Contacts of the helix formed by residues 160 - 169 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158E GLU 3.2 8.5 + - - -
159E ASN* 1.3 70.8 + - - +
161E MET* 1.3 63.9 + - - +
163E GLU* 3.3 5.8 + - - -
164E TYR* 3.1 18.5 + - - +
153W ARG* 3.2 43.0 - - - +
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Residues in contact with MET 161 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159E ASN* 3.4 10.6 + - - +
160E GLY* 1.3 72.8 - - - +
162E GLY* 1.3 64.9 + - - +
164E TYR* 3.4 1.9 + - - +
165E LEU* 3.1 24.7 + - + +
161L MET* 3.6 34.3 - - + +
153W ARG 3.6 3.8 + - - -
154W LEU* 4.0 27.6 - - + -
159W ASN* 3.8 24.0 - - - +
161W MET* 3.7 29.2 - - + +
162W GLY* 4.4 3.8 - - - -
165W LEU* 4.0 25.1 - - + -
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Residues in contact with GLY 162 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154E LEU* 3.3 35.1 - - - +
156E LEU* 3.9 5.8 - - - -
159E ASN* 3.3 23.7 + - - +
160E GLY 3.2 0.4 - - - -
161E MET* 1.3 80.0 - - - +
163E GLU* 1.3 62.2 + - - +
165E LEU* 3.5 2.1 + - - +
166E PHE* 3.1 17.8 + - - +
161L MET* 4.4 2.9 - - - -
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Residues in contact with GLU 163 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44E LEU* 3.9 20.6 - - + +
47E VAL* 5.8 0.2 - - - +
91E ASN* 3.5 13.0 - - - +
92E THR* 2.8 47.2 + - - +
156E LEU* 3.5 28.1 - - + +
159E ASN 3.3 9.4 + - - +
160E GLY* 3.3 10.5 + - - +
162E GLY* 1.3 73.8 - - - +
164E TYR* 1.3 65.2 + - - +
166E PHE* 3.3 6.7 + - - +
167E ASP* 3.2 20.1 + - - +
153W ARG* 3.4 21.1 + - - +
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Residues in contact with TYR 164 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44E LEU* 4.6 2.5 - - - -
160E GLY 3.1 13.2 + - - +
161E MET 3.6 6.7 - - - +
162E GLY 3.3 0.2 - - - -
163E GLU* 1.3 77.7 - - - +
165E LEU* 1.3 72.3 + - + +
167E ASP* 3.3 4.3 + - - +
168E LYS* 3.1 53.9 + - + +
150W ASN* 3.1 29.4 - - + -
153W ARG* 4.0 9.5 - - - +
154W LEU* 3.8 42.4 - - + -
165W LEU* 4.4 7.4 - - + -
166W PHE* 3.5 8.9 - - - -
169W HIS* 3.1 36.5 - + + +
170W SER* 2.9 30.5 + - - -
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Residues in contact with LEU 165 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154E LEU* 4.9 2.9 - - + -
161E MET* 3.1 25.7 + - + +
162E GLY* 3.8 5.2 - - - +
164E TYR* 1.3 82.4 - - + +
166E PHE* 1.3 66.5 - - - +
168E LYS* 3.1 3.1 + - + +
169E HIS* 3.0 48.9 + - + +
161L MET* 3.9 28.9 - - + -
164L TYR* 4.2 8.7 - - + -
165L LEU* 4.0 24.5 - - + -
165W LEU* 4.0 31.4 - - + -
169W HIS* 4.6 8.3 - - + +
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Residues in contact with PHE 166 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47E VAL* 4.3 7.2 - - + -
92E THR* 3.8 23.6 - - + -
96E MET* 4.3 6.3 - - + -
147E PHE* 3.6 45.3 - + + -
150E ASN* 4.6 2.7 - - + -
151E LEU* 3.5 34.3 - - + -
154E LEU* 3.8 13.2 - - + +
162E GLY 3.1 13.8 + - - +
163E GLU 3.5 9.4 - - - +
165E LEU* 1.3 76.7 - - - +
167E ASP* 1.3 63.9 + - - +
170E SER* 3.0 47.8 + - - -
171E VAL* 3.8 20.5 + - + +
164L TYR* 3.5 10.5 + + - -
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Residues in contact with ASP 167 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44E LEU* 3.3 27.5 - - + +
45E HIS* 4.4 2.3 + - - +
46E ASN* 3.0 67.3 + - - +
47E VAL* 3.1 23.3 + - + -
163E GLU 3.2 8.4 + - - +
164E TYR 3.4 9.9 - - - +
165E LEU 3.2 0.2 - - - -
166E PHE* 1.3 82.0 - - - +
168E LYS* 1.3 80.3 + - - +
169E HIS 3.6 0.2 + - - -
171E VAL* 4.4 7.7 + - - +
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Residues in contact with LYS 168 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44E LEU* 5.0 1.2 - - - +
46E ASN* 4.4 8.5 - - - +
164E TYR* 3.1 59.2 + - + +
165E LEU* 3.1 8.5 + - - +
167E ASP* 1.3 104.2 + - - +
169E HIS* 1.3 65.2 + - + +
171E VAL 5.3 1.6 - - - -
150W ASN* 4.8 2.2 + - - -
169W HIS* 3.8 51.5 + - + +
170W SER* 4.5 4.5 - - - +
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Residues in contact with HIS 169 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165E LEU* 3.0 34.5 + - + +
166E PHE 3.4 0.6 + - - -
168E LYS* 1.3 84.1 + - + +
170E SER* 1.3 62.1 + - - +
171E VAL 3.5 3.1 - - - -
164L TYR* 3.0 27.8 - + + +
165L LEU* 4.5 5.0 - - + +
168L LYS* 3.8 36.3 + - + +
169L HIS* 4.0 27.0 + + - -
169W HIS* 4.0 25.7 + + - -
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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