Contacts of the helix formed by residues 179 - 201 (chain 9) in PDB entry 6FF7
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 ASN 179 (chain 9).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1759 LYS* 5.1 2.9 - - + -
1769 GLU* 2.8 25.8 + - + +
1779 ARG 3.4 1.1 - - - +
1789 LYS* 1.3 79.5 - - - +
1809 ALA* 1.3 65.5 + - - +
1819 GLU* 4.9 1.3 - - + +
1829 TYR* 3.6 15.6 - - + +
1839 LYS* 3.0 24.1 + - - +
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Residues in contact with ALA 180 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1789 LYS 3.7 2.8 + - - -
1799 ASN* 1.3 68.2 - - - +
1819 GLU* 1.3 70.3 + - - +
1839 LYS* 2.9 17.8 + - - +
1849 ARG* 2.9 14.6 + - - +
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Residues in contact with GLU 181 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1529 LEU* 4.5 28.1 - - + +
1799 ASN* 3.7 1.9 - - + +
1809 ALA* 1.3 77.6 - - - +
1829 TYR* 1.3 56.9 + - - +
1849 ARG* 3.4 6.3 + - - +
1859 TYR* 2.9 31.3 + - - +
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Residues in contact with TYR 182 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1529 LEU* 5.3 4.9 - - - +
1759 LYS* 4.2 20.2 - - + -
1769 GLU 4.3 5.2 - - - +
1779 ARG* 5.7 1.8 - - - -
1799 ASN* 3.6 24.0 + - + +
1809 ALA 3.0 0.8 - - - -
1819 GLU* 1.3 78.4 - - - +
1839 LYS* 1.3 56.9 + - - +
1859 TYR* 3.3 7.5 + - - +
1869 LEU* 2.9 31.0 + - - +
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Residues in contact with LYS 183 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1779 ARG 5.1 9.1 + - - +
1799 ASN 3.0 15.6 + - - +
1809 ALA* 2.9 10.3 + - - +
1829 TYR* 1.3 72.9 - - - +
1849 ARG* 1.3 56.7 + - - +
1869 LEU* 3.5 7.5 + - - +
1879 GLU* 3.0 27.7 + - - +
2789 LEU* 4.8 20.5 - - + +
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Residues in contact with ARG 184 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1809 ALA 2.9 10.6 + - - +
1819 GLU* 3.6 11.4 - - - +
1839 LYS* 1.3 74.4 - - - +
1859 TYR* 1.3 67.3 - - - +
1879 GLU* 3.0 17.3 + - - +
1889 MET* 3.0 14.1 + - - +
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Residues in contact with TYR 185 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1489 LYS* 5.8 9.4 - - + +
1499 TYR* 6.0 1.8 - - - -
1529 LEU* 5.0 11.9 - - + -
1819 GLU 2.9 17.4 + - - +
1829 TYR* 3.5 7.4 - - - +
1849 ARG* 1.3 74.7 - - - +
1869 LEU* 1.3 63.9 + - - +
1889 MET* 2.9 19.3 + - - +
1899 LEU* 2.9 16.1 + - - +
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Residues in contact with LEU 186 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1829 TYR 2.9 20.9 + - - +
1839 LYS* 3.7 8.3 - - - +
1859 TYR* 1.3 72.5 - - - +
1879 GLU* 1.3 63.6 + - - +
1899 LEU* 3.8 5.9 - - - +
1909 LEU* 2.9 27.3 + - - +
2819 ARG* 5.6 1.8 - - - -
2829 ALA* 5.8 10.7 - - + +
2859 LEU* 5.3 1.4 - - - +
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Residues in contact with GLU 187 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1839 LYS 3.0 14.2 + - - +
1849 ARG* 3.0 12.3 + - - +
1869 LEU* 1.3 77.7 - - - +
1889 MET* 1.3 64.8 + - - +
1909 LEU* 3.5 5.1 - - - +
1919 GLU* 3.0 23.7 + - - +
2789 LEU* 6.3 2.2 - - - -
2819 ARG* 4.7 13.6 - - + +
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Residues in contact with MET 188 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1849 ARG 3.0 9.3 + - - +
1859 TYR* 2.9 14.0 + - - +
1879 GLU* 1.3 72.6 - - - +
1899 LEU* 1.3 59.3 + - - +
1919 GLU* 3.4 6.8 + - - +
1929 TYR* 3.0 27.3 + - - +
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Residues in contact with LEU 189 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1459 CYS* 5.4 12.8 - - + -
1859 TYR 2.9 15.1 + - - +
1869 LEU* 3.8 6.7 - - - +
1889 MET* 1.3 74.4 - - - +
1909 LEU* 1.3 66.4 + - - +
1929 TYR* 3.0 9.6 + - - +
1939 LEU* 2.9 23.7 + - - +
2859 LEU* 5.7 0.2 - - - -
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Residues in contact with LEU 190 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1869 LEU 2.9 19.9 + - - +
1879 GLU 3.5 3.8 - - - +
1899 LEU* 1.3 75.0 - - - +
1919 GLU* 1.3 64.9 + - - +
1939 LEU* 3.1 5.6 + - - +
1949 GLN* 3.0 23.9 + - - +
2819 ARG* 3.4 35.4 - - + +
2829 ALA* 5.5 0.2 - - - -
2849 ARG* 5.3 3.9 - - + +
2859 LEU* 3.9 23.1 + - + +
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Residues in contact with GLU 191 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1879 GLU 3.0 11.9 + - - +
1889 MET* 3.5 11.7 - - - +
1909 LEU* 1.3 76.1 - - - +
1929 TYR* 1.3 63.5 + - - +
1949 GLN* 3.3 5.9 + - - +
1959 ASP* 3.0 25.7 + - - +
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Residues in contact with TYR 192 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1889 MET 3.0 14.1 + - - +
1899 LEU* 3.0 11.0 + - - +
1919 GLU* 1.3 77.0 - - - +
1939 LEU* 1.3 63.6 + - - +
1959 ASP* 3.3 4.6 + - - +
1969 TYR* 2.9 26.4 + - - +
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Residues in contact with LEU 193 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1899 LEU 2.9 16.3 + - - +
1909 LEU* 3.1 9.8 + - - +
1929 TYR* 1.3 73.1 - - - +
1949 GLN* 1.3 57.8 + - - +
1969 TYR* 3.4 7.1 + - - +
1979 THR* 2.9 28.9 + - - -
2859 LEU* 5.3 8.5 - - + +
3019 PHE* 4.8 15.1 - - + +
3029 ALA* 5.5 5.8 - - + +
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Residues in contact with GLN 194 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1909 LEU 3.0 15.4 + - - +
1919 GLU* 3.7 6.3 - - - +
1939 LEU* 1.3 72.9 - - - +
1959 ASP* 1.3 66.9 + - - +
1979 THR* 3.0 17.5 + - - -
1989 ASP* 3.0 15.2 + - - +
2849 ARG* 5.7 8.3 - - + -
3019 PHE* 4.7 11.6 - - + +
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Residues in contact with ASP 195 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1919 GLU 3.0 17.5 + - - +
1929 TYR* 3.9 4.3 - - - +
1949 GLN* 1.3 76.0 - - - +
1969 TYR* 1.3 57.5 + - - +
1989 ASP* 3.5 4.1 + - - +
1999 ARG* 2.9 32.4 + - - +
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Residues in contact with TYR 196 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1409 LEU* 5.4 12.3 - - + -
1929 TYR 2.9 18.4 + - - +
1939 LEU* 3.5 8.7 - - - +
1959 ASP* 1.3 77.8 - - - +
1979 THR* 1.3 63.7 + - - +
1999 ARG* 3.4 6.9 - - - +
2009 VAL* 2.9 27.1 + - - +
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Residues in contact with THR 197 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1939 LEU 2.9 13.8 + - - -
1949 GLN* 3.0 12.3 + - - -
1969 TYR* 1.3 79.9 - - - +
1989 ASP* 1.3 62.9 + - - +
2009 VAL* 3.1 12.4 + - - +
2019 LYS* 3.3 14.6 + - - +
3019 PHE* 4.9 15.7 - - - -
3049 ASN* 6.2 2.7 - - - -
3059 PRO* 5.8 5.8 - - - -
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Residues in contact with ASP 198 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1949 GLN 3.0 9.9 + - - +
1959 ASP* 4.3 3.8 - - - +
1979 THR* 1.3 80.7 - - - +
1999 ARG* 1.3 61.0 + - - +
2009 VAL 3.3 0.2 - - - -
2019 LYS* 3.5 22.7 - - - +
2029 PRO* 3.6 6.2 - - - +
2069 GLN* 5.0 17.0 - - + -
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Residues in contact with ARG 199 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1299 GLU* 5.3 13.2 - - + +
1959 ASP 2.9 21.0 + - - +
1969 TYR* 3.4 8.7 - - - +
1979 THR 3.1 0.2 - - - -
1989 ASP* 1.3 78.1 - - - +
2009 VAL* 1.3 60.0 + - - +
2019 LYS 3.5 0.2 + - - -
2029 PRO* 4.3 8.5 - - - +
71n PRO* 5.0 12.5 - - - +
72n ASP 5.0 3.1 + - - -
73n SER* 5.9 1.4 + - - -
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Residues in contact with VAL 200 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1379 GLY* 4.3 24.0 - - - +
1969 TYR 2.9 16.0 + - - +
1979 THR* 3.9 4.9 - - - +
1999 ARG* 1.3 75.7 - - + +
2019 LYS* 1.3 60.1 + - + +
2029 PRO 3.9 0.9 - - - -
72n ASP* 4.7 16.8 - - + +
73n SER* 5.1 8.2 + - - -
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Residues in contact with LYS 201 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1979 THR 3.3 13.0 + - - +
1989 ASP* 3.5 10.3 - - - +
1999 ARG 3.3 0.2 - - - -
2009 VAL* 1.3 79.8 - - - +
2029 PRO* 1.3 66.0 - - - +
2039 LEU* 3.2 3.9 + - - +
2049 GLN* 3.3 23.6 + - + +
73n SER* 6.1 0.4 - - - -
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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
------------------------------------------------------------
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