Contacts of the helix formed by residues 160 - 169 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158A GLU 3.2 8.0 + - - -
159A ASN* 1.3 72.2 + - - +
161A MET* 1.3 64.1 + - - +
163A GLU* 3.3 5.9 + - - -
164A TYR* 3.1 19.1 + - - +
153O ARG* 3.3 42.9 + - - +
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Residues in contact with MET 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A ASN* 3.4 10.1 + - - +
160A GLY* 1.3 73.2 - - - +
162A GLY* 1.3 64.7 + - - +
164A TYR* 3.4 2.1 + - - +
165A LEU* 3.1 24.9 + - + +
161J MET* 3.6 29.8 - - + +
153O ARG 3.6 4.2 + - - -
154O LEU* 4.1 24.2 - - + -
159O ASN* 3.8 26.5 - - - +
161O MET* 3.6 34.1 - - + +
162O GLY* 4.4 4.3 - - - -
165O LEU* 4.0 24.0 - - + -
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Residues in contact with GLY 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A LEU* 3.3 36.0 - - - +
156A LEU* 3.9 5.8 - - - -
159A ASN* 3.3 23.9 + - - +
160A GLY 3.2 0.4 - - - -
161A MET* 1.3 79.4 - - - +
163A GLU* 1.3 60.4 + - - +
165A LEU* 3.5 2.1 + - - +
166A PHE* 3.1 17.5 + - - +
161J MET* 4.5 3.6 - - - -
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Residues in contact with GLU 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A LEU* 3.9 20.2 - - + +
91A ASN* 3.5 12.8 - - - +
92A THR* 2.8 46.6 + - + +
156A LEU* 3.5 27.8 - - + +
159A ASN 3.3 8.8 + - - +
160A GLY* 3.5 11.0 - - - +
162A GLY* 1.3 74.8 - - - +
164A TYR* 1.3 64.6 + - - +
166A PHE* 3.3 6.3 + - - +
167A ASP* 3.2 20.3 + - - +
153O ARG* 3.5 21.4 + - - +
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Residues in contact with TYR 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A LEU* 4.6 2.7 - - - -
160A GLY 3.1 13.0 + - - +
161A MET 3.6 7.0 - - - +
162A GLY 3.3 0.2 - - - -
163A GLU* 1.3 78.3 - - - +
165A LEU* 1.3 71.0 + - + +
167A ASP* 3.3 4.3 + - - -
168A LYS* 3.1 59.2 + - + +
150O ASN* 3.2 29.4 - - + -
153O ARG* 4.1 8.9 - - - +
154O LEU* 3.8 43.3 - - + -
165O LEU* 4.4 7.6 - - + -
166O PHE* 3.5 8.7 - - - -
169O HIS* 3.1 31.0 - + + +
170O SER* 2.9 30.2 + - - -
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Residues in contact with LEU 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A LEU* 4.9 2.7 - - + -
161A MET* 3.1 25.2 + - + +
162A GLY* 3.8 5.8 - - - +
163A GLU 3.3 0.2 - - - -
164A TYR* 1.3 82.9 - - + +
166A PHE* 1.3 67.2 + - - +
168A LYS* 3.1 3.7 + - + +
169A HIS* 3.0 46.0 + - + +
161J MET* 4.1 25.8 - - + -
164J TYR* 4.1 11.9 - - + -
165J LEU* 3.9 27.4 - - + -
165O LEU* 4.0 31.0 - - + -
169O HIS* 4.6 7.4 - - + +
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Residues in contact with PHE 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A VAL* 4.3 7.0 - - + -
92A THR* 3.8 23.6 - - + -
96A MET* 4.3 6.1 - - + -
147A PHE* 3.6 45.5 - + + -
150A ASN* 4.6 2.5 - - + -
151A LEU* 3.5 34.3 - - + -
154A LEU* 3.8 14.5 - - + +
162A GLY 3.1 14.1 + - - +
163A GLU 3.5 9.6 - - - +
164A TYR 3.3 0.2 - - - -
165A LEU* 1.3 76.2 - - - +
167A ASP* 1.3 63.9 + - - +
170A SER* 3.0 48.1 + - - -
171A VAL* 3.8 20.3 + - + -
164J TYR* 3.5 11.2 + + - -
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Residues in contact with ASP 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A LEU* 3.3 27.5 - - + +
45A HIS* 4.4 2.3 + - - +
46A ASN* 3.0 66.9 + - - +
47A VAL* 3.1 23.3 + - + -
163A GLU 3.2 9.0 + - - +
164A TYR 3.4 10.5 - - - +
166A PHE* 1.3 82.3 - - - +
168A LYS* 1.3 80.7 + - - +
171A VAL* 4.4 7.7 + - - +
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Residues in contact with LYS 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A LEU* 5.0 1.0 - - - +
46A ASN* 4.4 8.7 - - - +
164A TYR* 3.1 59.4 + - + +
165A LEU* 3.1 8.7 + - - +
167A ASP* 1.3 104.8 + - - +
169A HIS* 1.3 67.3 + - + +
171A VAL 5.3 1.3 - - - -
150O ASN* 4.8 2.2 + - - -
169O HIS* 3.8 48.9 + - + +
170O SER* 4.5 4.5 - - - +
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Residues in contact with HIS 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A LEU* 3.0 34.5 + - + +
167A ASP 3.4 0.2 - - - -
168A LYS* 1.3 84.1 + - + +
170A SER* 1.3 64.0 + - - +
171A VAL 3.5 3.5 - - - -
164J TYR* 3.2 21.8 - + - +
165J LEU* 4.7 4.6 - - + +
168J LYS* 3.8 37.4 + - + +
169J HIS* 4.0 29.3 + + - -
169O HIS* 4.1 25.1 + + - -
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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