Contacts of the helix formed by residues 160 - 169 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158F GLU 3.2 7.7 + - - -
159F ASN* 1.3 71.4 + - - +
161F MET* 1.3 64.8 + - - +
163F GLU* 3.3 6.1 + - - -
164F TYR* 3.1 18.7 + - - +
153V ARG* 3.3 42.4 + - - +
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Residues in contact with MET 161 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161C MET* 3.6 33.2 - - + +
159F ASN* 3.4 11.5 + - - +
160F GLY* 1.3 73.6 - - - +
162F GLY* 1.3 64.5 + - - +
164F TYR* 3.4 2.1 + - - +
165F LEU* 3.1 24.7 + - + +
153V ARG 3.7 4.0 + - - -
154V LEU* 4.1 26.0 - - + -
159V ASN* 3.8 24.9 - - - +
161V MET* 3.6 29.8 - - + +
162V GLY* 4.5 4.3 - - - -
165V LEU* 3.9 26.0 - - + -
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Residues in contact with GLY 162 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161C MET* 4.5 3.4 - - - -
154F LEU* 3.3 36.0 - - - +
156F LEU* 3.9 6.1 - - - -
159F ASN* 3.3 23.5 + - - +
160F GLY 3.2 0.6 - - - -
161F MET* 1.3 78.9 - - - +
163F GLU* 1.3 61.2 + - - +
165F LEU* 3.5 2.1 + - - +
166F PHE* 3.1 17.5 + - - +
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Residues in contact with GLU 163 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44F LEU* 3.9 19.6 - - + +
47F VAL* 5.8 0.3 - - - +
91F ASN* 3.5 12.2 - - - +
92F THR* 2.8 46.6 + - + +
156F LEU* 3.5 29.2 - - + +
159F ASN 3.3 9.2 + - - +
160F GLY* 3.3 10.6 + - - +
162F GLY* 1.3 75.1 - - - +
164F TYR* 1.3 63.2 + - - +
166F PHE* 3.3 6.5 + - - +
167F ASP* 3.2 20.4 + - - +
153V ARG* 3.5 21.7 + - - +
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Residues in contact with TYR 164 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44F LEU* 4.6 2.5 - - - -
160F GLY 3.1 12.8 + - - +
161F MET 3.6 7.6 - - - +
163F GLU* 1.3 77.8 - - - +
165F LEU* 1.3 71.7 + - + +
167F ASP* 3.3 3.5 + - - -
168F LYS* 3.1 53.8 + - + +
150V ASN* 3.2 29.8 - - + -
153V ARG* 4.1 8.6 - - - +
154V LEU* 3.8 42.8 - - + -
165V LEU* 4.4 8.3 - - + -
166V PHE* 3.6 8.3 - - - -
169V HIS* 3.1 37.1 - + + +
170V SER* 2.9 31.0 + - - -
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Residues in contact with LEU 165 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161C MET* 4.0 28.0 - - + -
164C TYR* 4.1 13.0 - - + -
165C LEU* 4.0 26.0 - - + -
154F LEU* 4.9 2.2 - - + -
161F MET* 3.1 26.1 + - + +
162F GLY* 3.8 5.4 - - - +
163F GLU 3.3 0.2 - - - -
164F TYR* 1.3 82.7 - - + +
166F PHE* 1.3 66.0 + - - +
168F LYS* 3.1 3.7 + - + +
169F HIS* 3.0 45.9 + - + +
165V LEU* 4.0 25.4 - - + -
169V HIS* 4.6 12.6 - - + +
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Residues in contact with PHE 166 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164C TYR* 3.5 10.1 + + - -
47F VAL* 4.3 7.2 - - + -
92F THR* 3.8 24.0 - - + -
96F MET* 4.3 5.8 - - + -
147F PHE* 3.6 45.1 - + + -
150F ASN* 4.6 2.5 - - + -
151F LEU* 3.5 34.1 - - + -
154F LEU* 3.8 14.1 - - + +
162F GLY 3.1 14.7 + - - +
163F GLU 3.5 9.2 - - - +
164F TYR 3.3 0.2 - - - -
165F LEU* 1.3 76.9 - - - +
167F ASP* 1.3 64.8 + - - +
170F SER* 3.0 48.4 + - - -
171F VAL* 3.8 20.6 + - + -
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Residues in contact with ASP 167 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44F LEU* 3.3 27.9 - - + +
45F HIS 4.4 1.9 + - - -
46F ASN* 2.9 67.6 + - - +
47F VAL* 3.1 23.1 + - + +
163F GLU 3.2 9.3 + - - +
164F TYR 3.4 10.1 - - - +
165F LEU 3.2 0.4 - - - -
166F PHE* 1.3 82.3 - - - +
168F LYS* 1.3 81.6 + - - +
169F HIS 3.6 0.2 + - - -
171F VAL* 4.4 7.1 + - - +
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Residues in contact with LYS 168 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44F LEU* 5.0 1.2 - - - +
46F ASN* 4.4 8.5 - - - +
164F TYR* 3.1 60.0 + - + +
165F LEU* 3.1 7.9 + - + +
167F ASP* 1.3 104.6 + - - +
169F HIS* 1.3 65.1 + - + +
171F VAL 5.3 1.6 - - - -
150V ASN* 4.9 2.4 + - - -
169V HIS* 3.9 50.5 + - + +
170V SER* 4.5 4.0 - - - +
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Residues in contact with HIS 169 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164C TYR* 3.1 24.0 - + - +
165C LEU* 4.6 4.4 - - + +
168C LYS* 3.8 37.4 - - + +
169C HIS* 4.0 28.4 + + - -
165F LEU* 3.0 34.7 + - + +
166F PHE 3.4 0.2 + - - -
167F ASP 3.4 0.2 - - - -
168F LYS* 1.3 84.0 + - + +
170F SER* 1.3 61.6 + - - +
171F VAL 3.5 3.3 - - - -
169V HIS* 4.0 24.4 + + - -
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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
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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