Contacts of the helix formed by residues 181 - 195 (chain 0) in PDB entry 1O1F
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 ALA 181 (chain 0).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1550 SER* 4.5 1.6 - - - +
1560 GLY 3.3 14.8 - - - +
1570 ASP 3.4 17.7 - - - +
1580 GLY 3.7 14.1 + - - -
1590 VAL 3.8 9.9 - - - +
1600 THR* 4.3 2.9 - - - +
1800 LEU* 1.3 77.5 - - - +
1820 GLY* 1.3 60.1 + - - +
1830 ARG 3.2 2.9 + - - -
1840 ASP* 3.2 10.8 + - - +
1850 LEU* 3.0 33.7 + - - +
3030 THR* 4.2 7.0 - - - -
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Residues in contact with GLY 182 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1560 GLY 3.0 11.2 + - - -
1570 ASP* 4.4 5.2 - - - -
1810 ALA* 1.3 76.3 - - - +
1830 ARG* 1.3 54.6 + - - +
1850 LEU* 3.5 7.8 - - - +
1860 THR* 3.0 18.2 + - - -
2130 LYS* 2.8 30.8 + - - -
3030 THR* 3.1 21.2 + - - -
3060 TYR* 4.6 0.2 - - - -
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Residues in contact with ARG 183 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140 SER* 2.8 36.0 + - - -
690 TYR* 3.5 29.6 + - - +
710 ILE 4.8 5.3 + - - -
720 GLU* 4.6 14.5 + - - +
730 HIS* 5.2 7.7 - - - +
1570 ASP* 2.9 47.7 + - - +
1580 GLY* 4.4 13.9 - - - -
1810 ALA 3.2 0.4 + - - -
1820 GLY* 1.3 71.4 - - - +
1840 ASP* 1.3 69.6 - - - +
1860 THR* 3.3 14.1 + - - -
1870 ASP* 3.3 24.7 + - - +
2060 ARG* 6.1 2.5 - - - +
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Residues in contact with ASP 184 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
730 HIS* 5.4 3.1 - - - -
1570 ASP 4.5 0.5 - - - +
1580 GLY* 4.7 5.0 - - - +
1790 ASP 3.9 12.1 - - - +
1800 LEU* 3.8 11.2 - - + +
1810 ALA* 3.2 28.4 + - - +
1830 ARG* 1.3 80.7 - - - +
1850 LEU* 1.3 61.4 + - + +
1870 ASP* 3.2 9.1 + - - +
1880 TYR* 3.1 27.7 + - - +
2670 ILE* 5.0 13.0 - - + +
2690 MET* 5.6 0.9 - - - +
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Residues in contact with LEU 185 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1800 LEU* 3.9 24.5 - - + -
1810 ALA 3.0 17.3 + - - +
1820 GLY 3.5 7.0 - - - +
1840 ASP* 1.3 78.2 - - + +
1860 THR* 1.3 62.1 + - - +
1880 TYR* 3.9 5.6 - - + +
1890 LEU* 3.3 8.7 + - - +
2130 LYS* 4.1 3.6 - - + -
2570 CYS* 3.2 38.6 - - - +
2580 PRO* 5.1 0.2 - - + -
2600 THR* 4.3 19.7 - - + -
2610 LEU* 4.0 11.2 - - + -
3030 THR* 3.8 18.2 - - + -
3060 TYR* 3.0 40.8 - - + +
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Residues in contact with THR 186 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1820 GLY 3.0 8.7 + - - -
1830 ARG* 3.3 8.1 + - - -
1850 LEU* 1.3 75.0 - - - +
1870 ASP* 1.3 67.1 + - - +
1890 LEU* 3.4 5.2 + - - +
1900 MET* 3.1 25.3 + - - +
2060 ARG* 4.6 10.1 - - - +
2090 VAL* 3.6 27.0 - - + +
2100 ARG* 3.7 25.8 - - + +
2130 LYS* 2.7 37.4 + - - +
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Residues in contact with ASP 187 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1830 ARG* 3.3 18.8 + - - +
1840 ASP* 3.2 11.0 + - - +
1860 THR* 1.3 79.6 - - - +
1880 TYR* 1.3 64.2 + - - +
1900 MET* 3.1 20.0 - - - +
1910 LYS* 3.3 9.5 + - - +
2060 ARG* 3.4 35.2 + - - -
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Residues in contact with TYR 188 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1840 ASP 3.1 15.5 + - - +
1850 LEU* 4.1 5.6 - - - +
1860 THR 3.3 0.2 - - - -
1870 ASP* 1.3 76.1 - - - +
1890 LEU* 1.3 66.3 + - - +
1910 LYS* 3.2 40.6 + - + +
1920 ILE* 3.0 44.3 + - + +
2560 ARG* 3.3 21.8 + - - +
2570 CYS* 3.9 11.0 - - + -
2600 THR* 3.2 24.0 - - + -
2660 PHE* 3.1 39.8 - + - +
2670 ILE* 3.5 24.9 - - + -
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Residues in contact with LEU 189 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1850 LEU 3.3 13.3 + - - +
1860 THR* 3.7 6.7 - - - +
1880 TYR* 1.3 77.9 - - - +
1900 MET* 1.3 55.2 + - - +
1920 ILE* 3.0 26.2 + - + +
1930 LEU* 2.8 52.9 + - + +
2090 VAL* 3.5 33.2 - - + +
2120 ILE* 3.7 12.1 - - + -
2130 LYS* 3.5 28.3 - - + +
2170 CYS* 4.6 7.4 - - - -
2500 ILE* 5.5 2.2 - - + -
2530 GLU* 4.6 16.4 - - + +
2540 ARG 5.3 0.7 - - - +
2570 CYS* 3.8 8.5 - - + -
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Residues in contact with MET 190 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1860 THR 3.1 9.6 + - - +
1870 ASP* 3.1 17.7 - - - +
1890 LEU* 1.3 78.6 - - - +
1910 LYS* 1.3 58.1 + - - +
1930 LEU* 3.3 3.1 + - - +
1940 THR* 2.9 37.7 + - + +
2000 PHE* 3.7 30.0 - - + +
2060 ARG* 3.7 44.2 - - + +
2090 VAL* 3.2 35.4 - - + -
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Residues in contact with LYS 191 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1870 ASP 3.3 5.3 + - - +
1880 TYR* 3.2 48.4 + - + +
1900 MET* 1.3 78.4 - - - +
1920 ILE* 1.3 65.3 + - - +
1930 LEU 2.8 7.3 + - - -
1940 THR* 2.9 10.7 + - - -
1950 GLU* 2.8 55.6 + - + +
2660 PHE 5.0 3.2 + - - -
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Residues in contact with ILE 192 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1880 TYR* 3.0 49.5 + - + +
1890 LEU* 3.0 23.1 + - + +
1910 LYS* 1.3 90.0 - - - +
1930 LEU* 1.3 54.9 + - - +
1950 GLU* 3.5 25.3 - - - +
1960 ARG* 3.2 21.1 + - - +
2530 GLU* 3.6 40.0 - - + +
2560 ARG* 3.6 32.2 + - + +
2570 CYS* 4.0 3.1 - - + +
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Residues in contact with LEU 193 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1890 LEU* 2.8 35.9 + - + +
1900 MET 3.6 4.0 - - - +
1910 LYS 2.8 0.8 + - - -
1920 ILE* 1.3 78.8 - - - +
1940 THR* 1.3 63.3 + - - +
1950 GLU 3.2 1.1 - - - -
1960 ARG* 3.3 7.2 + - + +
1980 TYR* 2.8 39.7 - - + +
2000 PHE* 3.6 27.4 - - + -
2090 VAL* 4.1 10.5 - - + -
2120 ILE* 4.2 17.7 - - + -
2480 ILE* 5.2 0.2 - - + -
2490 THR 4.5 1.1 - - - +
2500 ILE* 3.3 33.4 - - + -
2530 GLU* 4.1 13.7 - - + -
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Residues in contact with THR 194 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1900 MET* 2.9 27.6 + - + +
1910 LYS* 3.0 14.4 + - - -
1930 LEU* 1.3 76.1 - - - +
1950 GLU* 1.3 59.6 + - - +
1970 GLY* 2.9 9.4 + - - -
1980 TYR 2.9 38.4 + - - +
1990 SER* 4.9 0.2 - - - -
2000 PHE* 3.5 25.8 - - + +
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Residues in contact with GLU 195 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1910 LYS* 2.8 45.0 + - + +
1920 ILE* 3.5 23.4 - - - +
1940 THR* 1.3 76.7 + - - +
1960 ARG* 1.3 56.2 + - - +
1970 GLY* 3.0 8.5 + - - -
2560 ARG* 3.7 15.3 + - - +
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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