Contacts of the helix formed by residues 181 - 195 (chain 7) 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 7).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1557 SER* 4.5 0.9 - - - +
1567 GLY 3.3 16.2 - - - +
1577 ASP 3.4 17.7 - - - +
1587 GLY 3.7 13.0 - - - -
1597 VAL 3.8 9.9 - - - +
1607 THR* 4.3 3.8 - - - +
1807 LEU* 1.3 77.4 - - - +
1827 GLY* 1.3 61.1 + - - +
1837 ARG 3.2 2.7 + - - -
1847 ASP* 3.2 10.6 + - - +
1857 LEU* 3.0 33.4 + - - +
2617 LEU* 5.3 0.4 - - - -
3037 THR* 4.3 5.8 - - - -
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Residues in contact with GLY 182 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1567 GLY 3.0 10.4 + - - -
1577 ASP* 4.6 5.2 - - - -
1817 ALA* 1.3 75.7 - - - +
1837 ARG* 1.3 55.5 - - - +
1857 LEU* 3.5 7.7 - - - +
1867 THR* 3.0 17.7 + - - -
2137 LYS* 2.8 29.7 + - - -
3037 THR* 3.1 21.8 + - - -
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Residues in contact with ARG 183 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147 SER* 2.8 35.4 + - - -
697 TYR* 3.5 29.4 + - - +
717 ILE 4.8 6.1 + - - -
727 GLU* 4.6 13.7 + - - +
737 HIS* 5.2 7.5 - - - +
1577 ASP* 2.9 46.9 + - - +
1587 GLY* 4.4 15.4 - - - -
1817 ALA 3.2 0.2 + - - -
1827 GLY* 1.3 72.0 - - - +
1847 ASP* 1.3 71.3 + - - +
1867 THR* 3.3 13.9 + - - -
1877 ASP* 3.3 25.8 + - - +
2067 ARG* 6.1 2.2 - - - +
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Residues in contact with ASP 184 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
737 HIS* 5.4 3.1 - - - -
1577 ASP 4.5 0.9 - - - +
1587 GLY* 4.7 5.0 - - - +
1797 ASP 3.9 12.8 - - - +
1807 LEU* 3.8 11.1 - - + +
1817 ALA* 3.2 29.2 + - - +
1837 ARG* 1.3 83.2 - - - +
1857 LEU* 1.3 62.8 + - + +
1877 ASP* 3.2 8.6 + - - +
1887 TYR* 3.1 26.8 + - - +
2677 ILE* 5.0 13.3 - - + +
2697 MET* 5.6 0.9 - - - +
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Residues in contact with LEU 185 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1807 LEU* 3.9 24.0 - - + -
1817 ALA 3.0 18.1 + - - +
1827 GLY* 3.5 7.0 - - - +
1837 ARG 3.2 0.2 - - - -
1847 ASP* 1.3 77.2 - - + +
1867 THR* 1.3 62.3 + - - +
1887 TYR* 3.7 5.6 + - - +
1897 LEU* 3.3 8.8 + - - +
2137 LYS* 4.1 3.1 - - + -
2577 CYS* 3.2 38.4 - - - +
2587 PRO* 5.1 0.4 - - + -
2607 THR* 4.3 19.5 - - + -
2617 LEU* 4.0 11.2 - - + -
2677 ILE* 5.7 0.7 - - + -
3037 THR* 3.8 17.5 - - + -
3067 TYR* 3.0 40.8 - - + +
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Residues in contact with THR 186 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1827 GLY 3.0 6.6 + - - -
1837 ARG* 3.3 8.6 + - - -
1857 LEU* 1.3 76.4 - - - +
1877 ASP* 1.3 66.5 + - - +
1897 LEU* 3.4 5.5 + - - +
1907 MET* 3.1 25.3 + - - +
2067 ARG* 4.6 10.3 - - - +
2097 VAL* 3.6 26.7 - - + +
2107 ARG* 3.7 25.6 - - + +
2137 LYS* 2.7 38.2 + - - +
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Residues in contact with ASP 187 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1837 ARG* 3.4 18.1 - - - +
1847 ASP* 3.2 11.5 + - - +
1867 THR* 1.3 79.0 - - - +
1887 TYR* 1.3 64.0 + - - +
1907 MET* 3.1 19.7 - - - +
1917 LYS* 3.3 9.5 + - - +
2067 ARG* 3.4 34.8 + - - -
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Residues in contact with TYR 188 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1847 ASP 3.1 13.8 + - - +
1857 LEU* 4.1 6.3 - - + +
1867 THR 3.3 0.2 - - - -
1877 ASP* 1.3 76.3 - - - +
1897 LEU* 1.3 65.9 + - - +
1917 LYS* 3.2 40.7 + - + +
1927 ILE* 3.0 45.8 + - + +
2567 ARG* 3.3 21.3 + - - +
2577 CYS* 3.8 11.4 - - + -
2607 THR* 3.2 25.6 - - + +
2667 PHE* 3.1 41.1 + + - +
2677 ILE* 3.5 25.6 - - + -
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Residues in contact with LEU 189 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1857 LEU 3.3 13.6 + - - +
1867 THR* 3.7 7.4 - - - +
1877 ASP 3.4 0.2 - - - -
1887 TYR* 1.3 77.3 - - - +
1907 MET* 1.3 54.1 + - - +
1927 ILE* 3.0 25.0 + - + +
1937 LEU* 2.8 53.8 + - + +
2097 VAL* 3.5 33.0 - - + +
2127 ILE* 3.7 12.3 - - + -
2137 LYS* 3.5 28.5 - - + +
2177 CYS* 4.6 6.7 - - - -
2507 ILE* 5.5 2.5 - - + -
2537 GLU* 4.6 16.2 - - + +
2547 ARG 5.3 0.2 - - - +
2577 CYS* 3.8 8.5 - - + -
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Residues in contact with MET 190 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1867 THR 3.1 10.5 + - - +
1877 ASP* 3.1 18.2 - - - +
1897 LEU* 1.3 78.4 - - - +
1917 LYS* 1.3 57.6 + - - +
1937 LEU* 3.3 2.5 + - - +
1947 THR* 2.9 37.3 + - + +
2007 PHE* 3.7 28.6 - - + +
2067 ARG* 3.7 44.0 - - + +
2097 VAL* 3.2 35.7 - - + -
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Residues in contact with LYS 191 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1877 ASP 3.3 5.7 + - - +
1887 TYR* 3.2 48.7 + - + +
1907 MET* 1.3 77.3 - - - +
1927 ILE* 1.3 64.9 + - - +
1937 LEU 2.8 6.8 + - - -
1947 THR* 2.9 10.1 + - - -
1957 GLU* 2.8 56.6 + - + +
2567 ARG* 5.9 0.2 - - - +
2667 PHE 5.0 3.0 + - - -
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Residues in contact with ILE 192 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1887 TYR* 3.0 49.1 + - + +
1897 LEU* 3.0 22.0 + - + +
1917 LYS* 1.3 91.4 - - - +
1937 LEU* 1.3 56.2 + - - +
1957 GLU* 3.5 24.9 - - - +
1967 ARG* 3.2 21.3 + - - +
2537 GLU* 3.6 38.1 - - + +
2567 ARG* 3.6 32.4 + - + +
2577 CYS* 4.0 3.1 - - + +
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Residues in contact with LEU 193 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1897 LEU* 2.8 36.3 + - + +
1907 MET 3.6 4.3 - - - +
1917 LYS 2.8 0.8 + - - -
1927 ILE* 1.3 76.1 - - - +
1947 THR* 1.3 61.6 + - - +
1957 GLU 3.2 0.9 - - - -
1967 ARG* 3.3 7.5 + - + -
1987 TYR* 2.8 39.7 - - + -
2007 PHE* 3.6 28.7 - - + -
2097 VAL* 4.1 10.1 - - + -
2127 ILE* 4.2 18.6 - - + -
2497 THR 4.5 0.7 - - - +
2507 ILE* 3.3 34.3 - - + -
2537 GLU* 4.1 13.0 - - + -
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Residues in contact with THR 194 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1907 MET* 2.9 27.0 + - + +
1917 LYS* 3.0 14.3 + - - +
1937 LEU* 1.3 76.3 - - - +
1957 GLU* 1.3 58.0 + - - +
1977 GLY* 2.9 10.4 + - - -
1987 TYR* 2.9 37.4 + - - +
1997 SER* 4.9 0.2 - - - -
2007 PHE* 3.5 25.4 - - + +
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Residues in contact with GLU 195 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1126 PRO* 5.3 19.4 - - + +
1917 LYS* 2.8 46.2 + - + +
1927 ILE* 3.5 22.1 - - - +
1947 THR* 1.3 76.9 + - - +
1967 ARG* 1.3 53.9 + - - +
1977 GLY* 3.0 9.3 + - - -
2567 ARG* 3.7 14.8 + - - -
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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