Contacts of the helix formed by residues 202 - 217 (chain 5) 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 5).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2853 CYS 4.2 0.9 - - - +
2873 ILE* 1.3 117.4 - - + +
2903 ARG* 1.7 63.1 + - - +
2015 VAL* 1.3 77.8 - - + +
2035 THR* 1.3 52.8 + - - -
2055 GLU* 2.9 33.1 + - - +
2065 ARG* 3.1 10.8 + - - +
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Residues in contact with THR 203 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2863 ASP* 2.8 10.5 - - - +
2873 ILE* 1.6 34.4 - - - +
2883 ASP* 1.4 98.4 + - + +
625 ARG* 3.7 18.9 + - - +
2025 THR 1.3 66.7 - - - -
2045 ALA* 1.3 56.6 + - - -
2055 GLU 3.2 0.2 - - - -
2065 ARG* 3.7 11.7 - - - +
2075 GLU* 3.3 24.8 + - - +
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Residues in contact with ALA 204 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2873 ILE* 2.8 31.3 - - + +
2883 ASP* 4.0 9.0 - - - +
2913 LYS* 6.3 2.2 - - + -
2035 THR* 1.3 75.3 - - - +
2055 GLU* 1.3 64.3 + - - +
2075 GLU* 4.6 4.3 - - - -
2085 ILE* 3.6 12.2 + - - +
2435 PRO* 3.5 32.3 - - + +
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Residues in contact with GLU 205 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2873 ILE* 4.6 0.3 - - - +
2903 ARG* 5.8 0.3 + - - -
1995 SER 4.3 4.1 - - - +
2005 PHE* 3.4 34.6 - - + -
2015 VAL* 3.5 17.4 - - + +
2025 THR* 2.9 37.8 + - - +
2045 ALA* 1.3 86.0 - - - +
2065 ARG* 1.3 67.2 + - - +
2085 ILE* 3.1 21.1 - - - +
2095 VAL* 3.7 3.3 + - - +
2425 LEU* 3.7 23.1 - - - +
2435 PRO* 4.4 5.9 - - - +
2445 ASP* 5.1 2.9 - - - +
2465 GLN* 5.6 1.6 - - - +
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Residues in contact with ARG 206 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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625 ARG* 4.4 14.4 - - - +
1835 ARG* 6.1 2.8 - - - +
1865 THR* 4.6 11.4 - - - +
1875 ASP* 3.4 32.0 + - - -
1905 MET* 3.7 26.3 - - + +
2005 PHE* 4.2 3.8 - - + +
2015 VAL 5.9 0.7 - - - +
2025 THR 3.1 9.0 + - - +
2035 THR* 3.7 15.0 - - - +
2055 GLU* 1.3 77.1 - - - +
2075 GLU* 1.3 67.6 + - - +
2095 VAL* 3.0 29.7 + - - +
2105 ARG* 5.1 0.2 - - - +
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Residues in contact with GLU 207 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2883 ASP* 4.1 8.3 - - - +
595 GLN* 3.8 12.5 - - - +
625 ARG* 2.9 38.7 + - - +
2035 THR 3.3 13.6 + - - +
2045 ALA* 5.1 3.3 - - - -
2055 GLU 3.4 0.4 - - - -
2065 ARG* 1.3 82.5 - - - +
2085 ILE* 1.3 57.1 + - + +
2105 ARG* 3.1 39.2 + - - +
2115 ASP* 3.8 1.9 + - - +
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Residues in contact with ILE 208 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2005 PHE* 5.4 3.1 - - + -
2045 ALA 3.6 14.6 - - - +
2055 GLU* 3.1 19.3 - - - +
2075 GLU* 1.3 76.0 - - + +
2095 VAL* 1.4 58.4 + - - +
2105 ARG 3.1 1.6 - - - -
2115 ASP* 3.0 11.1 + - + +
2125 ILE* 2.9 33.8 + - + +
2405 TYR* 3.2 39.9 - - + +
2415 GLU 5.0 0.2 - - - +
2425 LEU* 4.4 14.1 - - + -
2435 PRO* 3.9 29.4 - - + -
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Residues in contact with VAL 209 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1865 THR* 3.6 21.8 - - + +
1895 LEU* 3.5 22.1 - - + +
1905 MET* 3.2 48.9 - - + +
1935 LEU* 4.1 13.2 - - + -
2005 PHE* 5.1 5.4 - - + -
2055 GLU 3.7 3.3 + - - +
2065 ARG* 3.0 24.6 + - - +
2085 ILE* 1.4 78.0 - - - +
2105 ARG* 1.3 59.3 + - - +
2125 ILE* 3.2 13.0 + - - +
2135 LYS 2.9 24.1 + - - -
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Residues in contact with ARG 210 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165 LEU* 6.1 2.6 - - - +
1865 THR* 3.7 31.6 - - + +
2065 ARG* 6.2 0.2 - - - +
2075 GLU* 3.1 24.8 + - - +
2095 VAL* 1.3 83.0 - - + +
2115 ASP* 1.3 61.4 + - - +
2135 LYS* 3.4 12.5 - - - +
2145 GLU* 2.8 68.2 + - - +
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Residues in contact with ASP 211 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2075 GLU 3.8 1.3 + - - +
2085 ILE* 3.0 18.7 + - + +
2105 ARG* 1.3 82.7 + - - +
2125 ILE* 1.3 60.9 + - - +
2145 GLU* 4.0 12.3 - - - +
2155 LYS* 2.7 63.5 + - - +
2405 TYR* 2.9 22.0 + - - +
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Residues in contact with ILE 212 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1895 LEU* 3.7 17.3 - - + -
1935 LEU* 4.2 23.3 - - + -
2005 PHE* 5.1 8.1 - - + -
2085 ILE* 2.9 20.3 + - + +
2095 VAL* 3.3 12.3 - - - +
2115 ASP* 1.3 74.0 - - - +
2135 LYS* 1.4 61.9 + - - +
2155 LYS 3.2 1.0 + - - -
2165 LEU* 2.9 41.9 + - + +
2175 CYS* 3.7 2.4 + - - -
2405 TYR* 3.9 40.4 - - + -
2425 LEU* 5.2 1.8 - - + -
2485 ILE* 4.3 15.7 - - + -
2505 ILE* 4.5 16.2 - - + -
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Residues in contact with LYS 213 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1575 ASP* 5.8 0.4 + - - -
1825 GLY* 2.8 25.2 + - - +
1855 LEU 4.1 2.7 - - - -
1865 THR* 2.7 40.6 + - - +
1895 LEU* 3.5 17.0 - - + +
2095 VAL 2.9 9.3 + - - +
2105 ARG* 3.4 21.4 - - - +
2125 ILE* 1.4 73.6 - - - +
2145 GLU* 1.3 78.1 + - - +
2175 CYS* 3.0 31.2 + - - +
2575 CYS* 4.2 12.6 - - - -
3035 THR* 5.1 1.2 + - - -
3065 TYR* 3.7 32.1 + - + +
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Residues in contact with GLU 214 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2105 ARG* 2.8 56.5 + - - +
2115 ASP* 4.2 10.8 - - - +
2125 ILE 3.3 0.4 - - - -
2135 LYS* 1.3 94.2 + - - +
2155 LYS* 1.3 63.6 + - + +
2175 CYS 4.3 5.7 + - - +
3065 TYR* 5.6 4.6 - - - -
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Residues in contact with LYS 215 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2115 ASP* 2.7 54.6 + - - +
2125 ILE* 3.2 0.9 + - - +
2145 GLU* 1.3 78.4 - - + +
2165 LEU* 1.3 72.8 + - + +
2175 CYS 4.9 0.7 - - - +
2185 TYR* 4.8 6.8 - - - -
2405 TYR* 4.1 15.2 + - + -
2545 ARG* 5.4 0.2 + - - -
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Residues in contact with LEU 216 (chain 5).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2125 ILE* 2.9 26.2 + - + +
2155 LYS* 1.3 86.0 - - + +
2175 CYS* 1.3 59.8 + - - +
2185 TYR* 3.3 5.2 - - - -
2385 LYS* 3.8 46.4 - - + +
2395 SER 5.8 1.1 - - - +
2405 TYR* 3.9 31.6 - - + +
2505 ILE* 4.6 12.3 - - + -
2545 ARG* 2.9 43.9 + - + +
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Residues in contact with CYS 217 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1895 LEU* 4.6 7.9 - - - -
2125 ILE* 4.6 2.2 - - - -
2135 LYS* 3.0 36.2 + - - +
2145 GLU 4.6 4.0 - - - +
2155 LYS 3.8 0.7 - - - +
2165 LEU* 1.3 72.0 - - - +
2185 TYR* 1.3 73.0 + - - +
2505 ILE* 6.2 0.9 - - - -
2535 GLU 4.7 0.2 - - - -
2545 ARG* 2.9 26.9 - - - +
2575 CYS* 4.2 19.5 - - - -
2585 PRO* 4.1 2.7 - - + -
3065 TYR* 4.0 22.5 - - + -
3075 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