Contacts of the helix formed by residues 160 - 169 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B GLU 3.2 8.2 + - - -
159B ASN* 1.3 71.5 + - - +
161B MET* 1.3 64.9 + - - +
163B GLU* 3.3 6.1 + - - -
164B TYR* 3.1 18.5 + - - +
153G ARG* 3.2 43.6 + - - +
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Residues in contact with MET 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159B ASN* 3.4 10.1 + - - +
160B GLY* 1.3 72.2 - - - +
162B GLY* 1.3 65.9 + - - +
164B TYR* 3.4 2.1 + - - +
165B LEU* 3.1 24.2 + - + +
153G ARG 3.6 4.2 + - - -
154G LEU* 4.0 24.7 - - + -
159G ASN* 3.8 25.8 - - - +
161G MET* 3.6 34.3 - - + +
162G GLY* 4.4 4.5 - - - -
165G LEU* 3.9 25.4 - - + -
161I MET* 3.6 29.6 - - + +
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Residues in contact with GLY 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B LEU* 3.3 36.2 - - - +
156B LEU* 3.9 6.1 - - - -
159B ASN* 3.3 24.1 + - - +
160B GLY 3.2 0.8 - - - -
161B MET* 1.3 79.6 - - - +
163B GLU* 1.3 60.8 + - - +
165B LEU* 3.5 1.7 + - - +
166B PHE* 3.1 17.5 + - - +
161I MET* 4.5 3.1 - - - -
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Residues in contact with GLU 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B LEU* 3.9 18.3 - - + +
91B ASN* 3.5 13.2 - - - +
92B THR* 2.8 45.5 + - - +
156B LEU* 3.5 27.4 - - + +
159B ASN 3.3 9.9 + - - +
160B GLY* 3.3 10.0 + - - +
162B GLY* 1.3 73.9 - - - +
164B TYR* 1.3 65.3 + - - +
166B PHE* 3.3 6.6 + - - +
167B ASP* 3.2 20.1 + - - +
153G ARG* 3.4 21.8 + - - +
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Residues in contact with TYR 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B LEU* 4.6 2.9 - - - -
160B GLY 3.1 13.4 + - - +
161B MET 3.6 7.4 - - - +
163B GLU* 1.3 77.2 - - - +
165B LEU* 1.3 71.1 + - + +
167B ASP* 3.3 3.7 + - - -
168B LYS* 3.1 53.2 + - + +
150G ASN* 3.1 29.6 - - + -
153G ARG* 4.0 9.1 - - - +
154G LEU* 3.8 42.4 - - + -
165G LEU* 4.3 8.5 - - + -
166G PHE* 3.5 8.5 - - - -
169G HIS* 3.1 37.1 - + + +
170G SER* 2.9 31.2 + - - -
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Residues in contact with LEU 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B LEU* 4.9 2.7 - - + -
161B MET* 3.1 20.6 + - + +
162B GLY* 3.8 5.8 - - - +
163B GLU 3.3 0.2 - - - -
164B TYR* 1.3 83.2 - - + +
166B PHE* 1.3 65.0 + - - +
168B LYS* 3.1 3.7 + - + +
169B HIS* 3.0 48.9 + - + +
165G LEU* 4.0 30.7 - - + -
169G HIS* 4.5 12.6 - - + +
161I MET* 4.0 27.8 - - + -
164I TYR* 4.2 9.2 - - + -
165I LEU* 4.0 25.4 - - + -
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Residues in contact with PHE 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B VAL* 4.3 7.0 - - + -
92B THR* 3.8 23.1 - - + -
96B MET* 4.3 6.1 - - + -
147B PHE* 3.6 45.3 - + + -
150B ASN* 4.6 4.0 - - + -
151B LEU* 3.5 35.2 - - + -
154B LEU* 3.8 14.1 - - + +
162B GLY 3.1 14.1 + - - +
163B GLU 3.5 9.9 - - - +
164B TYR 3.3 0.2 - - - -
165B LEU* 1.3 76.3 - - - +
167B ASP* 1.3 63.6 + - - +
170B SER* 3.0 48.4 + - - -
171B VAL* 3.8 20.7 + - + +
164I TYR* 3.6 8.0 + - - -
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Residues in contact with ASP 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B ALA 5.5 0.2 - - - +
44B LEU* 3.3 27.2 - - + +
45B HIS* 4.4 2.4 + - - +
46B ASN* 2.9 66.8 + - - +
47B VAL* 3.1 23.0 + - + -
163B GLU 3.2 8.9 + - - +
164B TYR 3.4 10.1 - - - +
165B LEU 3.2 0.4 - - - -
166B PHE* 1.3 82.6 - - - +
168B LYS* 1.3 81.2 + - - +
171B VAL* 4.4 7.5 + - - +
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Residues in contact with LYS 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B LEU* 5.0 0.8 - - - +
46B ASN* 4.4 8.7 - - - +
164B TYR* 3.1 59.3 + - + +
165B LEU* 3.1 8.5 + - - +
167B ASP* 1.3 104.4 + - - +
169B HIS* 1.3 65.0 + - + +
171B VAL 5.3 1.6 - - - -
150G ASN* 4.8 2.6 + - - -
169G HIS* 3.8 52.2 + - + +
170G SER* 4.4 4.5 - - - +
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Residues in contact with HIS 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B LEU* 3.0 34.5 + - + +
166B PHE 3.4 0.2 + - - -
167B ASP 3.4 0.2 - - - -
168B LYS* 1.3 83.8 + - + +
170B SER* 1.3 61.7 + - - +
171B VAL 3.5 2.9 - - - -
169G HIS* 4.0 25.7 + + - -
164I TYR* 3.0 27.4 - + + +
165I LEU* 4.7 4.8 - - + +
168I LYS* 3.9 34.8 - - + +
169I HIS* 4.1 27.5 + + - -
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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