Contacts of the helix formed by residues 146 - 164 (chain R) in PDB entry 3SN6
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 146 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A GLN* 6.0 5.6 - - + -
67R VAL* 4.2 7.4 - - - +
142R GLN 5.4 0.4 - - - +
143R SER 4.2 9.9 - - - +
144R LEU 3.4 11.8 + - - +
145R LEU* 1.3 79.9 - - - +
147R LYS* 1.3 59.5 + - - +
148R ASN* 3.8 6.0 + - - +
149R LYS* 3.2 25.8 + - - +
150R ALA* 2.9 28.1 + - - +
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Residues in contact with LYS 147 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A GLN* 6.0 3.6 - - - +
34A LYS* 4.7 17.9 - - - +
67R VAL* 4.5 24.4 - - + +
70R TYR* 5.0 16.2 + - + -
146R THR* 1.3 74.4 - - - +
148R ASN* 1.3 68.3 + - - +
150R ALA* 3.0 6.9 + - - +
151R ARG* 2.9 69.1 + - + +
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Residues in contact with ASN 148 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146R THR* 3.6 6.1 + - - +
147R LYS* 1.3 79.6 - - - +
149R LYS* 1.3 56.8 + - - +
151R ARG* 4.1 17.8 + - - +
152R VAL* 2.9 38.9 + - + +
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Residues in contact with LYS 149 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144R LEU 5.1 2.2 - - - +
145R LEU* 4.9 8.5 - - + -
146R THR* 3.2 28.9 + - - +
147R LYS 3.1 0.4 - - - -
148R ASN* 1.3 79.8 - - - +
150R ALA* 1.3 57.1 + - - +
152R VAL* 3.3 9.1 + - - +
153R ILE* 2.9 37.3 + - + +
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Residues in contact with ALA 150 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67R VAL* 4.0 23.8 - - + +
70R TYR* 5.5 5.8 - - + -
71R PHE* 3.4 27.7 - - + -
146R THR 2.9 18.3 + - - +
147R LYS* 3.0 4.9 + - - +
149R LYS* 1.3 72.4 - - - +
151R ARG* 1.3 63.4 + - + +
153R ILE* 2.8 21.5 + - - +
154R ILE* 2.9 15.5 + - - +
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Residues in contact with ARG 151 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70R TYR* 4.3 30.9 + - + +
147R LYS* 2.9 63.2 + - + +
148R ASN* 4.1 16.7 + - - +
150R ALA* 1.3 72.9 - - + +
152R VAL* 1.3 57.9 + - + +
154R ILE* 3.0 13.8 + - + +
155R LEU* 2.9 30.9 + - - +
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Residues in contact with VAL 152 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148R ASN* 2.9 29.2 + - + +
149R LYS* 3.3 9.9 - - - +
150R ALA 3.1 0.2 - - - -
151R ARG* 1.3 77.6 - - + +
153R ILE* 1.3 63.5 + - + +
155R LEU* 3.9 8.0 - - + +
156R MET* 2.9 31.3 + - + +
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Residues in contact with ILE 153 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71R PHE* 3.6 9.0 - - + -
126R VAL* 3.6 37.2 - - + -
145R LEU* 6.5 1.3 - - + -
149R LYS* 2.9 26.9 + - + +
150R ALA* 2.8 11.7 + - - +
152R VAL* 1.3 81.8 - - + +
154R ILE* 1.3 60.2 + - - +
156R MET* 3.3 8.5 + - + +
157R VAL* 2.9 34.4 + - + +
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Residues in contact with ILE 154 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70R TYR* 4.0 10.3 - - + +
71R PHE* 3.2 35.2 - - + +
74R SER* 3.3 38.6 - - - +
123R THR* 5.9 0.9 - - + -
126R VAL* 5.8 0.7 - - + -
150R ALA 2.9 12.5 + - - +
151R ARG* 3.0 15.0 + - + +
153R ILE* 1.3 75.0 - - - +
155R LEU* 1.3 63.9 + - - +
157R VAL* 2.9 19.8 + - + +
158R TRP* 2.9 25.0 + - + +
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Residues in contact with LEU 155 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151R ARG 2.9 17.2 + - - +
152R VAL* 4.0 7.4 - - + +
154R ILE* 1.3 75.7 - - - +
156R MET* 1.3 56.7 + - - +
158R TRP* 3.8 7.9 - - + +
159R ILE* 2.9 57.8 + - + +
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Residues in contact with MET 156 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152R VAL* 2.9 22.6 + - + +
153R ILE* 3.4 11.2 - - + +
155R LEU* 1.3 77.6 - - - +
157R VAL* 1.3 64.2 + - + +
159R ILE* 3.2 10.4 + - - +
160R VAL* 2.9 51.5 + - + +
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Residues in contact with VAL 157 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74R SER* 5.3 0.9 - - - +
119R ALA* 4.1 5.8 - - - +
122R GLU* 3.7 35.2 - - + +
123R THR* 3.8 18.8 - - - +
126R VAL* 3.5 31.0 - - + -
153R ILE* 2.9 23.0 + - + +
154R ILE* 2.9 11.0 + - + +
156R MET* 1.3 77.8 - - + +
158R TRP* 1.3 60.6 + - + +
160R VAL* 3.5 2.0 + - - +
161R SER* 2.6 40.3 + - - +
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Residues in contact with TRP 158 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74R SER* 3.1 23.0 + - - +
77R CYS* 4.4 8.4 - - + +
78R ALA* 3.4 46.2 - - + -
81R VAL* 5.6 4.7 - - + -
115R LEU* 4.0 36.5 - - + +
116R CYS* 5.3 5.6 - - - -
119R ALA* 3.4 25.8 - - + -
123R THR* 5.1 0.8 + - - -
154R ILE* 2.9 38.6 + - + +
155R LEU* 4.1 9.4 - - + +
157R VAL* 1.3 80.6 - - + +
159R ILE* 1.3 57.7 + - + +
161R SER* 3.7 3.3 - - - -
162R GLY* 2.9 24.8 + - - -
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Residues in contact with ILE 159 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155R LEU* 2.9 52.3 + - + +
156R MET* 3.2 10.5 + - - +
158R TRP* 1.3 75.2 - - + +
160R VAL* 1.3 65.7 + - + +
162R GLY* 3.3 1.0 + - - -
163R LEU* 2.9 59.3 + - + +
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Residues in contact with VAL 160 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118R THR* 5.9 0.4 - - + -
122R GLU* 4.5 14.8 - - - +
156R MET* 2.9 48.4 + - + +
157R VAL* 4.1 2.2 - - - +
159R ILE* 1.3 80.0 - - + +
161R SER* 1.3 61.4 + - - +
163R LEU* 4.0 7.6 - - + +
164R THR* 3.1 25.8 + - - +
206R VAL* 4.7 17.7 - - + -
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Residues in contact with SER 161 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115R LEU* 3.4 20.4 - - - +
118R THR* 3.2 33.3 + - - +
119R ALA* 3.4 18.4 + - - -
122R GLU* 4.2 1.9 - - - +
157R VAL* 2.6 27.2 + - - +
158R TRP* 3.7 5.6 - - - -
160R VAL* 1.3 78.1 - - - +
162R GLY* 1.3 51.0 + - - +
164R THR* 3.1 13.9 - - - +
165R SER* 2.7 24.8 + - - -
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Residues in contact with GLY 162 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115R LEU* 3.4 10.7 - - - +
158R TRP 2.9 15.8 + - - -
159R ILE* 3.8 1.1 - - - -
161R SER* 1.3 74.7 - - - +
163R LEU* 1.3 61.9 + - - +
164R THR 3.1 2.2 - - - -
165R SER* 3.1 7.7 + - - -
166R PHE* 2.8 34.1 + - - +
167R LEU* 3.4 7.5 + - - +
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Residues in contact with LEU 163 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159R ILE* 2.9 45.1 + - + +
160R VAL* 4.1 6.7 - - + +
162R GLY* 1.3 77.8 - - - +
164R THR* 1.3 57.8 + - - +
165R SER 3.4 0.2 - - - -
167R LEU* 3.5 32.8 - - + +
168R PRO* 3.0 19.9 - - - +
173R TRP* 5.4 1.6 - - - -
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Residues in contact with THR 164 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114R VAL* 4.3 3.0 - - + +
118R THR* 3.9 22.2 - - + +
160R VAL* 3.1 20.6 + - - +
161R SER* 3.1 17.9 - - - +
163R LEU* 1.3 75.8 - - - +
165R SER* 1.3 56.1 + - - +
168R PRO* 3.4 13.8 - - - +
199R TYR* 3.4 19.4 + - - -
203R SER* 4.7 13.0 + - - -
206R VAL* 4.5 18.6 - - + +
207R SER* 4.5 6.4 + - - +
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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
------------------------------------------------------------
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