Contacts of the helix formed by residues 181 - 195 (chain 9) 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 9).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1559 SER* 4.5 1.6 - - - +
1569 GLY 3.3 15.5 - - - +
1579 ASP 3.4 18.4 - - - +
1589 GLY 3.7 13.5 - - - -
1599 VAL 3.8 9.4 - - - +
1609 THR* 4.3 3.6 - - - +
1809 LEU* 1.3 77.4 - - - +
1829 GLY* 1.3 61.0 + - - +
1839 ARG 3.2 2.7 + - - -
1849 ASP* 3.2 10.4 + - - +
1859 LEU* 3.0 32.6 + - - +
3039 THR* 4.2 7.2 - - - -
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Residues in contact with GLY 182 (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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1569 GLY 3.0 11.1 + - - -
1579 ASP* 4.6 4.7 - - - -
1819 ALA* 1.3 75.6 - - - +
1839 ARG* 1.3 57.2 + - - +
1859 LEU* 3.5 8.0 - - - +
1869 THR* 3.0 17.7 + - - -
2139 LYS* 2.8 30.7 + - - -
3039 THR* 3.1 21.9 + - - -
3069 TYR* 4.6 0.2 - - - -
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Residues in contact with ARG 183 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149 SER* 2.8 35.4 + - - -
699 TYR* 3.5 30.6 + - - +
719 ILE 4.8 5.7 + - - -
729 GLU* 4.6 13.9 + - - +
739 HIS* 5.2 7.5 - - - +
1579 ASP* 2.9 46.4 + - - +
1589 GLY* 4.4 15.2 - - - -
1829 GLY* 1.3 71.4 - - - +
1849 ASP* 1.3 71.3 + - - +
1869 THR* 3.3 13.7 + - - -
1879 ASP* 3.3 25.9 + - - +
2069 ARG* 6.1 2.7 - - - +
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Residues in contact with ASP 184 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
739 HIS* 5.4 3.5 - - - -
1579 ASP 4.5 0.5 - - - +
1589 GLY* 4.7 5.0 - - - +
1799 ASP 3.9 12.8 - - - +
1809 LEU* 3.8 11.8 - - + +
1819 ALA* 3.2 28.8 + - - +
1839 ARG* 1.3 81.8 - - - +
1859 LEU* 1.3 62.0 + - + +
1879 ASP* 3.2 9.5 + - - +
1889 TYR* 3.1 27.7 + - - +
2679 ILE* 5.0 12.7 - - + +
2699 MET* 5.6 0.9 - - - +
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Residues in contact with LEU 185 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1809 LEU* 3.9 24.0 - - + -
1819 ALA 3.0 18.5 + - - +
1829 GLY 3.5 7.2 - - - +
1839 ARG 3.2 0.2 - - - -
1849 ASP* 1.3 78.1 - - + +
1869 THR* 1.3 60.7 + - - +
1889 TYR* 3.9 5.0 - - - +
1899 LEU* 3.3 8.7 + - - +
2139 LYS* 4.1 3.4 - - + -
2579 CYS* 3.2 38.8 - - - +
2589 PRO* 5.1 0.2 - - + -
2609 THR* 4.3 20.0 - - + -
2619 LEU* 4.0 11.4 - - + -
3039 THR* 3.8 17.5 - - + -
3069 TYR* 3.0 40.2 - - + +
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Residues in contact with THR 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 GLY 3.0 8.0 + - - -
1839 ARG* 3.3 8.0 + - - -
1859 LEU* 1.3 74.5 - - - +
1879 ASP* 1.3 65.4 + - - +
1899 LEU* 3.4 5.8 + - - +
1909 MET* 3.1 25.8 + - - +
2069 ARG* 4.6 10.1 - - - +
2099 VAL* 3.6 26.5 - - + +
2109 ARG* 3.7 26.3 - - + +
2139 LYS* 2.7 38.5 + - - +
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Residues in contact with ASP 187 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1839 ARG* 3.3 18.1 + - - +
1849 ASP* 3.2 11.5 + - - +
1869 THR* 1.3 79.2 - - - +
1889 TYR* 1.3 63.8 + - - +
1909 MET* 3.1 20.3 - - - +
1919 LYS* 3.3 9.5 + - - +
2069 ARG* 3.4 34.6 + - - -
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Residues in contact with TYR 188 (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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1849 ASP 3.1 15.1 + - - +
1859 LEU* 4.1 6.3 - - - +
1869 THR 3.3 0.2 - - - -
1879 ASP* 1.3 74.8 - - - +
1899 LEU* 1.3 66.7 + - - +
1919 LYS* 3.2 39.5 + - + +
1929 ILE* 3.0 45.8 + - + +
2569 ARG* 3.3 21.3 + - - +
2579 CYS* 3.9 10.8 - - + -
2609 THR* 3.2 24.9 - - + +
2669 PHE* 3.1 41.4 + + - +
2679 ILE* 3.5 26.5 - - + -
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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
----------------------------------------------------------
1859 LEU 3.3 13.9 + - - +
1869 THR 3.7 7.4 - - - +
1879 ASP 3.4 0.2 - - - -
1889 TYR* 1.3 76.7 - - - +
1909 MET* 1.3 55.8 - - - +
1929 ILE* 3.0 26.4 + - + +
1939 LEU* 2.8 52.4 + - + +
2099 VAL* 3.5 34.1 - - + +
2129 ILE* 3.7 12.3 - - + -
2139 LYS* 3.5 27.4 - - + +
2179 CYS* 4.6 7.4 - - - -
2509 ILE* 5.5 2.0 - - + -
2539 GLU* 4.6 15.9 - - + +
2549 ARG 5.3 0.4 - - - +
2579 CYS* 3.8 9.4 - - + -
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Residues in contact with MET 190 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1869 THR 3.1 11.1 + - - +
1879 ASP* 3.1 17.7 - - - +
1899 LEU* 1.3 77.9 - - - +
1919 LYS* 1.3 59.0 + - - +
1939 LEU* 3.3 2.9 + - - +
1949 THR* 2.9 37.3 + - + +
2009 PHE* 3.7 29.8 - - + +
2069 ARG* 3.7 43.3 - - + +
2099 VAL* 3.2 35.6 - - + +
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Residues in contact with LYS 191 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1879 ASP 3.3 5.6 + - - +
1889 TYR* 3.2 48.5 + - + +
1909 MET* 1.3 78.6 - - - +
1929 ILE* 1.3 64.2 + - - +
1939 LEU 2.8 7.4 + - - -
1949 THR* 2.9 12.0 + - - +
1959 GLU* 2.8 55.5 + - + +
2669 PHE 5.0 3.0 + - - -
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Residues in contact with ILE 192 (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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1889 TYR* 3.0 49.5 + - + +
1899 LEU* 3.2 23.1 - - + +
1919 LYS* 1.3 91.2 - - - +
1939 LEU* 1.3 55.0 + - - +
1959 GLU* 3.5 25.6 - - - +
1969 ARG* 3.2 21.1 + - - +
2539 GLU* 3.6 39.6 - - + +
2569 ARG* 3.6 31.7 + - + +
2579 CYS* 4.0 3.4 - - + +
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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* 2.8 35.4 + - + +
1909 MET 3.6 4.3 - - - +
1919 LYS 2.8 0.8 + - - -
1929 ILE* 1.3 76.9 - - - +
1949 THR* 1.3 63.1 + - - +
1959 GLU 3.2 1.1 - - - -
1969 ARG* 3.3 6.8 + - + -
1989 TYR* 2.8 40.6 + - + -
2009 PHE* 3.6 28.5 - - + -
2099 VAL* 4.1 10.5 - - + -
2129 ILE* 4.2 17.9 - - + -
2499 THR 4.5 1.1 - - - +
2509 ILE* 3.3 33.4 - - + -
2539 GLU* 4.1 13.9 - - + -
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Residues in contact with THR 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 MET* 2.9 26.8 + - + +
1919 LYS* 2.9 14.5 + - - -
1939 LEU* 1.3 76.2 - - - +
1959 GLU* 1.3 59.2 + - - +
1979 GLY* 2.9 9.9 + - - -
1989 TYR* 2.9 37.4 + - - +
1999 SER* 4.9 0.4 - - - -
2009 PHE* 3.5 25.8 - - + +
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Residues in contact with GLU 195 (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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1128 PRO* 5.3 18.1 - - + +
1919 LYS* 2.8 45.0 + - + +
1929 ILE* 3.5 24.4 - - - +
1949 THR* 1.3 77.4 + - - +
1969 ARG* 1.3 55.8 + - - +
1979 GLY* 3.0 9.3 + - - -
2569 ARG* 3.7 14.6 + - - -
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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