Contacts of the helix formed by residues 184 - 194 (chain 1) in PDB entry 6Q8O
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 GLU 184 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1801 TYR 4.7 0.2 + - - -
1811 ILE* 2.9 25.2 + - + +
1821 CYS 3.7 1.4 - - - +
1831 GLY* 1.3 77.1 - - - +
1851 GLU* 1.3 69.2 + - - +
1861 THR* 2.3 47.2 + - - -
1871 ALA* 2.9 16.9 + - + +
1881 LEU 3.1 10.4 + - - -
1991 PRO* 4.7 3.4 - - + -
2021 LYS* 2.6 37.1 + - - +
4001 CYS* 4.5 19.2 - - + -
4011 PRO* 4.8 9.8 - - + +
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Residues in contact with GLU 185 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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751 LYS* 4.8 15.0 + - - -
921 ASN* 5.6 2.9 - - - +
1831 GLY 3.4 5.0 + - - -
1841 GLU* 1.3 84.4 + - - +
1861 THR* 1.3 66.6 + - + +
1881 LEU* 3.8 6.5 + - - +
1891 MET* 3.3 30.2 + - - +
2021 LYS* 3.9 17.1 + - - +
2061 PRO* 3.6 26.3 - - + +
2181 ILE* 3.6 37.0 + - + +
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Residues in contact with THR 186 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1841 GLU* 2.3 40.4 + - - +
1851 GLU* 1.3 80.7 - - + +
1871 ALA* 1.3 60.0 + - - +
1891 MET* 3.8 14.8 + - + +
1901 ASN* 3.6 13.7 + - - -
1991 PRO* 3.2 18.1 - - - +
2001 ARG* 3.2 48.0 + - + +
2011 LEU 5.5 0.7 - - - +
2021 LYS* 4.5 19.9 - - + +
2061 PRO* 5.4 7.0 - - + -
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Residues in contact with ALA 187 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1811 ILE* 3.2 46.2 - - + +
1821 CYS* 4.7 0.2 - - - -
1841 GLU* 2.9 7.3 + - + +
1861 THR* 1.3 79.2 + - - +
1881 LEU* 1.3 58.6 + - - +
1891 MET 3.4 0.2 + - - -
1901 ASN* 3.4 1.2 + - - +
1911 SER* 2.9 28.8 + - - -
1971 ALA* 3.5 20.1 - - + +
1981 ASN 4.3 2.5 - - - -
1991 PRO* 4.0 14.1 - - + -
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Residues in contact with LEU 188 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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901 ILE* 4.2 24.0 - - + -
921 ASN* 3.4 30.7 - - + +
1331 TYR* 3.5 48.1 - - + -
1821 CYS* 3.2 26.3 + - - +
1831 GLY 5.5 0.4 - - - +
1841 GLU 3.1 10.4 + - - +
1851 GLU* 4.1 7.4 - - - +
1871 ALA* 1.3 77.6 - - - +
1891 MET* 1.3 61.4 + - + +
1911 SER* 3.3 6.9 + - - -
1921 LEU* 2.9 34.7 + - + +
2181 ILE* 5.8 3.6 - - + -
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Residues in contact with MET 189 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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901 ILE* 4.3 13.9 - - + -
1851 GLU 3.3 21.5 + - - +
1861 THR* 4.2 15.3 - - + +
1871 ALA 3.3 0.4 - - - -
1881 LEU* 1.3 80.4 - - + +
1901 ASN* 1.3 58.2 + - - +
1921 LEU* 3.4 0.8 + - - -
1931 GLU* 2.9 30.3 + - - +
2001 ARG* 4.0 26.7 - - - +
2061 PRO* 4.0 24.0 - - + -
2091 SER 5.0 0.7 - - - +
2101 GLY* 4.0 3.6 - - - -
2111 LEU* 3.4 35.6 - - + +
2161 THR* 3.4 23.3 - - - -
2181 ILE* 4.3 10.3 - - + -
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Residues in contact with ASN 190 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1861 THR 3.6 2.1 + - - +
1871 ALA 3.4 6.6 + - - +
1881 LEU 3.4 0.2 - - - -
1891 MET* 1.3 74.8 - - - +
1911 SER* 1.3 62.9 + - - +
1931 GLU* 3.4 4.6 + - - -
1951 LEU* 2.8 50.8 + - + +
1961 ARG 3.4 16.3 + - - +
1981 ASN* 2.5 28.3 + - - +
1991 PRO 4.2 1.0 + - - -
2001 ARG* 2.4 51.2 + - - +
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Residues in contact with SER 191 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1331 TYR* 3.6 14.4 + - - -
1821 CYS* 4.1 4.8 - - - -
1871 ALA 2.9 18.1 + - - -
1881 LEU* 3.3 8.9 + - - -
1901 ASN* 1.3 77.5 - - - +
1921 LEU* 1.3 63.1 + - - +
1941 GLY* 3.2 11.6 + - - -
1951 LEU 3.4 13.5 - - - +
1971 ALA* 3.7 14.5 - - - +
282 MET* 3.5 23.4 - - - +
672 TYR* 2.7 21.8 + - - -
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Residues in contact with LEU 192 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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901 ILE* 6.1 0.7 - - + -
1311 TYR* 4.3 23.8 - - + -
1331 TYR* 4.6 11.6 - - + -
1741 HIS* 3.7 51.3 - - + +
1881 LEU* 2.9 25.4 + - + +
1891 MET* 4.0 4.3 - - - +
1911 SER* 1.3 71.5 - - - +
1931 GLU* 1.3 63.8 + - - +
1941 GLY 2.9 6.4 + - - -
2111 LEU* 3.6 26.5 - - + -
2121 TRP* 3.9 19.3 - - + -
182 TYR* 4.2 8.7 - - + -
252 ALA* 3.1 23.0 - - - +
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Residues in contact with GLU 193 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1891 MET 2.9 14.8 + - - +
1901 ASN 3.7 6.1 - - - +
1911 SER 3.3 0.2 - - - -
1921 LEU* 1.3 77.2 - - - +
1941 GLY* 1.3 57.7 + - - +
1951 LEU* 3.7 23.9 - - + +
2001 ARG* 2.4 34.0 + - - -
2111 LEU* 4.2 3.2 - - + +
2121 TRP* 3.6 55.1 + - + +
222 GLY* 4.1 5.5 - - - +
242 ARG* 3.9 6.4 - - - +
252 ALA* 3.3 14.5 + - - +
4403 ARG* 5.3 4.3 + - - +
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Residues in contact with GLY 194 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1911 SER 3.2 6.1 + - - -
1921 LEU 2.9 6.5 + - - -
1931 GLU* 1.3 77.9 - - - +
1951 LEU* 1.3 59.3 + - - +
242 ARG* 2.5 56.6 + - - +
252 ALA* 3.8 2.7 - - - -
272 ILE* 4.9 1.8 - - - +
282 MET* 5.2 4.5 - - - -
632 VAL* 3.7 12.0 - - - +
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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
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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