Contacts of the helix formed by residues 160 - 169 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153E ARG* 3.2 43.5 - - - +
158L GLU 3.2 8.2 + - - -
159L ASN* 1.3 72.1 + - - +
161L MET* 1.3 64.6 + - - +
163L GLU* 3.3 6.0 + - - -
164L TYR* 3.1 19.1 + - - +
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Residues in contact with MET 161 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153E ARG 3.6 3.4 + - - -
154E LEU* 4.0 25.8 - - + +
159E ASN* 3.8 24.9 - - - +
161E MET* 3.6 33.4 - - + +
162E GLY* 4.4 4.3 - - - -
165E LEU* 3.9 26.9 - - + -
159L ASN* 3.4 10.1 + - - +
160L GLY* 1.3 74.0 - - - +
162L GLY* 1.3 65.2 + - - +
164L TYR* 3.4 2.1 + - - +
165L LEU* 3.1 24.6 + - + +
161P MET* 3.6 30.3 - - + +
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Residues in contact with GLY 162 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154L LEU* 3.3 36.2 - - - +
156L LEU* 3.9 5.4 - - - -
159L ASN* 3.3 23.5 + - - +
160L GLY 3.2 0.8 - - - -
161L MET* 1.3 79.5 - - - +
163L GLU* 1.3 60.4 + - - +
165L LEU* 3.5 1.9 + - - +
166L PHE* 3.1 18.2 + - - +
161P MET* 4.5 3.4 - - - -
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Residues in contact with GLU 163 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153E ARG* 3.4 22.6 + - - +
44L LEU* 3.9 19.2 - - + +
47L VAL* 5.8 0.3 - - - +
91L ASN* 3.5 13.7 - - - +
92L THR* 2.8 46.2 + - + +
156L LEU* 3.5 27.2 - - + +
159L ASN 3.3 9.5 + - - +
160L GLY* 3.3 10.3 + - - +
162L GLY* 1.3 73.9 - - - +
164L TYR* 1.3 66.1 + - - +
166L PHE* 3.3 6.6 + - - +
167L ASP* 3.2 20.6 + - - +
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Residues in contact with TYR 164 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150E ASN* 3.2 28.7 - - + -
153E ARG* 4.1 9.6 - - - +
154E LEU* 3.8 40.4 - - + -
165E LEU* 4.3 8.5 - - + -
166E PHE* 3.5 8.4 - - - -
169E HIS* 3.0 37.9 - + + +
170E SER* 2.9 30.9 + - - -
44L LEU* 4.6 3.1 - - - -
160L GLY 3.1 13.4 + - - +
161L MET 3.6 7.0 - - - +
163L GLU* 1.3 77.5 - - - +
165L LEU* 1.3 71.4 + - + +
167L ASP* 3.3 3.8 + - - +
168L LYS* 3.1 53.7 + - + +
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Residues in contact with LEU 165 (chain L).
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* 4.0 26.2 - - + -
169E HIS* 4.5 12.3 - - + +
154L LEU* 4.9 2.7 - - + -
161L MET* 3.1 26.4 + - + +
162L GLY* 3.8 5.4 - - - +
163L GLU 3.3 0.4 - - - -
164L TYR* 1.3 82.7 - - + +
166L PHE* 1.3 64.5 + - - +
168L LYS* 3.1 3.3 + - + +
169L HIS* 3.0 46.3 + - + +
161P MET* 4.0 26.0 - - + -
164P TYR* 4.1 12.6 - - + -
165P LEU* 4.0 26.7 - - + -
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Residues in contact with PHE 166 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47L VAL* 4.3 7.2 - - + -
92L THR* 3.8 22.9 - - + -
96L MET* 4.3 6.3 - - + -
147L PHE* 3.6 45.3 - + + -
150L ASN* 4.6 2.9 - - + -
151L LEU* 3.5 34.3 - - + -
154L LEU* 3.8 13.6 - - + +
162L GLY 3.1 14.3 + - - +
163L GLU 3.5 9.6 - - - +
164L TYR 3.3 0.4 - - - -
165L LEU* 1.3 77.5 - - - +
167L ASP* 1.3 65.4 + - - +
170L SER* 3.0 47.7 + - - -
171L VAL* 3.8 19.5 + - + -
164P TYR* 3.5 9.4 + + - -
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Residues in contact with ASP 167 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44L LEU* 3.3 27.9 - - + +
45L HIS* 4.4 2.4 + - - +
46L ASN* 3.0 68.7 + - - +
47L VAL* 3.1 22.8 + - + +
163L GLU 3.2 8.5 + - - +
164L TYR 3.4 9.6 - - - +
165L LEU 3.2 0.2 - - - -
166L PHE* 1.3 82.7 - - - +
168L LYS* 1.3 80.5 + - - +
171L VAL* 4.4 7.2 + - - +
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Residues in contact with LYS 168 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150E ASN* 4.9 2.2 + - - -
169E HIS* 3.8 50.0 + - + +
170E SER* 4.5 4.7 - - - +
44L LEU* 5.0 1.2 - - - +
46L ASN* 4.4 9.2 - - - +
164L TYR* 3.1 59.3 + - + +
165L LEU* 3.1 8.3 + - - +
167L ASP* 1.3 104.6 + - - +
169L HIS* 1.3 64.7 + - + +
171L VAL 5.3 1.3 - - - -
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Residues in contact with HIS 169 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169E HIS* 4.0 25.5 + + - -
165L LEU* 3.0 35.2 + - + +
166L PHE 3.4 0.2 + - - -
167L ASP 3.4 0.4 - - - -
168L LYS* 1.3 84.7 + - + +
170L SER* 1.3 61.2 + - - +
171L VAL 3.5 3.3 - - - -
164P TYR* 3.1 24.0 - + - +
165P LEU* 4.7 3.8 - - + +
168P LYS* 3.9 37.8 + - + +
169P HIS* 4.1 27.9 + + - -
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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