Contacts of the helix formed by residues 202 - 217 (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 THR 202 (chain 9).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2857 CYS 3.6 2.5 - - - +
2877 ILE* 0.6 288.8 - - + +
2907 ARG* 2.2 60.6 - - - +
2019 VAL* 1.3 73.2 - - - +
2039 THR* 1.3 52.4 + - - -
2059 GLU* 2.9 17.8 + - - +
2069 ARG* 3.1 10.7 + - - +
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Residues in contact with THR 203 (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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2867 ASP* 2.3 34.1 - - - +
2877 ILE* 1.4 37.2 - - - +
2887 ASP* 1.3 77.9 + - + +
629 ARG* 3.7 24.7 + - + +
2029 THR 1.3 66.5 - - - -
2049 ALA* 1.3 53.6 + - - -
2059 GLU 3.2 0.2 - - - -
2069 ARG* 3.7 10.7 - - - +
2079 GLU* 3.3 23.7 + - - +
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Residues in contact with ALA 204 (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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2877 ILE* 2.8 32.9 - - + +
2887 ASP* 2.7 20.5 + - - +
2917 LYS* 5.6 4.5 - - + -
2039 THR* 1.3 73.7 - - - +
2059 GLU* 1.3 63.5 + - - +
2079 GLU* 4.6 2.9 - - - -
2089 ILE* 3.6 10.9 - - - +
2439 PRO* 3.5 32.2 - - + +
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Residues in contact with GLU 205 (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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2877 ILE* 3.0 28.8 - - + +
2907 ARG* 5.3 3.0 + - - -
1999 SER 4.2 3.8 - - - +
2009 PHE* 3.4 33.6 - - + -
2019 VAL* 3.5 17.8 - - + +
2029 THR* 2.9 15.5 + - - +
2049 ALA* 1.3 85.0 - - - +
2069 ARG* 1.3 68.0 + - - +
2079 GLU 3.4 0.2 - - - -
2089 ILE* 3.1 21.5 - - - +
2099 VAL* 3.7 2.8 + - - +
2429 LEU* 3.7 23.4 - - + +
2439 PRO* 4.4 5.5 - - - +
2449 ASP* 5.1 2.4 - - - +
2469 GLN* 5.6 1.4 - - - +
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Residues in contact with ARG 206 (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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629 ARG* 4.4 12.6 - - - +
1839 ARG* 6.1 2.8 - - - +
1869 THR* 4.6 11.2 - - - +
1879 ASP* 3.4 32.4 + - - -
1909 MET* 3.7 26.9 - - + +
2009 PHE* 4.2 3.4 - - + +
2019 VAL 5.9 0.2 - - - +
2029 THR 3.1 8.2 + - - +
2039 THR* 3.7 15.9 - - - +
2059 GLU* 1.3 77.3 - - - +
2079 GLU* 1.3 67.3 + - - +
2099 VAL* 3.0 29.4 + - - +
2109 ARG* 5.1 0.8 - - - +
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Residues in contact with GLU 207 (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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2887 ASP* 4.1 11.0 - - - +
599 GLN* 3.8 13.0 - - - +
629 ARG* 2.9 39.7 + - - +
2039 THR 3.3 13.4 + - - +
2049 ALA* 5.1 2.0 - - - -
2059 GLU 3.4 0.2 + - - -
2069 ARG* 1.3 83.7 - - - +
2089 ILE* 1.3 58.5 + - + +
2109 ARG* 3.1 39.8 + - - +
2119 ASP* 3.8 1.9 + - - +
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Residues in contact with ILE 208 (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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2009 PHE* 5.4 2.9 - - + -
2049 ALA 3.6 15.7 + - - +
2059 GLU* 3.1 19.7 - - - +
2079 GLU* 1.3 75.4 - - + +
2099 VAL* 1.4 58.7 + - - +
2109 ARG 3.1 2.0 - - - -
2119 ASP* 3.0 10.9 + - + +
2129 ILE* 2.9 32.6 + - + +
2409 TYR* 3.2 40.2 - - + +
2419 GLU 5.0 0.2 - - - +
2429 LEU* 4.4 14.4 - - + -
2439 PRO* 3.9 29.2 - - + -
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Residues in contact with VAL 209 (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 THR* 3.6 22.4 - - + +
1899 LEU* 3.5 21.4 - - + +
1909 MET* 3.2 48.2 - - + +
1939 LEU* 4.1 13.2 - - + -
2009 PHE* 5.1 5.8 - - + -
2059 GLU 3.7 3.1 + - - +
2069 ARG* 3.0 24.5 + - - +
2089 ILE* 1.4 77.7 - - - +
2109 ARG* 1.3 58.7 + - - +
2129 ILE* 3.2 12.1 + - - +
2139 LYS* 2.9 24.4 + - - +
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Residues in contact with ARG 210 (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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169 LEU* 6.1 2.4 - - - +
1869 THR* 3.7 31.9 - - + +
2069 ARG* 5.1 0.4 - - - +
2079 GLU* 3.1 24.8 + - - +
2099 VAL* 1.3 81.4 - - - +
2119 ASP* 1.3 61.6 + - - +
2139 LYS* 3.4 13.5 - - - +
2149 GLU* 2.8 67.5 + - - +
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Residues in contact with ASP 211 (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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2079 GLU 3.8 1.0 + - - +
2089 ILE* 3.0 19.0 + - + +
2109 ARG* 1.3 83.3 + - - +
2129 ILE* 1.3 60.7 + - - +
2149 GLU* 4.0 12.9 - - - +
2159 LYS* 2.7 62.7 + - - +
2409 TYR* 2.9 21.6 + - - +
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Residues in contact with ILE 212 (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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1899 LEU* 3.7 17.0 - - + -
1939 LEU* 4.2 23.8 - - + -
2009 PHE* 5.1 7.9 - - + -
2089 ILE* 2.9 20.7 + - + +
2099 VAL* 3.3 11.7 - - - +
2119 ASP* 1.3 75.1 - - - +
2139 LYS* 1.4 61.6 + - - +
2159 LYS 3.2 0.9 + - - -
2169 LEU* 2.9 42.4 + - + +
2179 CYS* 3.7 2.5 + - - -
2409 TYR* 3.9 39.0 - - + -
2429 LEU* 5.2 1.6 - - + -
2489 ILE* 4.3 15.7 - - + -
2509 ILE* 4.5 15.7 - - + -
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Residues in contact with LYS 213 (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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1579 ASP* 5.8 0.6 + - - -
1829 GLY* 2.8 25.6 + - - +
1859 LEU 4.1 3.4 - - - -
1869 THR* 2.7 40.2 + - - +
1899 LEU* 3.6 18.2 - - + -
2099 VAL 2.9 8.1 + - - +
2109 ARG* 3.4 20.5 - - - +
2129 ILE* 1.4 74.6 - - - +
2149 GLU* 1.3 76.7 + - - +
2179 CYS* 3.0 31.4 + - - +
2579 CYS* 4.2 13.5 - - - -
3039 THR* 5.1 1.2 + - - -
3069 TYR* 3.7 32.1 - - + +
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Residues in contact with GLU 214 (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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2109 ARG* 2.8 55.2 + - - +
2119 ASP* 4.2 10.8 - - - +
2139 LYS* 1.3 95.2 + - - +
2159 LYS* 1.3 64.4 + - + +
2179 CYS 4.3 5.5 + - - +
3069 TYR* 5.6 4.4 - - - -
3079 PRO* 5.7 2.4 - - - +
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Residues in contact with LYS 215 (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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2119 ASP* 2.7 53.7 + - - +
2129 ILE* 4.1 0.7 - - - +
2149 GLU* 1.3 78.2 - - + +
2169 LEU* 1.3 73.5 + - + +
2179 CYS 4.9 0.7 - - - +
2189 TYR* 4.8 6.8 - - - -
2409 TYR* 4.1 16.0 + - + -
2549 ARG* 5.4 0.2 + - - -
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Residues in contact with LEU 216 (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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2129 ILE* 2.9 28.4 + - + +
2159 LYS* 1.3 86.9 - - + +
2179 CYS* 1.3 61.9 + - - +
2189 TYR* 3.3 6.1 - - - -
2389 LYS* 3.8 46.4 - - + +
2399 SER 4.9 1.6 - - - +
2409 TYR* 3.9 31.4 - - + +
2509 ILE* 4.6 11.0 - - + -
2549 ARG* 2.9 42.9 + - + +
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Residues in contact with CYS 217 (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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1899 LEU* 4.6 8.1 - - - -
2129 ILE* 3.7 2.7 + - - -
2139 LYS* 3.0 37.7 + - - +
2149 GLU 4.6 4.0 - - - +
2159 LYS 3.8 0.9 - - - +
2169 LEU* 1.3 73.0 - - - +
2189 TYR* 1.3 72.3 - - - +
2509 ILE* 6.2 0.2 - - - -
2539 GLU 4.7 0.2 - - - -
2549 ARG* 2.9 26.7 - - - +
2579 CYS* 4.2 19.1 - - - -
2589 PRO* 4.1 2.9 - - + -
3069 TYR* 4.0 22.0 - - + -
3079 PRO* 3.4 17.7 - - - +
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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