Contacts of the helix formed by residues 202 - 217 (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 THR 202 (chain 6).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2854 CYS 4.5 0.7 - - - +
2874 ILE* 1.6 57.2 - - + +
2904 ARG* 1.6 61.0 + - - +
2016 VAL* 1.3 77.8 - - + +
2036 THR* 1.3 54.1 + - - -
2056 GLU* 2.9 36.4 + - + +
2066 ARG* 3.1 11.4 + - - +
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Residues in contact with THR 203 (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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2864 ASP* 3.0 7.0 - - - +
2874 ILE* 1.6 36.0 - - - +
2884 ASP* 1.7 86.5 + - + +
626 ARG* 3.7 17.7 + - - +
2026 THR 1.3 66.5 - - - -
2046 ALA* 1.3 56.9 + - - -
2056 GLU 3.2 0.7 - - - -
2066 ARG* 3.7 10.8 - - - +
2076 GLU* 3.3 27.2 + - - +
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Residues in contact with ALA 204 (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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2874 ILE* 2.7 35.2 - - + +
2884 ASP* 4.5 5.6 - - - +
2026 THR* 4.1 0.7 - - - +
2036 THR* 1.3 71.7 - - - +
2056 GLU* 1.3 62.1 + - - +
2076 GLU* 4.6 5.4 - - - -
2086 ILE* 3.6 10.8 - - - +
2436 PRO* 3.5 31.9 - - + +
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Residues in contact with GLU 205 (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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1996 SER 4.2 4.4 - - - +
2006 PHE* 3.4 34.5 - - + -
2016 VAL* 3.5 17.4 - - + +
2026 THR* 2.9 39.4 + - - +
2046 ALA* 1.3 87.3 - - - +
2066 ARG* 1.3 66.9 + - - +
2086 ILE* 3.1 21.9 - - - +
2096 VAL 3.7 2.6 + - - -
2426 LEU* 3.7 22.3 - - - +
2436 PRO* 4.4 5.5 - - - +
2446 ASP* 5.1 2.9 - - - +
2466 GLN* 5.6 1.4 - - - +
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Residues in contact with ARG 206 (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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626 ARG* 4.4 12.6 - - - +
1836 ARG* 6.1 2.8 - - - +
1866 THR* 4.6 11.4 - - - +
1876 ASP* 3.4 33.2 + - - -
1906 MET* 3.7 27.9 - - + +
2006 PHE* 4.2 3.6 - - + +
2016 VAL 5.9 0.4 - - - +
2026 THR 3.1 8.0 + - - +
2036 THR* 3.5 15.7 + - - +
2056 GLU* 1.3 76.6 - - - +
2076 GLU* 1.3 68.2 + - - +
2096 VAL* 3.0 30.6 + - - +
2106 ARG* 5.1 0.6 - - - +
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Residues in contact with GLU 207 (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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2884 ASP* 4.3 8.5 - - - +
596 GLN* 3.8 12.3 - - - +
626 ARG* 2.9 37.4 + - - +
2036 THR 3.3 13.7 + - - +
2046 ALA* 5.1 3.5 - - - -
2056 GLU 3.4 0.2 - - - -
2066 ARG* 1.3 83.7 - - - +
2086 ILE* 1.3 57.8 + - + +
2106 ARG* 3.1 39.5 + - - +
2116 ASP* 3.8 2.3 + - - +
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Residues in contact with ILE 208 (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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2006 PHE* 5.4 3.1 - - + -
2046 ALA 3.6 14.5 + - - +
2056 GLU* 3.1 19.7 - - - +
2076 GLU* 1.3 75.5 - - - +
2096 VAL* 1.4 58.1 + - - +
2106 ARG 3.1 1.8 - - - -
2116 ASP* 3.0 11.5 + - + +
2126 ILE* 2.9 33.2 + - + +
2406 TYR* 3.2 41.1 - - + +
2426 LEU* 4.4 14.6 - - + -
2436 PRO* 3.9 29.8 - - + -
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Residues in contact with VAL 209 (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* 3.6 22.0 - - + +
1896 LEU* 3.5 22.6 - - + +
1906 MET* 3.2 48.9 - - + +
1936 LEU* 4.1 13.7 - - + -
2006 PHE* 5.1 6.1 - - + -
2056 GLU 3.7 2.9 + - - +
2066 ARG* 3.0 24.5 + - - +
2086 ILE* 1.4 78.1 - - - +
2106 ARG* 1.3 59.3 + - - +
2126 ILE* 3.2 12.5 + - - +
2136 LYS* 3.0 24.8 + - - +
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Residues in contact with ARG 210 (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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166 LEU* 6.1 2.4 - - - +
1866 THR* 3.7 31.4 - - + +
2066 ARG* 6.2 0.2 - - - +
2076 GLU* 3.1 24.0 + - - +
2096 VAL* 1.3 83.3 - - + +
2116 ASP* 1.3 60.8 + - - +
2136 LYS* 3.4 13.0 - - - +
2146 GLU* 2.8 68.6 + - - +
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Residues in contact with ASP 211 (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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2076 GLU 3.8 1.3 + - - +
2086 ILE* 3.0 18.8 + - + +
2106 ARG* 1.3 83.4 + - - +
2126 ILE* 1.3 60.3 + - - +
2146 GLU* 4.0 14.1 - - - +
2156 LYS* 2.7 63.4 + - - +
2406 TYR* 2.9 21.4 + - - +
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Residues in contact with ILE 212 (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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1896 LEU* 3.7 17.7 - - + -
1936 LEU* 4.2 24.0 - - + -
2006 PHE* 5.1 7.9 - - + -
2086 ILE* 2.9 21.4 + - + +
2096 VAL* 3.3 12.1 - - - +
2116 ASP* 1.3 74.2 - - - +
2136 LYS* 1.4 60.9 + - - +
2156 LYS 3.2 0.7 + - - -
2166 LEU* 2.9 42.6 + - + +
2176 CYS* 3.7 2.9 + - - -
2406 TYR* 3.9 37.9 - - + -
2426 LEU* 5.2 1.6 - - + -
2486 ILE* 4.3 15.3 - - + -
2506 ILE* 4.5 15.9 - - + -
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Residues in contact with LYS 213 (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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1576 ASP* 5.8 0.2 + - - -
1826 GLY* 2.8 25.4 + - - +
1856 LEU* 4.1 2.9 - - + -
1866 THR* 2.7 40.6 + - - +
1896 LEU* 3.6 17.7 - - + -
2096 VAL 3.0 8.7 + - - +
2106 ARG* 3.4 20.0 - - - +
2126 ILE* 1.4 73.8 - - - +
2146 GLU* 1.3 77.9 + - - +
2176 CYS* 3.0 31.6 + - - +
2576 CYS* 4.2 13.5 - - - -
3036 THR* 5.1 1.0 + - - -
3066 TYR* 3.7 31.9 + - + +
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Residues in contact with GLU 214 (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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2106 ARG* 2.8 56.9 + - - +
2116 ASP* 4.2 10.8 - - - +
2126 ILE 3.3 0.2 - - - -
2136 LYS* 1.3 95.4 + - - +
2156 LYS* 1.3 63.6 + - + +
2176 CYS 4.3 5.7 + - - +
3066 TYR* 5.6 3.7 - - - -
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Residues in contact with LYS 215 (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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2116 ASP* 2.7 53.5 + - - +
2126 ILE* 4.1 0.4 - - - +
2146 GLU* 1.3 78.3 - - + +
2166 LEU* 1.3 73.5 + - + +
2176 CYS 4.9 0.7 - - - +
2186 TYR* 4.8 6.8 - - - -
2406 TYR* 4.1 14.9 + - + -
2546 ARG* 5.4 0.2 + - - -
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Residues in contact with LEU 216 (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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2126 ILE* 2.9 27.1 + - + +
2156 LYS* 1.3 85.7 - - + +
2176 CYS* 1.3 61.9 + - - +
2186 TYR* 3.3 4.9 - - - -
2386 LYS* 3.8 46.4 - - + +
2396 SER 5.8 0.7 - - - +
2406 TYR* 3.9 32.3 - - + +
2506 ILE* 4.6 11.4 - - + -
2546 ARG* 2.9 43.9 + - + +
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Residues in contact with CYS 217 (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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1896 LEU* 4.6 7.9 - - - -
2126 ILE* 3.7 2.9 + - - -
2136 LYS* 3.0 36.0 + - - +
2146 GLU 4.6 3.6 - - - +
2156 LYS 3.8 1.3 - - - +
2166 LEU* 1.3 72.7 - - - +
2186 TYR* 1.3 72.8 - - - +
2506 ILE* 6.2 0.4 - - - -
2536 GLU 4.7 0.4 - - - -
2546 ARG* 2.9 27.4 - - - +
2576 CYS* 4.2 19.3 - - - -
2586 PRO* 4.1 2.9 - - + -
3066 TYR* 4.0 21.5 - - + -
3076 PRO* 3.4 17.5 - - - +
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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