Contacts of the helix formed by residues 181 - 195 (chain 2) 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 2).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1552 SER* 4.5 1.1 - - - +
1562 GLY 3.3 15.3 - - - +
1572 ASP 3.4 18.2 - - - +
1582 GLY* 3.7 13.2 - - - -
1592 VAL 3.8 9.6 - - - +
1602 THR* 4.3 2.7 - - - +
1802 LEU* 1.3 77.7 - - - +
1822 GLY* 1.3 61.4 + - - +
1832 ARG 3.2 3.2 + - - -
1842 ASP* 3.2 10.9 + - - +
1852 LEU* 3.0 33.7 + - - +
2612 LEU* 5.3 0.2 - - - -
3032 THR* 4.2 6.5 - - - -
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Residues in contact with GLY 182 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1562 GLY 3.0 10.0 + - - -
1572 ASP* 4.6 4.5 - - - -
1812 ALA* 1.3 76.1 - - - +
1832 ARG* 1.3 55.4 + - - +
1852 LEU* 3.5 8.2 - - - +
1862 THR* 3.0 18.4 + - - -
2132 LYS* 2.8 30.8 + - - -
3032 THR* 3.1 21.3 + - - -
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Residues in contact with ARG 183 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142 SER* 2.8 36.4 + - - -
692 TYR* 3.5 30.0 + - - +
712 ILE 4.8 5.7 + - - -
722 GLU* 4.6 13.9 + - - +
732 HIS* 5.2 7.4 - - - +
1572 ASP* 2.9 46.9 + - - +
1582 GLY* 4.4 14.9 - - - -
1812 ALA 3.2 0.2 + - - -
1822 GLY* 1.3 71.6 - - - +
1842 ASP* 1.3 69.9 - - - +
1862 THR* 3.3 13.7 + - - -
1872 ASP* 3.3 25.5 + - - +
2062 ARG* 6.1 2.2 - - - +
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Residues in contact with ASP 184 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
732 HIS* 5.4 2.8 - - - -
1572 ASP 4.5 1.0 - - - +
1582 GLY* 4.7 5.0 - - - +
1792 ASP 3.9 12.4 - - - +
1802 LEU* 3.8 11.3 - - + +
1812 ALA* 3.2 29.1 + - - +
1832 ARG* 1.3 81.1 - - - +
1852 LEU* 1.3 63.1 + - + +
1872 ASP* 3.2 9.4 + - - +
1882 TYR* 3.1 27.3 + - - +
2672 ILE* 5.0 13.2 - - + +
2692 MET* 5.6 1.0 - - - +
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Residues in contact with LEU 185 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1802 LEU* 3.9 23.8 - - + -
1812 ALA 3.0 19.4 + - - +
1822 GLY* 3.5 7.2 - - - +
1832 ARG 3.2 0.2 - - - -
1842 ASP* 1.3 77.5 - - + +
1862 THR* 1.3 61.5 + - - +
1872 ASP 3.3 0.2 - - - -
1882 TYR* 3.9 5.0 - - - +
1892 LEU 3.3 8.3 + - - -
2132 LYS* 4.1 2.7 - - + -
2572 CYS* 3.2 39.6 - - - +
2602 THR* 4.3 19.5 - - + -
2612 LEU* 4.0 11.7 - - + -
3032 THR* 3.8 17.3 - - + -
3062 TYR* 3.0 41.5 - - + +
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Residues in contact with THR 186 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1822 GLY 3.0 6.6 + - - -
1832 ARG* 3.3 7.7 + - - -
1852 LEU* 1.3 75.7 - - - +
1872 ASP* 1.3 67.3 + - - +
1892 LEU* 3.4 5.3 + - - +
1902 MET* 3.1 25.1 + - - +
2062 ARG* 4.6 10.5 - - - +
2092 VAL* 3.6 26.7 - - + +
2102 ARG* 3.7 26.0 - - + +
2132 LYS* 2.7 38.3 + - - +
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Residues in contact with ASP 187 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1832 ARG* 3.4 17.3 - - - +
1842 ASP* 3.2 11.3 + - - +
1862 THR* 1.3 78.6 - - - +
1882 TYR* 1.3 64.9 + - - +
1902 MET* 3.1 19.3 - - - +
1912 LYS* 3.3 9.9 + - - +
2062 ARG* 3.4 35.1 + - - -
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Residues in contact with TYR 188 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1842 ASP 3.1 15.1 + - - +
1852 LEU* 4.1 5.2 - - - +
1862 THR 3.3 0.2 - - - -
1872 ASP* 1.3 76.0 - - - +
1892 LEU* 1.3 66.6 + - - +
1912 LYS* 3.2 40.3 + - + +
1922 ILE* 3.0 45.8 + - + +
2562 ARG* 3.3 20.9 + - - +
2572 CYS* 3.8 11.7 - - + -
2602 THR* 3.2 25.1 - - + +
2662 PHE* 3.1 40.4 - + - +
2672 ILE* 3.5 25.8 - - + -
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Residues in contact with LEU 189 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1852 LEU 3.3 13.2 + - - +
1862 THR 3.4 8.0 + - - +
1872 ASP 3.4 0.2 - - - -
1882 TYR* 1.3 76.9 - - - +
1902 MET* 1.3 54.0 + - - +
1922 ILE* 3.0 26.0 + - + +
1932 LEU* 2.8 54.0 + - + +
2092 VAL* 3.5 33.2 - - + +
2122 ILE* 3.7 12.6 - - + -
2132 LYS* 3.5 28.3 - - + +
2172 CYS* 4.6 6.5 - - - -
2502 ILE* 5.5 2.5 - - + -
2532 GLU* 4.6 15.9 - - + +
2572 CYS* 3.8 9.0 - - + -
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Residues in contact with MET 190 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1862 THR 3.1 10.3 + - - +
1872 ASP* 3.1 17.3 - - - +
1892 LEU* 1.3 77.9 - - - +
1912 LYS* 1.3 58.2 + - - +
1932 LEU* 3.3 2.9 + - - +
1942 THR* 2.9 37.4 + - + +
2002 PHE* 3.7 28.8 - - + +
2062 ARG* 3.7 44.2 - - + +
2092 VAL* 3.2 35.4 - - + -
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Residues in contact with LYS 191 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1872 ASP 3.3 5.3 + - - +
1882 TYR* 3.2 49.5 + - + +
1902 MET* 1.3 77.5 - - - +
1922 ILE* 1.3 65.4 + - - +
1932 LEU 2.8 7.1 + - - -
1942 THR* 2.9 10.2 + - - -
1952 GLU* 2.8 56.1 + - + +
2562 ARG* 5.9 0.2 - - - +
2662 PHE 5.0 3.6 + - - -
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Residues in contact with ILE 192 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1882 TYR* 3.0 49.3 + - + +
1892 LEU* 3.0 21.5 + - + +
1912 LYS* 1.3 91.5 - - - +
1932 LEU* 1.3 55.1 + - - +
1952 GLU* 3.5 26.0 - - - +
1962 ARG* 3.2 21.1 + - - +
2532 GLU* 3.6 38.8 - - + +
2562 ARG* 3.6 32.3 + - + +
2572 CYS* 4.0 4.3 - - + +
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Residues in contact with LEU 193 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1892 LEU* 2.8 35.4 + - + +
1902 MET 3.6 4.0 - - - +
1912 LYS 2.8 1.0 + - - -
1922 ILE* 1.3 76.5 - - - +
1942 THR* 1.3 62.1 + - - +
1952 GLU 3.2 0.9 - - - -
1962 ARG* 3.3 8.2 + - + -
1982 TYR* 2.8 39.7 - - + -
2002 PHE* 3.6 28.7 - - + -
2092 VAL* 4.1 10.5 - - + -
2122 ILE* 4.2 17.5 - - + -
2482 ILE* 5.2 0.2 - - + -
2492 THR 4.5 0.9 - - - +
2502 ILE* 3.3 34.8 - - + -
2532 GLU* 4.1 13.2 - - + -
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Residues in contact with THR 194 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1902 MET* 2.9 26.6 + - + +
1912 LYS* 3.0 14.7 + - - +
1932 LEU* 1.3 75.4 - - - +
1952 GLU* 1.3 59.0 + - - +
1972 GLY* 2.9 10.2 + - - -
1982 TYR* 2.9 38.9 + - - +
1992 SER* 4.9 0.2 - - - -
2002 PHE* 3.5 25.4 - - + +
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Residues in contact with GLU 195 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1121 PRO* 5.3 18.2 - - + +
1912 LYS* 2.8 44.7 + - + +
1922 ILE* 3.5 23.1 - - - +
1942 THR* 1.3 77.2 + - - +
1962 ARG* 1.3 55.6 + - - +
1972 GLY* 3.0 9.0 + - - -
2562 ARG* 3.7 15.0 + - - -
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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