Contacts of the helix formed by residues 181 - 195 (chain 5) 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 5).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1555 SER* 4.5 1.3 - - - +
1565 GLY 3.3 15.0 - - - +
1575 ASP 3.4 17.7 - - - +
1585 GLY 3.7 13.7 - - - -
1595 VAL 3.8 9.6 - - - +
1605 THR* 4.3 2.7 - - - +
1795 ASP 4.4 0.2 - - - -
1805 LEU* 1.3 76.9 - - - +
1825 GLY* 1.3 61.0 + - - +
1835 ARG 3.2 2.9 + - - -
1845 ASP* 3.2 10.4 + - - +
1855 LEU* 3.0 34.0 + - - +
3035 THR* 4.2 7.2 - - - -
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Residues in contact with GLY 182 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1565 GLY 3.0 10.6 + - - -
1575 ASP* 4.6 4.9 - - - -
1815 ALA* 1.3 76.7 - - - +
1835 ARG* 1.3 55.7 + - - +
1855 LEU* 3.5 8.1 + - - +
1865 THR* 3.0 17.5 + - - -
2135 LYS* 2.8 31.7 + - - -
3035 THR* 3.1 19.9 + - - -
3065 TYR* 4.6 0.2 - - - -
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Residues in contact with ARG 183 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145 SER* 2.8 35.8 + - - -
695 TYR* 3.5 29.2 + - - +
715 ILE 4.8 5.5 + - - -
725 GLU* 4.6 14.5 + - - +
735 HIS* 5.2 6.8 - - - +
1575 ASP* 2.9 48.6 + - - +
1585 GLY* 4.4 14.9 - - - -
1815 ALA 3.2 0.2 - - - -
1825 GLY* 1.3 70.7 - - - +
1845 ASP* 1.3 69.3 + - - +
1865 THR* 3.3 14.1 + - - -
1875 ASP* 3.3 24.8 + - - +
2065 ARG* 6.1 2.5 - - - +
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Residues in contact with ASP 184 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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735 HIS* 5.4 3.1 - - - -
1575 ASP 4.5 0.9 - - - +
1585 GLY* 4.7 5.0 - - - +
1795 ASP 3.9 12.0 - - - +
1805 LEU* 3.8 11.3 - - + +
1815 ALA* 3.2 29.0 + - - +
1835 ARG* 1.3 81.1 - - - +
1855 LEU* 1.3 63.2 + - + +
1875 ASP* 3.2 8.9 + - - +
1885 TYR* 3.1 27.1 + - - +
2675 ILE* 5.0 12.7 - - + +
2695 MET* 5.6 1.4 - - - +
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Residues in contact with LEU 185 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1805 LEU* 3.9 24.0 - - + -
1815 ALA 3.0 17.4 + - - +
1825 GLY 3.5 6.7 - - - +
1835 ARG 3.2 0.2 - - - -
1845 ASP* 1.3 77.8 - - + +
1865 THR* 1.3 61.9 + - - +
1885 TYR* 3.7 5.1 + - - +
1895 LEU 3.3 8.5 + - - -
2135 LYS* 4.1 3.1 - - + -
2575 CYS* 3.2 38.3 - - - +
2585 PRO* 5.1 0.9 - - + -
2605 THR* 4.3 19.5 - - + -
2615 LEU* 4.0 11.7 - - + -
2675 ILE* 5.7 0.4 - - + -
3035 THR* 3.8 17.3 - - + -
3065 TYR* 3.0 40.8 - - + +
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Residues in contact with THR 186 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1825 GLY 3.0 7.6 + - - -
1835 ARG* 3.3 7.3 + - - -
1855 LEU* 1.3 75.9 - - - +
1875 ASP* 1.3 67.5 + - - +
1895 LEU* 3.4 4.7 + - - +
1905 MET* 3.1 25.6 + - - +
2065 ARG* 4.6 10.1 - - - +
2095 VAL* 3.6 25.8 - - + +
2105 ARG* 3.7 26.1 - - + +
2135 LYS* 2.7 38.0 + - - +
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Residues in contact with ASP 187 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1835 ARG* 3.3 17.8 + - - +
1845 ASP* 3.2 10.4 + - - +
1865 THR* 1.3 78.5 - - - +
1885 TYR* 1.3 64.5 + - - +
1905 MET* 3.1 19.6 - - - +
1915 LYS* 3.3 9.5 + - - +
2065 ARG* 3.4 34.9 + - - -
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Residues in contact with TYR 188 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1845 ASP 3.1 14.7 + - - +
1855 LEU* 4.1 6.5 - - - +
1875 ASP* 1.3 76.7 - - - +
1895 LEU* 1.3 67.0 + - - +
1915 LYS* 3.2 39.9 + - + +
1925 ILE* 3.0 44.9 + - + +
2565 ARG* 3.3 21.2 + - - +
2575 CYS* 3.9 11.0 - - + -
2605 THR* 3.2 25.8 - - + +
2665 PHE* 3.1 41.1 + + - +
2675 ILE* 3.5 25.4 - - + -
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Residues in contact with LEU 189 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1855 LEU 3.3 13.7 + - - +
1865 THR 3.7 6.3 - - - +
1875 ASP 3.4 0.2 - - - -
1885 TYR* 1.3 78.4 - - - +
1905 MET* 1.3 55.5 + - - +
1925 ILE* 3.0 25.3 + - + +
1935 LEU* 2.8 52.0 + - + +
2095 VAL* 3.5 34.3 - - + +
2125 ILE* 3.7 11.2 - - + -
2135 LYS* 3.5 28.5 - - + +
2175 CYS* 4.6 6.3 - - - -
2505 ILE* 5.5 2.7 - - + -
2535 GLU* 4.6 16.2 - - + +
2545 ARG 5.3 0.7 - - - +
2575 CYS* 3.8 9.0 - - + -
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Residues in contact with MET 190 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1865 THR 3.1 9.8 + - - +
1875 ASP* 3.1 17.0 - - - +
1895 LEU* 1.3 77.7 - - - +
1915 LYS* 1.3 58.7 + - - +
1935 LEU* 3.3 2.7 + - - +
1945 THR* 2.9 37.3 + - + +
2005 PHE* 3.7 29.0 - - + +
2065 ARG* 3.7 44.0 - - + +
2095 VAL* 3.2 35.9 - - + +
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Residues in contact with LYS 191 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1875 ASP 3.3 6.3 + - - +
1885 TYR* 3.2 47.6 + - + +
1905 MET* 1.3 77.5 - - - +
1925 ILE* 1.3 65.2 + - - +
1935 LEU 2.8 7.4 + - - -
1945 THR* 2.9 10.7 + - - -
1955 GLU* 2.8 55.2 + - + +
2665 PHE 5.0 3.9 + - - -
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Residues in contact with ILE 192 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1885 TYR* 3.0 49.9 + - + +
1895 LEU* 3.0 23.3 + - + +
1915 LYS* 1.3 90.0 - - - +
1935 LEU* 1.3 55.2 + - - +
1955 GLU* 3.5 24.7 - - - +
1965 ARG* 3.2 21.0 + - - +
2535 GLU* 3.6 40.0 - - + +
2565 ARG* 3.6 32.3 + - + +
2575 CYS* 4.0 3.6 - - + +
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Residues in contact with LEU 193 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1895 LEU* 2.8 35.9 + - + +
1905 MET 3.6 4.0 - - - +
1915 LYS 2.8 0.8 + - - -
1925 ILE* 1.3 79.2 - - - +
1945 THR* 1.3 62.0 + - - +
1955 GLU 3.2 1.3 - - - -
1965 ARG* 3.3 7.1 + - + -
1985 TYR* 2.8 40.1 - - + +
2005 PHE* 3.6 28.0 - - + -
2095 VAL* 4.1 10.1 - - + -
2125 ILE* 4.2 18.6 - - + -
2495 THR 4.5 0.9 - - - +
2505 ILE* 3.3 34.1 - - + -
2535 GLU* 4.1 13.2 - - + -
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Residues in contact with THR 194 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1905 MET* 2.9 27.2 + - + +
1915 LYS* 3.0 14.3 + - - +
1935 LEU* 1.3 75.7 - - - +
1955 GLU* 1.3 60.0 + - - +
1975 GLY* 2.9 9.9 + - - -
1985 TYR* 2.9 37.8 + - - +
1995 SER* 4.9 0.7 - - - -
2005 PHE* 3.5 25.6 - - + +
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Residues in contact with GLU 195 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1124 PRO* 5.3 19.5 - - + +
1915 LYS* 2.8 45.3 + - + +
1925 ILE* 3.5 24.4 - - - +
1945 THR* 1.3 77.4 + - - +
1965 ARG* 1.3 55.6 + - - +
1975 GLY* 3.0 9.2 + - - -
2565 ARG* 3.7 15.1 + - - -
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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
------------------------------------------------------------
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