Contacts of the helix formed by residues 202 - 217 (chain 7) 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 7).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2017 VAL* 1.3 84.8 - - + +
2037 THR* 1.4 59.3 + - - +
2047 ALA* 3.8 11.9 + - - +
2057 GLU* 2.9 38.7 + - + +
2067 ARG* 3.1 11.1 + - - +
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Residues in contact with THR 203 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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627 ARG* 3.7 31.2 + - + +
2027 THR* 1.4 74.1 - - - +
2047 ALA* 1.3 62.5 + - + +
2057 GLU 3.2 0.4 - - - -
2067 ARG* 3.7 11.2 - - - +
2077 GLU* 3.3 28.2 + - - +
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Residues in contact with ALA 204 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2027 THR* 3.2 9.7 + - - +
2037 THR* 1.3 80.0 - - + +
2057 GLU* 1.3 64.2 + - - +
2077 GLU* 4.6 5.4 - - - -
2087 ILE* 3.6 11.9 - - - +
2437 PRO* 3.5 32.1 - - + +
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Residues in contact with GLU 205 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1997 SER 4.2 4.1 - - - +
2007 PHE* 3.4 34.2 - - + -
2017 VAL* 3.5 17.4 - - + +
2027 THR* 2.9 37.2 + - - +
2047 ALA* 1.3 86.9 - - - +
2067 ARG* 1.3 66.7 + - - +
2077 GLU 3.4 0.2 - - - -
2087 ILE* 3.1 21.4 - - - +
2097 VAL 3.7 2.8 + - - -
2427 LEU* 3.7 23.3 - - + +
2437 PRO* 4.4 5.5 - - - +
2447 ASP* 5.1 3.1 - - - +
2467 GLN* 5.6 1.2 - - - +
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Residues in contact with ARG 206 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
627 ARG* 4.4 13.3 - - - +
1837 ARG* 6.1 2.8 - - - +
1867 THR* 4.6 12.4 - - - +
1877 ASP* 3.4 32.2 + - - -
1907 MET* 3.7 26.8 - - + +
2007 PHE* 4.2 3.6 - - - +
2017 VAL 5.9 0.4 - - - +
2027 THR 3.1 8.4 + - - +
2037 THR* 3.7 14.8 - - - +
2057 GLU* 1.3 78.0 - - - +
2077 GLU* 1.3 66.7 + - - +
2097 VAL* 3.0 30.0 + - - +
2107 ARG* 5.1 0.4 - - - +
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Residues in contact with GLU 207 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597 GLN* 3.8 12.8 - - - +
627 ARG* 2.9 38.2 + - - +
2037 THR 3.3 13.9 + - - +
2047 ALA* 5.1 3.8 - - - -
2067 ARG* 1.3 82.2 - - - +
2087 ILE* 1.3 57.8 + - - +
2107 ARG* 3.1 41.0 + - - +
2117 ASP* 3.8 1.7 + - - +
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Residues in contact with ILE 208 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2007 PHE* 5.4 3.1 - - + -
2047 ALA 3.6 13.9 - - - +
2057 GLU* 3.1 20.8 - - - +
2077 GLU* 1.3 75.9 - - - +
2097 VAL* 1.4 58.6 + - - +
2107 ARG 3.1 2.0 - - - -
2117 ASP* 3.0 11.0 + - + +
2127 ILE* 2.9 32.9 + - + +
2407 TYR* 3.2 40.4 - - + +
2427 LEU* 4.4 13.9 - - + -
2437 PRO* 3.9 29.2 - - + -
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Residues in contact with VAL 209 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1867 THR* 3.6 22.2 - - + +
1897 LEU* 3.5 21.2 - - + +
1907 MET* 3.2 48.2 - - + +
1937 LEU* 4.1 13.5 - - + -
2007 PHE* 5.1 5.4 - - + -
2057 GLU 3.7 3.3 + - - +
2067 ARG* 3.0 25.0 + - - +
2087 ILE* 1.4 78.4 - - - +
2107 ARG* 1.3 59.1 + - + +
2127 ILE* 3.2 12.2 + - - +
2137 LYS* 2.9 25.1 + - - +
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Residues in contact with ARG 210 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167 LEU* 6.1 2.8 - - - +
1867 THR* 3.7 31.9 - - + +
2067 ARG* 6.2 0.4 - - - +
2077 GLU* 3.1 23.3 + - - +
2097 VAL* 1.3 83.1 - - + +
2117 ASP* 1.3 61.2 + - - +
2137 LYS* 3.4 12.9 - - - +
2147 GLU* 2.8 70.0 + - - +
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Residues in contact with ASP 211 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2077 GLU 3.8 1.7 + - - +
2087 ILE* 3.0 18.7 + - + +
2107 ARG* 1.3 81.9 + - - +
2127 ILE* 1.3 60.9 + - - +
2147 GLU* 4.0 13.5 - - - +
2157 LYS* 2.7 62.2 + - - +
2407 TYR* 2.9 20.9 + - - +
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Residues in contact with ILE 212 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1897 LEU* 3.7 17.5 - - + -
1937 LEU* 4.2 23.1 - - + -
2007 PHE* 5.1 8.1 - - + -
2087 ILE* 2.9 19.4 + - + +
2097 VAL* 3.2 12.8 + - - +
2117 ASP* 1.3 74.3 - - - +
2137 LYS* 1.4 62.2 + - - +
2157 LYS 3.2 1.0 + - - -
2167 LEU* 2.9 42.1 + - + +
2177 CYS* 3.7 2.8 + - - -
2407 TYR* 3.9 39.7 - - + -
2427 LEU* 5.2 1.3 - - + -
2487 ILE* 4.3 15.9 - - + -
2507 ILE* 4.5 15.7 - - + -
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Residues in contact with LYS 213 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1577 ASP* 5.8 0.4 + - - -
1827 GLY* 2.8 25.6 + - - +
1857 LEU 4.1 2.9 - - - -
1867 THR* 2.7 40.4 + - - +
1897 LEU* 3.5 17.7 - - + +
2097 VAL 2.9 9.3 + - - +
2107 ARG* 3.4 21.2 - - - +
2127 ILE* 1.4 73.2 - - - +
2147 GLU* 1.3 75.7 + - - +
2177 CYS* 3.0 31.4 + - - +
2577 CYS* 4.2 13.5 - - - -
3037 THR* 5.1 0.6 + - - -
3067 TYR* 3.7 31.7 + - + +
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Residues in contact with GLU 214 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2107 ARG* 2.8 55.5 + - - +
2117 ASP* 4.2 11.0 - - - +
2137 LYS* 1.3 94.1 + - - +
2157 LYS* 1.3 65.2 + - + +
2177 CYS 4.3 5.9 + - - +
3067 TYR* 5.6 4.4 - - - -
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Residues in contact with LYS 215 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2117 ASP* 2.7 52.2 + - - +
2127 ILE* 4.1 0.4 - - - +
2147 GLU* 1.3 77.9 - - + +
2167 LEU* 1.3 72.9 + - + +
2177 CYS 4.9 0.7 - - - +
2187 TYR* 4.8 6.8 - - - -
2407 TYR* 4.1 15.3 + - + -
2547 ARG* 5.4 0.2 + - - -
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Residues in contact with LEU 216 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2127 ILE* 2.9 26.4 + - + +
2157 LYS* 1.3 86.4 - - + +
2177 CYS* 1.3 61.8 + - - +
2187 TYR* 3.3 5.6 - - - -
2387 LYS* 3.8 46.7 - - + +
2397 SER 5.8 1.1 - - - +
2407 TYR* 3.9 31.4 - - + +
2507 ILE* 4.6 11.4 - - + -
2547 ARG* 2.9 44.1 + - + +
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Residues in contact with CYS 217 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1897 LEU* 4.6 7.2 - - - -
2127 ILE* 3.7 2.9 + - - -
2137 LYS* 3.0 35.5 + - - +
2147 GLU 4.6 4.2 - - - +
2157 LYS 3.8 0.9 - - - +
2167 LEU* 1.3 72.2 - - - +
2187 TYR* 1.3 72.8 + - - +
2507 ILE* 6.2 0.2 - - - -
2537 GLU 4.7 0.4 - - - -
2547 ARG* 2.9 27.4 - - - +
2577 CYS* 4.2 19.5 - - - -
2587 PRO* 4.1 2.7 - - + -
3067 TYR* 4.0 22.2 - - + -
3077 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