Contacts of the helix formed by residues 190 - 202 (chain 5) in PDB entry 5LN3
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 GLY 190 (chain 5).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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615 THR* 3.3 19.9 + - - -
1895 SER* 1.3 80.4 + - - +
1915 SER* 1.4 51.3 + - - -
1925 VAL 3.2 3.1 - - - -
1935 TYR* 2.8 37.9 + - - +
1945 ALA* 3.1 11.6 + - - +
2225 ALA* 4.7 11.9 - - - +
2255 ARG* 5.4 5.2 - - - -
2265 ASP* 5.5 2.5 - - - -
2295 SER* 5.4 0.9 - - - -
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Residues in contact with SER 191 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615 THR* 3.5 7.6 - - - +
1865 SER* 3.3 32.7 + - - -
1875 VAL* 3.5 7.5 - - - -
1885 GLY 3.4 32.3 + - - -
1895 SER 3.2 1.1 + - - +
1905 GLY* 1.4 74.0 - - - +
1925 VAL* 1.4 64.7 + - - +
1945 ALA 3.4 0.2 + - - -
1955 TYR* 2.9 34.6 + - - +
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Residues in contact with VAL 192 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254 ILE* 5.2 14.8 - - + -
264 VAL* 4.6 20.2 - - + -
1895 SER 3.9 15.3 - - - +
1915 SER* 1.4 83.7 + - - +
1935 TYR* 1.3 78.4 + - + +
1955 TYR* 3.3 21.9 + - - +
1965 GLY* 3.4 5.5 + - - -
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Residues in contact with TYR 193 (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 SER 4.6 4.0 - - - -
1905 GLY* 2.8 20.7 + - - +
1925 VAL* 1.3 93.9 - - + +
1945 ALA* 1.4 66.0 - - - +
1965 GLY* 3.3 10.2 + - - -
1975 VAL* 3.7 7.4 + - - +
2185 ALA 5.3 1.1 - - - +
2215 GLN* 3.7 28.6 - - + +
2225 ALA* 5.1 4.9 - - - -
2255 ARG* 3.1 64.7 + - + -
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Residues in contact with ALA 194 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615 THR* 4.4 7.0 - - + -
635 LEU* 3.8 19.5 - - + -
1865 SER* 3.4 21.8 - - - +
1905 GLY 3.1 8.0 + - - +
1915 SER* 3.6 4.0 - - - +
1935 TYR* 1.4 78.9 - - - +
1955 TYR* 1.3 58.6 + - - +
1975 VAL* 3.3 6.3 + - - +
1985 MET* 3.0 30.7 + - - +
2185 ALA* 4.0 21.2 - - + +
2195 ILE* 5.4 1.6 - - + -
2225 ALA* 5.8 1.3 - - + -
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Residues in contact with TYR 195 (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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224 ALA* 4.0 13.4 - - + +
264 VAL* 5.1 17.7 - - + -
284 MET* 3.7 43.5 - - + +
1845 THR* 3.0 38.4 + - - -
1855 PHE* 3.5 11.9 - + - -
1865 SER* 3.7 29.4 - - - -
1915 SER* 2.9 21.1 + - - +
1925 VAL* 3.3 14.6 - - - +
1935 TYR 3.1 0.4 - - - -
1945 ALA* 1.3 75.3 - - - +
1965 GLY* 1.4 56.2 - - - +
1985 MET* 3.4 17.9 + - + +
1995 ASP* 2.8 37.7 + - + +
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Residues in contact with GLY 196 (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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284 MET* 5.8 1.6 - - - -
1925 VAL 3.4 6.5 + - - -
1935 TYR 3.3 8.6 + - - -
1945 ALA 3.3 0.8 - - - -
1955 TYR* 1.4 79.3 - - - +
1975 VAL* 1.4 59.2 + - - +
1995 ASP* 3.4 5.9 + - - +
2005 ARG* 3.3 29.2 + - - +
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Residues in contact with VAL 197 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1935 TYR 3.7 5.8 - - - +
1945 ALA 3.3 7.8 + - - +
1965 GLY* 1.4 72.5 - - - +
1985 MET* 1.4 60.3 + - - +
2005 ARG* 3.7 6.8 + - - +
2015 GLY 3.6 8.7 + - - -
2145 LEU* 3.4 27.1 - - + +
2175 ARG* 4.8 13.0 - - + +
2185 ALA* 3.9 32.1 - - + +
2215 GLN* 3.2 32.1 - - + +
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Residues in contact with MET 198 (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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635 LEU* 3.9 22.2 - - + -
645 ALA 3.9 9.9 - - - +
655 PHE* 4.2 25.4 - - + -
1845 THR* 4.7 6.5 - - + -
1855 PHE 3.3 32.1 - - - +
1865 SER* 3.6 24.0 - - - -
1945 ALA 3.0 18.3 + - - +
1955 TYR* 3.5 21.1 - - + +
1975 VAL* 1.4 73.4 - - - +
1995 ASP* 1.4 54.3 + - - +
2015 GLY 3.2 2.6 + - - -
2025 TYR* 2.7 37.6 + - - +
2145 LEU* 4.2 13.9 - - + +
2155 ALA* 6.4 0.9 - - - -
2185 ALA* 5.0 3.6 - - + -
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Residues in contact with ASP 199 (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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284 MET* 3.7 33.0 - - + +
1955 TYR* 2.8 20.7 + - + +
1965 GLY* 3.6 7.2 - - - +
1975 VAL 3.4 0.2 - - - -
1985 MET* 1.4 76.4 - - - +
2005 ARG* 1.3 69.3 + - + +
2025 TYR* 3.4 38.6 + - - +
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Residues in contact with ARG 200 (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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1965 GLY 3.3 15.5 + - - +
1975 VAL* 3.7 6.9 + - - +
1985 MET 3.2 1.0 - - - -
1995 ASP* 1.3 83.8 + - + +
2015 GLY* 1.4 57.4 + - - +
2025 TYR 3.8 3.1 + - - +
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Residues in contact with GLY 201 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1975 VAL 3.6 4.2 + - - -
1985 MET 3.2 5.7 + - - -
2005 ARG* 1.4 77.4 - - - +
2025 TYR* 1.4 63.0 + - - +
2035 SER* 3.2 10.4 + - - -
2065 LEU* 4.6 13.1 - - - +
2145 LEU* 3.9 27.7 - - - +
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Residues in contact with TYR 202 (chain 5).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1845 THR* 5.0 20.6 - - + -
1985 MET 2.7 19.9 + - - +
1995 ASP* 3.5 32.5 - - - +
2005 ARG 3.4 4.3 - - - +
2015 GLY* 1.4 71.0 - - - +
2035 SER* 1.4 72.6 + - - +
2045 TYR 5.7 0.4 - - - -
2065 LEU* 6.0 0.7 - - - -
2145 LEU* 5.2 2.2 - - - -
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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