Contacts of the helix formed by residues 202 - 217 (chain 3) 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 3).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2831 MET* 5.2 7.6 - - + -
2871 ILE* 4.2 7.9 - - - -
2901 ARG* 2.8 35.4 - - - +
2013 VAL* 1.3 84.4 - - + +
2033 THR* 1.3 60.1 + - - +
2043 ALA* 3.8 11.9 + - - +
2053 GLU* 2.9 38.7 + - - +
2063 ARG* 3.1 11.0 + - - +
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Residues in contact with THR 203 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2871 ILE* 2.2 65.0 - - + +
2881 ASP* 4.3 9.9 + - - +
623 ARG* 3.7 26.3 + - - -
2023 THR* 1.3 74.1 - - - +
2043 ALA* 1.3 60.9 + - + +
2053 GLU 3.2 0.2 - - - -
2063 ARG* 3.7 11.7 - - - +
2073 GLU* 3.3 27.9 + - - +
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Residues in contact with ALA 204 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2871 ILE* 5.3 1.6 - - + -
2023 THR* 3.2 10.8 + - - +
2033 THR* 1.3 80.4 - - + +
2053 GLU* 1.3 64.1 + - - +
2073 GLU* 4.6 5.2 - - - -
2083 ILE* 3.6 12.2 - - - +
2433 PRO* 3.5 31.3 - - + +
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Residues in contact with GLU 205 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1993 SER 4.3 4.1 - - - +
2003 PHE* 3.4 33.4 - - + -
2013 VAL* 3.5 17.5 - - + +
2023 THR* 2.9 37.4 + - - +
2043 ALA* 1.3 86.3 - - - +
2063 ARG* 1.3 67.2 + - - +
2073 GLU 3.4 0.2 - - - -
2083 ILE* 3.1 21.7 - - - +
2093 VAL* 3.7 3.3 + - - +
2423 LEU* 3.7 23.1 - - + +
2433 PRO* 4.4 5.5 - - - +
2443 ASP* 5.1 3.0 - - - +
2463 GLN* 5.6 1.6 - - - +
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Residues in contact with ARG 206 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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623 ARG* 4.4 13.3 - - - +
1833 ARG* 6.1 3.2 - - - +
1863 THR* 4.6 12.3 - - - +
1873 ASP* 3.4 32.0 + - - -
1903 MET* 3.7 26.8 - - + +
2003 PHE* 4.2 3.8 - - + +
2013 VAL 5.9 0.4 - - - +
2023 THR 3.1 9.1 + - - +
2033 THR* 3.7 15.0 - - - +
2053 GLU* 1.3 77.3 - - - +
2073 GLU* 1.3 67.5 + - - +
2093 VAL* 3.0 29.9 + - - +
2103 ARG* 5.1 0.4 - - - +
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Residues in contact with GLU 207 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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593 GLN* 3.8 12.6 - - - +
623 ARG* 2.9 38.3 + - - +
2033 THR 3.3 14.1 + - - +
2043 ALA* 5.1 3.8 - - - -
2053 GLU 3.4 0.2 - - - -
2063 ARG* 1.3 83.7 - - - +
2083 ILE* 1.3 57.6 + - + +
2103 ARG* 3.1 39.8 + - - +
2113 ASP* 3.8 1.9 + - - +
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Residues in contact with ILE 208 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2003 PHE* 5.4 2.9 - - + -
2043 ALA 3.6 14.5 + - - +
2053 GLU* 3.1 20.8 - - - +
2073 GLU* 1.3 75.1 - - + +
2093 VAL* 1.4 58.2 + - - +
2103 ARG 3.1 2.0 - - - -
2113 ASP* 3.0 10.7 + - + +
2123 ILE* 2.9 32.8 + - + +
2403 TYR* 3.2 40.6 - - + +
2423 LEU* 4.4 14.1 - - + -
2433 PRO* 3.9 29.2 - - + -
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Residues in contact with VAL 209 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1863 THR* 3.6 22.2 - - + +
1893 LEU* 3.5 22.1 - - + +
1903 MET* 3.2 48.7 - - + +
1933 LEU* 4.1 13.0 - - + -
2003 PHE* 5.1 6.1 - - + -
2053 GLU 3.7 2.9 + - - +
2063 ARG* 3.0 25.2 + - - +
2083 ILE* 1.4 77.9 - - - +
2103 ARG* 1.3 59.5 + - - +
2123 ILE* 3.2 12.5 + - - +
2133 LYS* 2.9 24.4 + - - +
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Residues in contact with ARG 210 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163 LEU* 6.1 2.8 - - - +
1863 THR* 3.7 31.4 - - + +
2063 ARG* 6.2 0.4 - - - +
2073 GLU* 3.1 24.2 + - - +
2093 VAL* 1.3 82.6 - - + +
2113 ASP* 1.3 61.6 + - - +
2133 LYS* 3.4 13.4 - - - +
2143 GLU* 2.8 69.5 + - - +
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Residues in contact with ASP 211 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2073 GLU 3.8 1.7 + - - +
2083 ILE* 3.0 19.2 + - + +
2103 ARG* 1.3 83.5 + - - +
2123 ILE* 1.3 60.8 + - - +
2143 GLU* 4.0 13.9 - - - +
2153 LYS* 2.7 63.1 + - - +
2403 TYR* 2.9 20.9 + - - +
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Residues in contact with ILE 212 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1893 LEU* 3.7 17.9 - - + -
1933 LEU* 4.2 23.6 - - + -
2003 PHE* 5.1 7.9 - - + -
2083 ILE* 2.9 19.6 + - + +
2093 VAL* 3.2 12.8 + - - +
2113 ASP* 1.3 74.2 - - - +
2133 LYS* 1.4 61.8 + - - +
2153 LYS 3.2 1.2 + - - -
2163 LEU* 2.9 42.3 + - + +
2173 CYS* 3.7 2.8 + - - -
2403 TYR* 3.9 40.8 - - + -
2423 LEU* 5.2 1.1 - - + -
2483 ILE* 4.3 15.9 - - + -
2503 ILE* 4.5 15.9 - - + -
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Residues in contact with LYS 213 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1573 ASP* 5.8 0.6 + - - -
1823 GLY* 2.8 24.8 + - - +
1853 LEU 4.1 3.1 - - - -
1863 THR* 2.7 40.6 + - - +
1893 LEU* 3.5 17.2 - - + +
2093 VAL 2.9 9.1 + - - +
2103 ARG* 3.4 21.2 - - - +
2123 ILE* 1.4 73.6 - - - +
2143 GLU* 1.3 76.3 + - - +
2173 CYS* 3.0 31.0 + - - +
2573 CYS* 4.2 13.0 - - - -
3033 THR* 5.1 1.2 + - - -
3063 TYR* 3.7 32.3 - - + +
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Residues in contact with GLU 214 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2103 ARG* 2.8 56.7 + - - +
2113 ASP* 4.2 10.4 - - - +
2133 LYS* 1.3 94.4 + - - +
2153 LYS* 1.3 65.2 + - + +
2173 CYS 4.3 5.7 + - - +
3063 TYR* 5.6 4.7 - - - -
3073 PRO* 5.7 2.4 - - - +
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Residues in contact with LYS 215 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2113 ASP* 2.7 53.6 + - - +
2123 ILE* 4.1 1.1 - - - +
2143 GLU* 1.3 77.3 - - + +
2163 LEU* 1.3 73.0 + - + +
2173 CYS 4.9 0.9 - - - +
2183 TYR* 4.8 6.4 - - - -
2403 TYR* 4.1 15.6 + - + -
2543 ARG* 5.4 0.2 + - - -
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Residues in contact with LEU 216 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2123 ILE* 2.9 27.3 + - + +
2153 LYS* 1.3 86.0 - - + +
2173 CYS* 1.3 62.2 + - - +
2183 TYR* 3.3 4.9 - - - -
2383 LYS* 3.8 46.2 - - + +
2393 SER 5.8 1.1 - - - +
2403 TYR* 3.9 31.9 - - + +
2503 ILE* 4.6 11.9 - - + -
2543 ARG* 2.9 43.3 + - + +
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Residues in contact with CYS 217 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1893 LEU* 4.6 7.9 - - - -
2123 ILE* 4.6 2.5 - - - -
2133 LYS* 3.0 35.6 + - - +
2143 GLU 4.6 4.0 - - - +
2153 LYS 3.8 0.9 - - - +
2163 LEU* 1.3 72.1 - - - +
2183 TYR* 1.3 74.4 + - - +
2503 ILE* 6.2 0.2 - - - -
2533 GLU 4.7 0.2 - - - -
2543 ARG* 2.9 27.4 - - - +
2573 CYS* 4.2 19.5 - - - -
2583 PRO* 4.1 2.5 - - + -
3063 TYR* 4.0 21.9 - - + -
3073 PRO* 3.4 17.8 - - - +
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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