Contacts of the helix formed by residues 181 - 195 (chain 1) 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 1).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1551 SER* 4.5 1.3 - - - +
1561 GLY 3.3 14.8 - - - +
1571 ASP 3.4 17.7 - - - +
1581 GLY 3.7 13.7 - - - -
1591 VAL 3.8 9.9 - - - +
1601 THR* 4.3 2.9 - - - +
1791 ASP 4.4 0.2 - - - -
1801 LEU* 1.3 76.2 - - - +
1821 GLY* 1.3 61.4 + - - +
1831 ARG 3.2 2.7 + - - -
1841 ASP* 3.2 10.7 + - - +
1851 LEU* 3.0 33.6 + - - +
3031 THR* 4.2 7.0 - - - -
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Residues in contact with GLY 182 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1561 GLY 3.0 10.8 + - - -
1571 ASP* 4.6 4.7 - - - -
1811 ALA* 1.3 77.4 - - - +
1831 ARG* 1.3 54.4 + - - +
1851 LEU* 3.5 8.4 + - - +
1861 THR* 3.0 17.8 + - - -
2131 LYS* 2.8 31.6 + - - -
3031 THR* 3.1 20.5 + - - -
3061 TYR* 4.6 0.2 - - - -
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Residues in contact with ARG 183 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141 SER* 2.8 36.0 + - - -
691 TYR* 3.5 28.7 + - - +
711 ILE 4.8 5.5 + - - -
721 GLU* 4.6 14.1 + - - +
731 HIS* 5.2 6.8 - - - +
1571 ASP* 2.9 49.2 + - - +
1581 GLY* 4.4 14.9 - - - -
1811 ALA 3.2 0.2 - - - -
1821 GLY* 1.3 70.9 - - - +
1841 ASP* 1.3 70.9 - - - +
1861 THR* 3.3 14.0 + - - -
1871 ASP* 3.4 25.4 + - - +
2061 ARG* 6.1 2.5 - - - +
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Residues in contact with ASP 184 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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731 HIS* 5.4 3.3 - - - -
1571 ASP 4.5 0.9 - - - +
1581 GLY* 4.7 5.2 - - - +
1791 ASP 3.9 12.0 - - - +
1801 LEU* 3.8 11.5 - - + +
1811 ALA* 3.2 28.7 + - - +
1831 ARG* 1.3 80.6 - - - +
1851 LEU* 1.3 62.9 + - + +
1871 ASP* 3.2 9.3 + - - +
1881 TYR* 3.1 27.4 + - - +
2671 ILE* 5.0 12.4 - - + +
2691 MET* 5.6 1.4 - - - +
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Residues in contact with LEU 185 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1801 LEU* 3.9 24.2 - - + -
1811 ALA 3.0 17.8 + - - +
1821 GLY 3.5 6.7 - - - +
1831 ARG 3.2 0.2 - - - -
1841 ASP* 1.3 78.2 - - + +
1861 THR* 1.3 61.9 + - - +
1881 TYR* 3.9 5.0 - - + +
1891 LEU 3.3 8.7 + - - -
2131 LYS* 4.1 3.4 - - + -
2571 CYS* 3.2 38.4 - - - +
2581 PRO* 5.1 0.4 - - + -
2601 THR* 4.3 18.8 - - + -
2611 LEU* 4.0 11.4 - - + -
2671 ILE* 5.7 0.4 - - + -
3031 THR* 3.8 17.0 - - + -
3061 TYR* 3.0 41.3 - - + +
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Residues in contact with THR 186 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1821 GLY 3.0 7.1 + - - -
1831 ARG* 3.3 7.1 + - - -
1851 LEU* 1.3 76.5 - - - +
1871 ASP* 1.3 67.4 + - - +
1891 LEU* 3.4 5.3 + - - +
1901 MET* 3.1 25.1 + - - +
2061 ARG* 4.6 10.3 - - - +
2091 VAL* 3.6 26.2 - - + +
2101 ARG* 3.7 25.5 - - + +
2131 LYS* 2.7 38.3 + - - +
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Residues in contact with ASP 187 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1831 ARG* 3.4 18.4 - - - +
1841 ASP* 3.2 10.8 + - - +
1861 THR* 1.3 79.0 - - - +
1881 TYR* 1.3 64.3 + - - +
1901 MET* 3.1 19.2 - - - +
1911 LYS* 3.3 9.5 + - - +
2061 ARG* 3.4 35.5 + - - -
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Residues in contact with TYR 188 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1841 ASP 3.1 14.5 + - - +
1851 LEU* 4.1 6.3 - - - +
1861 THR 3.3 0.2 - - - -
1871 ASP* 1.3 77.1 - - - +
1891 LEU* 1.3 66.6 + - - +
1911 LYS* 3.2 39.2 + - + +
1921 ILE* 3.0 45.2 + - + +
2561 ARG* 3.3 21.6 + - - +
2571 CYS* 3.9 11.2 - - + -
2601 THR* 3.2 24.2 - - + -
2661 PHE* 3.1 41.3 + + - +
2671 ILE* 3.5 25.8 - - + -
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Residues in contact with LEU 189 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1851 LEU 3.3 13.5 + - - +
1861 THR 3.7 7.0 - - - +
1871 ASP 3.4 0.2 - - - -
1881 TYR* 1.3 77.3 - - - +
1901 MET* 1.3 54.6 + - - +
1921 ILE* 3.0 25.7 + - + +
1931 LEU* 2.8 53.0 + - + +
2091 VAL* 3.5 33.7 - - + +
2121 ILE* 3.7 12.1 - - + -
2131 LYS* 3.5 29.2 - - + +
2171 CYS* 4.6 6.5 - - - -
2501 ILE* 5.5 2.7 - - + -
2531 GLU* 4.6 16.2 - - + +
2541 ARG 5.3 0.2 - - - +
2571 CYS* 3.8 9.0 - - + -
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Residues in contact with MET 190 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1861 THR 3.1 11.0 + - - +
1871 ASP* 3.1 17.7 - - - +
1891 LEU* 1.3 76.2 - - - +
1911 LYS* 1.3 58.8 + - - +
1931 LEU* 3.3 2.8 + - - +
1941 THR* 2.9 36.7 + - + +
2001 PHE* 3.7 29.6 - - + +
2061 ARG* 3.7 43.3 - - + +
2091 VAL* 3.2 34.7 - - + +
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Residues in contact with LYS 191 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1871 ASP 3.3 5.8 + - - +
1881 TYR* 3.2 48.0 + - + +
1901 MET* 1.3 77.9 - - - +
1921 ILE* 1.3 64.8 + - - +
1931 LEU 2.8 7.3 + - - -
1941 THR* 2.9 10.3 + - - -
1951 GLU* 2.8 55.7 + - + +
2661 PHE 5.0 3.6 + - - -
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Residues in contact with ILE 192 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1881 TYR* 3.0 50.4 + - + +
1891 LEU* 3.0 22.4 + - + +
1911 LYS* 1.3 90.2 - - - +
1931 LEU* 1.3 55.0 + - - +
1951 GLU* 3.5 25.5 - - - +
1961 ARG* 3.2 21.0 + - - +
2531 GLU* 3.6 40.0 - - + +
2561 ARG* 3.6 31.7 + - + +
2571 CYS* 4.0 4.3 - - + +
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Residues in contact with LEU 193 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1891 LEU* 2.8 36.1 + - + +
1901 MET 3.6 4.0 - - - +
1911 LYS 2.8 1.0 + - - -
1921 ILE* 1.3 78.6 - - - +
1941 THR* 1.3 62.0 + - - +
1951 GLU 3.2 1.3 - - - -
1961 ARG* 3.3 7.8 + - + -
1981 TYR* 2.8 39.8 - - + -
2001 PHE* 3.6 28.7 - - + -
2091 VAL* 4.1 10.1 - - + -
2121 ILE* 4.2 18.2 - - + -
2491 THR 4.5 0.9 - - - +
2501 ILE* 3.3 33.7 - - + -
2531 GLU* 4.1 13.7 - - + -
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Residues in contact with THR 194 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1901 MET* 2.9 26.6 + - + +
1911 LYS* 3.0 14.5 + - - +
1931 LEU* 1.3 75.4 - - - +
1951 GLU* 1.3 60.0 + - - +
1971 GLY* 2.9 9.9 + - - -
1981 TYR* 2.9 38.4 + - - +
1991 SER* 4.9 0.7 - - - -
2001 PHE* 3.5 25.6 - - + +
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Residues in contact with GLU 195 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1120 PRO* 5.3 19.1 - - + +
1911 LYS* 2.8 44.9 + - + +
1921 ILE* 3.5 22.9 - - - +
1941 THR* 1.3 76.7 + - - +
1961 ARG* 1.3 54.9 + - - +
1971 GLY* 3.0 8.6 + - - -
2561 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
------------------------------------------------------------
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