3.5 26.8 - - + +
741S ALA* 3.6 11.4 - - + -
755S LEU 3.0 4.2 + - - +
756S MET* 3.5 19.5 - - - +
758S LYS* 1.3 78.8 - - - +
760S LEU* 1.3 60.5 + - - +
761S GLU* 3.3 7.5 - - - +
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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