Contacts of the helix formed by residues 181 - 195 (chain 4) 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 4).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1554 SER* 4.5 1.1 - - - +
1564 GLY 3.3 14.8 - - - +
1574 ASP 3.4 17.5 - - - +
1584 GLY 3.7 14.1 + - - -
1594 VAL 3.8 10.1 - - - +
1604 THR* 4.3 3.1 - - - +
1804 LEU* 1.3 77.8 - - - +
1824 GLY* 1.3 61.1 + - - +
1834 ARG 3.2 2.5 + - - -
1844 ASP* 3.2 10.8 + - - +
1854 LEU* 3.0 34.0 + - - +
2614 LEU* 5.3 0.2 - - - -
3034 THR* 4.2 6.5 - - - -
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Residues in contact with GLY 182 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1564 GLY 3.0 11.4 + - - -
1574 ASP* 4.6 4.7 - - - -
1814 ALA* 1.3 75.7 - - - +
1834 ARG* 1.3 54.8 + - - +
1854 LEU* 3.5 7.8 - - - +
1864 THR* 3.0 17.7 + - - -
2134 LYS* 2.8 31.3 + - - -
3034 THR* 3.1 21.8 + - - -
3064 TYR* 4.6 0.2 - - - -
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Residues in contact with ARG 183 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144 SER* 2.8 35.8 + - - -
694 TYR* 3.5 29.8 + - - +
714 ILE 4.8 5.3 + - - -
724 GLU* 4.6 14.8 + - - +
734 HIS* 5.2 7.4 - - - +
1574 ASP* 2.9 48.3 + - - +
1584 GLY* 4.4 14.7 - - - -
1814 ALA 3.2 0.2 - - - -
1824 GLY* 1.3 70.9 - - - +
1844 ASP* 1.3 70.8 + - - +
1864 THR* 3.3 13.9 + - - -
1874 ASP* 3.3 25.1 + - - +
2064 ARG* 6.1 2.7 - - - +
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Residues in contact with ASP 184 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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734 HIS* 5.4 3.3 - - - -
1574 ASP 4.5 0.7 - - - +
1584 GLY* 4.7 5.0 - - - +
1794 ASP 3.9 12.5 - - - +
1804 LEU* 3.8 11.4 - - + +
1814 ALA* 3.2 29.1 + - - +
1834 ARG* 1.3 81.1 - - - +
1854 LEU* 1.3 62.0 + - + +
1874 ASP* 3.2 9.0 + - - +
1884 TYR* 3.1 26.7 + - - +
2674 ILE* 5.0 13.4 - - + +
2694 MET* 5.6 0.9 - - - +
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Residues in contact with LEU 185 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1804 LEU* 3.9 24.0 - - + -
1814 ALA 3.0 16.3 + - - +
1824 GLY 3.5 6.5 - - - +
1844 ASP* 1.3 78.7 - - + +
1864 THR* 1.3 61.9 + - - +
1884 TYR* 3.7 5.4 + - + +
1894 LEU 3.3 8.5 + - - -
2134 LYS* 4.1 3.1 - - + -
2574 CYS* 3.2 38.9 - - - +
2584 PRO* 5.1 0.2 - - + -
2604 THR* 4.3 19.7 - - + -
2614 LEU* 4.0 10.5 - - + -
3034 THR* 3.8 18.6 - - + -
3064 TYR* 3.0 41.1 - - + +
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Residues in contact with THR 186 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1824 GLY 3.0 7.9 + - - -
1834 ARG* 3.3 8.2 + - - -
1854 LEU* 1.3 74.3 - - - +
1874 ASP* 1.3 66.7 + - - +
1894 LEU* 3.4 5.2 + - - +
1904 MET* 3.1 25.5 + - - +
2064 ARG* 4.6 9.9 - - - +
2094 VAL* 3.6 26.6 - - + +
2104 ARG* 3.7 25.8 - - + +
2134 LYS* 2.7 37.9 + - - +
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Residues in contact with ASP 187 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1834 ARG* 3.3 18.4 + - - +
1844 ASP* 3.2 10.9 + - - +
1864 THR* 1.3 78.5 - - - +
1884 TYR* 1.3 64.5 + - - +
1904 MET* 3.1 19.6 - - - +
1914 LYS* 3.3 9.5 + - - +
2064 ARG* 3.4 35.2 + - - -
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Residues in contact with TYR 188 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1844 ASP 3.1 14.7 + - - +
1854 LEU* 4.1 6.3 - - - +
1874 ASP* 1.3 76.5 - - - +
1894 LEU* 1.3 66.5 + - - +
1914 LYS* 3.2 39.7 + - + +
1924 ILE* 3.0 46.1 + - + +
2564 ARG* 3.3 21.9 + - - +
2574 CYS* 3.8 11.2 - - + -
2604 THR* 3.2 24.9 - - + +
2664 PHE* 3.1 40.1 - + - +
2674 ILE* 3.5 25.1 - - + -
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Residues in contact with LEU 189 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1854 LEU 3.3 13.5 + - - +
1864 THR* 3.7 7.0 - - - +
1874 ASP 3.4 0.2 - - - -
1884 TYR* 1.3 77.1 - - - +
1904 MET* 1.3 55.2 - - - +
1924 ILE* 3.0 25.9 + - + +
1934 LEU* 2.8 52.8 + - + +
2094 VAL* 3.5 33.2 - - + +
2124 ILE* 3.7 12.1 - - + -
2134 LYS* 3.5 29.2 - - + +
2174 CYS* 4.6 7.2 - - - -
2504 ILE* 5.5 2.2 - - + -
2534 GLU* 4.6 16.4 - - + +
2544 ARG 5.3 0.7 - - - +
2574 CYS* 3.8 8.5 - - + -
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Residues in contact with MET 190 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1864 THR 3.1 9.2 + - - +
1874 ASP* 3.1 18.4 - - - +
1894 LEU* 1.3 77.8 - - - +
1914 LYS* 1.3 57.6 + - - +
1934 LEU* 3.3 3.7 + - - +
1944 THR* 2.9 37.0 + - + +
2004 PHE* 3.7 29.7 - - + +
2064 ARG* 3.7 44.0 - - + +
2094 VAL* 3.2 35.4 - - + -
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Residues in contact with LYS 191 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1874 ASP 3.3 5.1 + - - +
1884 TYR* 3.2 49.1 + - + +
1904 MET* 1.3 79.1 - - - +
1924 ILE* 1.3 64.6 + - - +
1934 LEU 2.8 6.9 + - - -
1944 THR* 2.9 10.5 + - - -
1954 GLU* 2.8 56.2 + - + +
2664 PHE 5.0 3.0 + - - -
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Residues in contact with ILE 192 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1884 TYR* 3.0 49.9 + - + +
1894 LEU* 3.0 22.6 + - + +
1914 LYS* 1.3 90.4 - - - +
1934 LEU* 1.3 55.1 + - - +
1954 GLU* 3.5 25.0 - - - +
1964 ARG* 3.2 20.8 + - - +
2534 GLU* 3.6 38.8 - - + +
2564 ARG* 3.6 33.3 + - + +
2574 CYS* 4.0 3.1 - - + +
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Residues in contact with LEU 193 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1894 LEU* 2.8 35.6 + - + +
1904 MET* 3.6 4.7 - - - +
1914 LYS 2.8 0.8 + - - -
1924 ILE* 1.3 79.1 - - - +
1944 THR* 1.3 62.5 + - - +
1954 GLU 3.2 0.9 - - - -
1964 ARG* 3.3 7.0 + - + +
1984 TYR* 2.8 40.3 - - + -
2004 PHE* 3.6 27.6 - - + -
2094 VAL* 4.1 10.3 - - + -
2124 ILE* 4.2 17.9 - - + -
2494 THR 4.5 0.9 - - - +
2504 ILE* 3.3 33.9 - - + -
2534 GLU* 4.1 13.7 - - + -
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Residues in contact with THR 194 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1904 MET* 2.9 27.2 + - + +
1914 LYS* 3.0 14.4 + - - +
1934 LEU* 1.3 76.1 - - - +
1954 GLU* 1.3 59.3 + - - +
1974 GLY* 2.9 9.7 + - - -
1984 TYR 2.9 37.7 + - - +
1994 SER* 4.9 0.2 - - - -
2004 PHE* 3.5 26.2 - - + +
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Residues in contact with GLU 195 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1123 PRO* 5.3 19.6 - - + +
1914 LYS* 2.8 44.2 + - + +
1924 ILE* 3.5 23.5 - - - +
1944 THR* 1.3 76.9 + - - +
1964 ARG* 1.3 54.2 + - - +
1974 GLY* 3.0 9.4 + - - -
2564 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
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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