Contacts of the helix formed by residues 202 - 217 (chain 4) 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 4).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2852 CYS 4.7 0.4 - - - +
2872 ILE* 1.9 51.5 - - + +
2902 ARG* 1.5 57.6 + - - +
2014 VAL* 1.3 79.8 - - + +
2034 THR* 1.3 54.1 + - - -
2044 ALA* 4.1 0.7 - - - +
2054 GLU* 2.9 38.8 + - - +
2064 ARG* 3.1 10.8 + - - +
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Residues in contact with THR 203 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2862 ASP* 3.3 3.4 - - - +
2872 ILE* 1.7 40.2 - - + +
2882 ASP* 2.1 83.7 + - - +
624 ARG* 3.7 16.6 + - - -
2024 THR 1.3 65.7 - - - -
2044 ALA* 1.3 56.8 + - - -
2054 GLU 3.2 0.7 - - - -
2064 ARG* 3.7 11.3 - - - +
2074 GLU* 3.3 26.9 + - - +
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Residues in contact with ALA 204 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2872 ILE* 2.6 33.8 - - + +
2882 ASP* 5.0 3.1 - - - -
2024 THR* 4.1 1.3 - - - +
2034 THR* 1.3 70.0 - - - +
2054 GLU* 1.3 61.7 + - - +
2074 GLU* 4.6 4.5 - - - -
2084 ILE* 3.6 12.3 - - - +
2434 PRO* 3.5 31.8 - - + +
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Residues in contact with GLU 205 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1994 SER 4.2 4.4 - - - +
2004 PHE* 3.4 34.7 - - + -
2014 VAL* 3.5 17.4 - - + +
2024 THR* 2.9 39.0 + - - +
2044 ALA* 1.3 87.2 - - - +
2064 ARG* 1.3 67.4 + - - +
2084 ILE* 3.1 21.9 - - - +
2094 VAL* 3.7 2.8 + - - +
2424 LEU* 3.7 22.6 - - - +
2434 PRO* 4.4 5.5 - - - +
2444 ASP* 5.1 2.8 - - - +
2464 GLN* 5.6 1.4 - - - +
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Residues in contact with ARG 206 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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624 ARG* 4.4 13.1 - - - +
1834 ARG* 6.1 2.8 - - - +
1864 THR* 4.6 11.4 - - - +
1874 ASP* 3.4 33.4 + - - -
1904 MET* 3.7 27.9 - - + +
2004 PHE* 4.2 3.4 - - + +
2014 VAL 5.9 0.7 - - - +
2024 THR 3.1 8.2 + - - +
2034 THR* 3.7 15.7 - - - +
2054 GLU* 1.3 76.6 - - - +
2074 GLU* 1.3 67.9 + - - +
2094 VAL* 3.0 29.9 + - - +
2104 ARG* 5.1 0.6 - - - +
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Residues in contact with GLU 207 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2882 ASP* 4.5 6.2 - - - +
594 GLN* 3.8 12.1 - - - +
624 ARG* 2.9 38.6 + - - +
2034 THR 3.3 14.7 + - - +
2044 ALA* 5.1 4.0 - - - -
2054 GLU 3.4 0.2 - - - -
2064 ARG* 1.3 82.6 - - - +
2084 ILE* 1.3 58.1 + - + +
2104 ARG* 3.1 39.3 + - - +
2114 ASP* 3.8 1.9 + - - +
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Residues in contact with ILE 208 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2004 PHE* 5.4 2.9 - - + -
2044 ALA 3.6 13.9 + - - +
2054 GLU* 3.1 19.9 - - - +
2074 GLU* 1.3 76.2 - - - +
2094 VAL* 1.4 58.0 + - - +
2104 ARG 3.1 2.2 - - - -
2114 ASP* 3.0 11.6 + - + +
2124 ILE* 2.9 33.6 + - + +
2404 TYR* 3.2 39.9 - - + +
2424 LEU* 4.4 14.8 - - + -
2434 PRO* 3.9 29.4 - - + -
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Residues in contact with VAL 209 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1864 THR* 3.6 22.4 - - + +
1894 LEU* 3.5 22.1 - - + +
1904 MET* 3.2 49.1 - - + +
1934 LEU* 4.1 13.5 - - + -
2004 PHE* 5.1 5.6 - - + -
2054 GLU 3.7 2.7 + - - +
2064 ARG* 3.0 24.6 + - - +
2084 ILE* 1.4 79.0 - - - +
2104 ARG* 1.3 59.1 + - - +
2124 ILE* 3.2 12.2 + - - +
2134 LYS* 3.0 24.6 + - - +
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Residues in contact with ARG 210 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164 LEU* 6.1 2.2 - - - +
1864 THR* 3.7 31.9 - - + +
2064 ARG* 6.2 0.2 - - - +
2074 GLU* 3.1 23.3 + - - +
2094 VAL* 1.3 82.7 - - + +
2114 ASP* 1.3 61.4 + - - +
2134 LYS* 3.4 12.7 - - - +
2144 GLU* 2.8 68.2 + - - +
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Residues in contact with ASP 211 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2074 GLU 3.8 1.5 + - - +
2084 ILE* 3.0 19.6 + - + +
2104 ARG* 1.3 82.3 + - - +
2124 ILE* 1.3 60.7 + - - +
2144 GLU* 4.0 13.9 - - - +
2154 LYS* 2.7 63.4 + - - +
2404 TYR* 2.9 21.7 + - - +
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Residues in contact with ILE 212 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1894 LEU* 3.7 17.3 - - + -
1934 LEU* 4.2 23.8 - - + -
2004 PHE* 5.1 7.4 - - + -
2084 ILE* 2.9 21.3 + - + +
2094 VAL* 3.3 12.6 - - - +
2114 ASP* 1.3 73.4 - - - +
2134 LYS* 1.4 61.2 - - - +
2154 LYS 3.2 0.7 + - - -
2164 LEU* 2.9 42.8 + - + +
2174 CYS* 3.7 2.8 + - - -
2404 TYR* 3.9 38.6 - - + -
2424 LEU* 5.2 1.3 - - + -
2484 ILE* 4.3 15.3 - - + -
2504 ILE* 4.5 15.7 - - + -
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Residues in contact with LYS 213 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1574 ASP* 5.8 0.2 + - - -
1824 GLY* 2.8 25.6 + - - +
1854 LEU* 4.1 2.9 - - + -
1864 THR* 2.7 42.0 + - - +
1894 LEU* 3.6 17.3 - - + -
2094 VAL 3.0 8.7 + - - +
2104 ARG* 3.4 19.9 - - - +
2124 ILE* 1.4 74.0 - - - +
2144 GLU* 1.3 77.6 + - - +
2174 CYS* 3.0 32.0 + - - +
2574 CYS* 4.2 13.5 - - - -
3034 THR* 5.1 0.6 + - - -
3064 TYR* 3.7 32.8 + - + +
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Residues in contact with GLU 214 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2104 ARG* 2.8 57.0 + - - +
2114 ASP* 4.2 10.4 - - - +
2124 ILE 3.3 0.4 - - - -
2134 LYS* 1.3 95.4 + - - +
2154 LYS* 1.3 64.0 + - + +
2174 CYS 4.3 5.7 + - - +
3064 TYR* 5.6 4.1 - - - -
3074 PRO* 5.7 2.1 - - - +
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Residues in contact with LYS 215 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2114 ASP* 2.7 53.5 + - - +
2124 ILE* 4.1 0.7 - - - +
2144 GLU* 1.3 78.7 - - + +
2164 LEU* 1.3 72.2 + - + +
2174 CYS 4.9 0.7 - - - +
2184 TYR* 4.8 7.3 - - - -
2404 TYR* 4.1 15.1 + - + -
2544 ARG* 5.4 0.2 + - - -
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Residues in contact with LEU 216 (chain 4).
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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2124 ILE* 2.9 27.7 + - + +
2154 LYS* 1.3 85.3 - - + +
2174 CYS* 1.3 62.1 + - - +
2184 TYR* 3.3 5.6 - - - -
2384 LYS* 3.8 46.9 - - + +
2394 SER 5.8 0.7 - - - +
2404 TYR* 3.9 32.8 - - + +
2504 ILE* 4.6 11.4 - - + -
2544 ARG* 2.9 43.6 + - + +
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Residues in contact with CYS 217 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1894 LEU* 4.6 7.9 - - - -
2124 ILE* 3.7 2.9 + - - -
2134 LYS* 3.0 36.8 + - - +
2144 GLU 4.6 3.3 - - - +
2154 LYS 3.8 1.1 - - - +
2164 LEU* 1.3 72.4 - - - +
2184 TYR* 1.4 73.2 + - - +
2504 ILE* 6.2 0.4 - - - -
2534 GLU 4.7 0.4 - - - -
2544 ARG* 2.9 27.6 - - - +
2574 CYS* 4.2 19.3 - - - -
2584 PRO* 4.1 3.1 - - + -
3064 TYR* 4.0 21.2 - - + -
3074 PRO* 3.4 18.2 - - - +
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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