Contacts of the helix formed by residues 181 - 195 (chain 6) in PDB entry 1MVW
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 6).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1556 SER* 4.5 1.1 - - - +
1566 GLY 3.3 15.0 - - - +
1576 ASP 3.4 18.2 - - - +
1586 GLY* 3.7 13.7 - - - -
1596 VAL 3.8 9.4 - - - +
1606 THR* 4.3 2.7 - - - +
1806 LEU* 1.3 77.7 - - - +
1826 GLY* 1.3 61.2 + - - +
1836 ARG 3.2 2.8 + - - -
1846 ASP* 3.2 10.5 + - - +
1856 LEU* 3.0 33.6 + - - +
2616 LEU* 5.3 0.2 - - - -
3036 THR* 4.2 6.7 - - - -
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Residues in contact with GLY 182 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1566 GLY 3.0 10.0 + - - -
1576 ASP* 4.6 4.7 - - - -
1816 ALA* 1.3 76.1 - - - +
1836 ARG* 1.3 55.1 + - - +
1856 LEU* 3.5 8.2 - - - +
1866 THR* 3.0 18.2 + - - -
2136 LYS* 2.8 30.8 + - - -
3036 THR* 3.1 21.4 + - - -
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Residues in contact with ARG 183 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146 SER* 2.8 36.4 + - - -
696 TYR* 3.5 30.2 + - - +
716 ILE 4.8 5.5 + - - -
726 GLU* 4.6 13.9 + - - +
736 HIS* 5.2 7.4 - - - +
1576 ASP* 2.9 48.6 + - - +
1586 GLY* 4.4 15.1 - - - -
1816 ALA 3.2 0.2 - - - -
1826 GLY* 1.3 71.2 - - - +
1846 ASP* 1.3 70.5 - - - +
1866 THR* 3.3 13.3 + - - -
1876 ASP* 3.4 25.6 + - - +
2066 ARG* 6.1 2.5 - - - +
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Residues in contact with ASP 184 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
736 HIS* 5.4 2.9 - - - -
1576 ASP 4.5 1.0 - - - +
1586 GLY* 4.7 5.0 - - - +
1796 ASP 3.9 12.2 - - - +
1806 LEU* 3.8 11.2 - - + +
1816 ALA* 3.2 28.9 + - - +
1836 ARG* 1.3 81.4 - - - +
1856 LEU* 1.3 63.3 + - + +
1876 ASP* 3.2 9.4 + - - +
1886 TYR* 3.1 27.5 + - - +
2676 ILE* 5.0 13.5 - - + +
2696 MET* 5.6 1.2 - - - +
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Residues in contact with LEU 185 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1806 LEU* 3.9 24.0 - - + -
1816 ALA 3.0 18.5 + - - +
1826 GLY* 3.5 7.0 - - - +
1836 ARG 3.2 0.4 - - - -
1846 ASP* 1.3 77.6 - - + +
1866 THR* 1.3 61.5 + - - +
1876 ASP 3.3 0.2 - - - -
1886 TYR* 3.9 5.2 - - + +
1896 LEU 3.3 8.5 + - - -
2136 LYS* 4.1 2.7 - - + -
2576 CYS* 3.2 39.2 - - - +
2606 THR* 4.3 19.3 - - + -
2616 LEU* 4.0 11.2 - - + -
3036 THR* 3.8 17.3 - - + -
3066 TYR* 3.0 41.5 - - + +
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Residues in contact with THR 186 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1826 GLY 3.0 6.7 + - - -
1836 ARG* 3.3 7.9 + - - -
1856 LEU* 1.3 75.9 - - - +
1876 ASP* 1.3 66.7 + - - +
1896 LEU* 3.4 4.9 + - - +
1906 MET* 3.1 25.3 + - - +
2066 ARG* 4.6 10.8 - - - +
2096 VAL* 3.6 26.5 - - + +
2106 ARG* 3.7 26.2 - - + +
2136 LYS* 2.7 38.3 + - - +
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Residues in contact with ASP 187 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1836 ARG* 3.4 17.5 - - - +
1846 ASP* 3.2 11.3 + - - +
1866 THR* 1.3 78.4 - - - +
1886 TYR* 1.3 64.0 + - - +
1906 MET* 3.1 19.3 - - - +
1916 LYS* 3.3 9.9 + - - +
2066 ARG* 3.4 35.5 + - - -
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Residues in contact with TYR 188 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1846 ASP 3.1 15.3 + - - +
1856 LEU* 4.1 5.2 - - - +
1866 THR 3.3 0.2 - - - -
1876 ASP* 1.3 76.0 - - - +
1896 LEU* 1.3 66.6 + - - +
1916 LYS* 3.2 40.1 + - + +
1926 ILE* 3.0 44.9 + - + +
2566 ARG* 3.3 21.6 + - - +
2576 CYS* 3.8 11.4 - - + -
2606 THR* 3.2 24.7 - - + +
2666 PHE* 3.1 40.4 + + - +
2676 ILE* 3.5 25.8 - - + -
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Residues in contact with LEU 189 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1856 LEU 3.3 13.6 + - - +
1866 THR 3.4 7.8 + - - +
1876 ASP 3.4 0.2 - - - -
1886 TYR* 1.3 76.9 - - - +
1906 MET* 1.3 54.2 + - - +
1926 ILE* 3.0 26.3 + - + +
1936 LEU* 2.8 53.7 + - + +
2096 VAL* 3.5 34.1 - - + +
2126 ILE* 3.7 12.6 - - + -
2136 LYS* 3.5 28.3 - - + +
2176 CYS* 4.6 6.5 - - - -
2506 ILE* 5.5 2.9 - - + -
2536 GLU* 4.6 15.9 - - + +
2576 CYS* 3.8 9.0 - - + -
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Residues in contact with MET 190 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1866 THR 3.1 10.3 + - - +
1876 ASP* 3.1 17.3 - - - +
1896 LEU* 1.3 77.8 - - - +
1916 LYS* 1.3 58.4 + - - +
1936 LEU* 3.3 2.7 + - - +
1946 THR* 2.9 37.4 + - + +
2006 PHE* 3.7 29.0 - - + +
2066 ARG* 3.7 43.7 - - + +
2096 VAL* 3.2 35.9 - - + +
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Residues in contact with LYS 191 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1105 LEU* 6.5 1.6 - - + -
1876 ASP 3.3 5.3 + - - +
1886 TYR* 3.2 49.3 + - + +
1906 MET* 1.3 77.9 - - - +
1926 ILE* 1.3 65.3 + - - +
1936 LEU 2.8 6.8 + - - -
1946 THR* 2.9 10.6 + - - -
1956 GLU* 2.8 56.3 + - + +
2666 PHE 5.0 3.6 + - - -
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Residues in contact with ILE 192 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1886 TYR* 3.0 49.9 + - + +
1896 LEU* 3.0 21.1 + - + +
1916 LYS* 1.3 90.9 - - - +
1936 LEU* 1.3 55.1 + - - +
1956 GLU* 3.5 25.3 - - - +
1966 ARG* 3.2 21.0 + - - +
2536 GLU* 3.6 39.0 - - + +
2566 ARG* 3.6 32.8 + - + +
2576 CYS* 4.0 4.5 - - + +
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Residues in contact with LEU 193 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1896 LEU* 2.8 35.2 + - + +
1906 MET* 3.6 4.3 - - - +
1916 LYS 2.8 1.0 + - - -
1926 ILE* 1.3 77.1 - - - +
1946 THR* 1.3 62.0 + - - +
1956 GLU 3.2 0.9 - - - -
1966 ARG* 3.3 7.8 + - + -
1986 TYR* 2.8 39.6 - - + -
2006 PHE* 3.6 28.0 - - + -
2096 VAL* 4.1 10.1 - - + -
2126 ILE* 4.2 18.2 - - + -
2486 ILE* 5.2 0.2 - - + -
2496 THR 4.5 0.9 - - - +
2506 ILE* 3.3 34.5 - - + -
2536 GLU* 4.1 13.2 - - + -
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Residues in contact with THR 194 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1125 PRO* 5.6 1.4 - - - +
1906 MET* 2.9 26.8 + - + +
1916 LYS* 3.0 14.5 + - - +
1936 LEU* 1.3 75.2 - - - +
1956 GLU* 1.3 59.5 + - - +
1976 GLY* 2.9 9.9 + - - -
1986 TYR* 2.9 39.0 + - - +
1996 SER* 4.9 0.4 - - - -
2006 PHE* 3.5 25.4 - - + +
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Residues in contact with GLU 195 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1105 LEU* 5.3 11.1 - - + +
1125 PRO* 4.0 33.9 - - + +
1916 LYS* 2.8 44.9 + - + +
1926 ILE* 3.5 23.1 - - - +
1946 THR* 1.3 77.4 + - - +
1966 ARG* 1.3 55.5 + - - +
1976 GLY* 3.0 8.5 + - - -
2566 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
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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