Contacts of the helix formed by residues 202 - 217 (chain 8) 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 8).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2018 VAL* 1.3 84.8 - - + +
2038 THR* 1.4 60.5 + - - +
2048 ALA* 3.8 10.9 + - - +
2058 GLU* 2.9 38.9 + - + +
2068 ARG* 3.1 11.2 + - - +
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Residues in contact with THR 203 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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628 ARG* 3.7 30.4 + - + +
2028 THR* 1.4 74.1 - - - +
2048 ALA* 1.3 62.0 + - + +
2058 GLU 3.2 0.4 - - - -
2068 ARG* 3.7 11.1 - - - +
2078 GLU* 3.3 27.5 + - - +
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Residues in contact with ALA 204 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2028 THR* 3.2 10.0 + - - +
2038 THR* 1.3 80.8 - - + +
2058 GLU* 1.3 64.1 + - - +
2078 GLU* 4.6 5.3 - - - +
2088 ILE* 3.6 11.2 - - - +
2438 PRO* 3.5 31.9 - - + +
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Residues in contact with GLU 205 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1998 SER 4.2 4.3 - - - +
2008 PHE* 3.4 34.5 - - + -
2018 VAL* 3.5 17.0 - - + +
2028 THR* 2.9 38.1 + - - +
2048 ALA* 1.3 87.0 - - - +
2068 ARG* 1.3 65.9 + - - +
2078 GLU 3.4 0.2 - - - -
2088 ILE* 3.1 21.8 - - - +
2098 VAL* 3.7 2.9 + - - +
2428 LEU* 3.7 23.3 - - + +
2438 PRO* 4.4 5.4 - - - +
2448 ASP* 5.1 2.6 - - - +
2468 GLN* 5.6 1.4 - - - +
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Residues in contact with ARG 206 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628 ARG* 4.4 12.9 - - - +
1838 ARG* 6.1 2.6 - - - +
1868 THR* 4.6 11.6 - - - +
1878 ASP* 3.4 32.8 + - - -
1908 MET* 3.7 27.9 - - + +
2008 PHE* 4.2 3.2 - - + +
2018 VAL 5.9 0.2 - - - +
2028 THR 3.1 8.4 + - - +
2038 THR* 3.5 15.9 + - - +
2058 GLU* 1.3 77.3 - - - +
2078 GLU* 1.3 67.1 + - - +
2098 VAL* 3.0 29.9 + - - +
2108 ARG* 6.2 0.4 - - - +
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Residues in contact with GLU 207 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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598 GLN* 3.8 12.8 - - - +
628 ARG* 2.8 38.6 + - - +
2038 THR 3.3 13.7 + - - +
2048 ALA* 5.1 4.0 - - - -
2068 ARG* 1.3 83.9 - - - +
2088 ILE* 1.3 58.9 + - + +
2108 ARG* 3.1 39.5 + - - +
2118 ASP* 3.8 1.9 + - - +
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Residues in contact with ILE 208 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2008 PHE* 5.4 3.6 - - + -
2048 ALA 3.6 14.3 + - - +
2058 GLU* 3.1 20.1 - - - +
2078 GLU* 1.3 75.3 - - - +
2098 VAL* 1.4 58.6 + - - +
2108 ARG 3.1 1.6 - - - -
2118 ASP* 3.0 11.4 + - + +
2128 ILE* 2.9 32.8 + - + +
2408 TYR* 3.2 40.4 - - + +
2428 LEU* 4.4 14.4 - - + -
2438 PRO* 3.9 29.8 - - + -
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Residues in contact with VAL 209 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1868 THR* 3.6 21.8 - - + +
1898 LEU* 3.5 21.8 - - + +
1908 MET* 3.2 48.7 - - + +
1938 LEU* 4.1 13.2 - - + -
2008 PHE* 5.1 5.2 - - + -
2058 GLU 3.7 2.9 + - - +
2068 ARG* 3.0 24.1 + - - +
2088 ILE* 1.4 78.4 - - - +
2108 ARG* 1.3 58.6 + - + +
2128 ILE* 3.2 11.8 + - - +
2138 LYS 3.0 24.4 + - - -
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Residues in contact with ARG 210 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168 LEU* 6.1 2.6 - - - +
1868 THR* 3.7 31.0 - - + +
2068 ARG* 5.1 0.4 - - - +
2078 GLU* 3.1 24.9 + - - +
2098 VAL* 1.3 83.1 - - + +
2118 ASP* 1.3 61.0 + - - +
2138 LYS* 3.4 13.8 - - - +
2148 GLU* 2.8 69.1 + - - +
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Residues in contact with ASP 211 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2078 GLU 3.8 1.3 + - - +
2088 ILE* 3.0 18.8 + - + +
2108 ARG* 1.3 83.7 + - - +
2128 ILE* 1.3 60.1 + - - +
2148 GLU* 4.0 12.9 - - - +
2158 LYS* 2.7 63.3 + - - +
2408 TYR* 2.9 20.8 + - - +
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Residues in contact with ILE 212 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1898 LEU* 3.7 16.8 - - + -
1938 LEU* 4.2 24.5 - - + -
2008 PHE* 5.1 7.6 - - + -
2088 ILE* 2.9 20.5 + - + +
2098 VAL* 3.3 12.3 - - - +
2118 ASP* 1.3 74.5 - - - +
2138 LYS* 1.4 61.5 + - - +
2158 LYS 3.2 1.0 + - - -
2168 LEU* 2.9 42.4 + - + +
2178 CYS* 3.7 2.8 + - - -
2408 TYR* 3.9 38.6 - - + -
2428 LEU* 5.2 1.3 - - + -
2488 ILE* 4.3 15.9 - - + -
2508 ILE* 4.5 15.9 - - + -
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Residues in contact with LYS 213 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1578 ASP* 5.8 0.4 + - - -
1828 GLY* 2.8 25.6 + - - +
1858 LEU* 4.1 2.9 - - + -
1868 THR* 2.7 40.6 + - - +
1898 LEU* 3.6 17.7 - - + -
2098 VAL 3.0 8.7 + - - +
2108 ARG* 3.4 20.1 - - - +
2128 ILE* 1.4 73.7 - - - +
2148 GLU* 1.3 77.9 + - - +
2178 CYS* 3.0 32.0 + - - +
2578 CYS* 4.2 13.2 - - - -
3038 THR* 5.1 1.2 + - - -
3068 TYR* 3.7 32.6 + - + +
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Residues in contact with GLU 214 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2108 ARG* 2.8 56.9 + - - +
2118 ASP* 4.2 10.8 - - - +
2138 LYS* 1.3 94.7 + - - +
2158 LYS* 1.3 64.5 + - + +
2178 CYS 4.3 5.7 + - - +
3068 TYR* 5.6 4.7 - - - -
3078 PRO* 5.7 2.6 - - - +
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Residues in contact with LYS 215 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2118 ASP* 2.7 54.5 + - - +
2128 ILE* 4.1 0.4 - - - +
2148 GLU* 1.3 78.2 - - + +
2168 LEU* 1.3 73.8 + - + +
2178 CYS 4.9 0.7 - - - +
2188 TYR* 4.8 6.6 - - - -
2408 TYR* 4.1 15.8 + - + -
2548 ARG* 5.4 0.3 + - - -
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Residues in contact with LEU 216 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2128 ILE* 2.9 27.9 + - + +
2158 LYS* 1.3 85.3 - - + +
2178 CYS* 1.3 61.9 + - - +
2188 TYR* 3.3 5.2 - - - -
2388 LYS* 3.8 46.9 - - + +
2398 SER 5.8 0.9 - - - +
2408 TYR* 3.9 31.6 - - + +
2508 ILE* 4.6 11.2 - - + -
2548 ARG* 2.9 43.8 + - + +
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Residues in contact with CYS 217 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1898 LEU* 4.6 7.6 - - - -
2128 ILE* 3.7 2.4 + - - -
2138 LYS* 3.0 36.5 + - - +
2148 GLU 4.6 4.3 - - - +
2158 LYS 3.8 0.9 - - - +
2168 LEU* 1.3 72.8 - - - +
2188 TYR* 1.3 72.7 - - - +
2508 ILE* 6.2 0.4 - - - -
2538 GLU 4.7 0.2 - - - -
2548 ARG* 2.9 27.8 - - - +
2578 CYS* 4.2 19.1 - - - -
2588 PRO* 4.1 3.4 - - + -
3068 TYR* 4.0 21.7 - - + -
3078 PRO* 3.4 17.3 - - - +
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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