Contacts of the helix formed by residues 160 - 169 (chain R) in PDB entry 1MFR
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 160 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153J ARG* 3.2 43.1 + - - +
158R GLU 3.2 8.2 + - - -
159R ASN* 1.3 72.5 + - - +
161R MET* 1.3 64.8 + - - +
163R GLU* 3.3 5.8 + - - -
164R TYR* 3.1 18.9 + - - +
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Residues in contact with MET 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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153J ARG 3.7 3.8 + - - -
154J LEU* 4.0 27.4 - - + -
159J ASN* 3.9 23.6 - - - +
161J MET* 3.6 29.4 - - + +
162J GLY* 4.5 4.5 - - - -
165J LEU* 3.9 25.6 - - + -
161O MET* 3.6 33.9 - - + +
159R ASN* 3.4 10.7 + - - +
160R GLY* 1.3 72.4 - - - +
162R GLY* 1.3 65.5 + - - +
164R TYR* 3.4 1.7 + - - +
165R LEU* 3.1 25.0 + - + +
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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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161O MET* 4.5 3.4 - - - -
154R LEU* 3.3 36.6 - - - +
156R LEU* 3.9 6.3 - - - -
159R ASN* 3.3 24.2 + - - +
160R GLY 3.2 0.6 - - - -
161R MET* 1.3 78.9 - - - +
163R GLU* 1.3 59.3 + - - +
165R LEU* 3.5 2.1 + - - +
166R PHE* 3.1 17.5 + - - +
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Residues in contact with GLU 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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153J ARG* 3.4 21.8 + - - +
44R LEU* 3.9 19.3 - - + +
47R VAL* 5.8 0.2 - - - +
91R ASN* 3.5 12.6 - - - +
92R THR* 2.8 46.7 + - - +
156R LEU* 3.5 28.2 - - + +
159R ASN 3.3 10.1 + - - +
160R GLY* 3.3 9.7 + - - +
162R GLY* 1.3 73.9 - - - +
164R TYR* 1.3 64.5 + - - +
166R PHE* 3.3 6.5 + - - +
167R ASP* 3.2 20.1 + - - +
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Residues in contact with TYR 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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150J ASN* 3.1 29.6 - - + -
153J ARG* 4.1 9.1 - - - +
154J LEU* 3.9 40.4 - - + -
165J LEU* 4.4 8.1 - - + -
166J PHE* 3.6 8.4 - - - -
169J HIS* 3.0 38.5 - + + +
170J SER* 2.9 31.4 + - - -
44R LEU* 4.6 2.7 - - - -
160R GLY 3.1 13.3 + - - +
161R MET 3.6 7.2 - - - +
162R GLY 3.3 0.2 - - - -
163R GLU* 1.3 77.9 - - - +
165R LEU* 1.3 73.3 + - + +
167R ASP* 3.3 3.6 + - - +
168R LYS* 3.1 53.1 + - + +
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Residues in contact with LEU 165 (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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165J LEU* 4.1 25.6 - - + -
169J HIS* 4.5 13.0 - - + +
161O MET* 4.0 27.6 - - + -
164O TYR* 4.1 11.9 - - + -
165O LEU* 4.0 26.2 - - + -
154R LEU* 4.9 2.9 - - + -
161R MET* 3.1 24.4 + - + +
162R GLY* 3.8 5.6 - - - +
163R GLU 3.3 0.2 - - - -
164R TYR* 1.3 82.3 - - + +
166R PHE* 1.3 65.0 + - - +
168R LYS* 3.1 3.7 + - + +
169R HIS* 3.0 45.7 + - + +
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Residues in contact with PHE 166 (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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164O TYR* 3.5 8.1 - - - -
47R VAL* 4.3 7.0 - - + -
92R THR* 3.8 23.6 - - + -
96R MET* 4.3 5.6 - - + -
147R PHE* 3.6 44.6 - + + -
150R ASN* 4.6 3.8 - - + -
151R LEU* 3.5 34.8 - - + -
154R LEU* 3.8 15.0 - - + +
162R GLY 3.1 14.2 + - - +
163R GLU* 3.5 9.2 - - - +
164R TYR 3.3 0.2 - - - -
165R LEU* 1.3 76.6 - - - +
167R ASP* 1.3 65.1 + - - +
170R SER* 3.0 47.9 + - - -
171R VAL* 3.8 20.0 + - + +
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Residues in contact with ASP 167 (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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44R LEU* 3.3 27.8 - - + +
45R HIS* 4.4 2.3 + - - +
46R ASN* 2.9 67.2 + - - +
47R VAL* 3.1 23.0 + - + -
163R GLU 3.2 9.1 + - - +
164R TYR 3.4 9.9 - - - +
165R LEU 3.2 0.4 - - - -
166R PHE* 1.3 82.8 - - - +
168R LYS* 1.3 82.0 + - - +
169R HIS 3.6 0.2 + - - -
171R VAL* 4.4 7.1 + - - +
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Residues in contact with LYS 168 (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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150J ASN* 4.9 2.4 + - - -
169J HIS* 3.8 50.7 + - + +
170J SER* 4.5 3.6 - - - +
44R LEU* 5.0 1.2 - - - +
46R ASN* 4.4 9.0 - - - +
164R TYR* 3.1 59.6 + - + +
165R LEU* 3.1 9.1 + - - +
167R ASP* 1.3 103.8 + - - +
169R HIS* 1.3 66.3 + - + +
171R VAL 5.3 1.3 - - - -
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Residues in contact with HIS 169 (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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169J HIS* 4.0 25.0 + + - -
164O TYR* 3.1 28.3 - + + +
165O LEU* 4.6 5.0 - - + +
168O LYS* 3.8 35.6 + - + +
169O HIS* 4.1 27.3 + + - -
165R LEU* 3.0 35.0 + - + +
166R PHE 3.4 0.6 + - - -
167R ASP 3.4 0.2 - - - -
168R LYS* 1.3 83.4 + - + +
170R SER* 1.3 61.3 + - - +
171R VAL 3.5 3.5 - - - -
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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