Contacts of the helix formed by residues 160 - 169 (chain U) 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 U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153N ARG* 3.3 42.3 - - - +
158U GLU 3.2 8.0 + - - -
159U ASN* 1.3 71.6 + - - +
161U MET* 1.3 64.4 + - - +
163U GLU* 3.3 6.0 + - - -
164U TYR* 3.1 18.9 + - - +
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Residues in contact with MET 161 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153N ARG 3.6 3.6 + - - -
154N LEU* 4.1 25.1 - - + -
159N ASN* 3.7 26.2 - - - +
161N MET* 3.6 29.8 - - + +
162N GLY* 4.5 3.4 - - - -
165N LEU* 4.0 24.9 - - + -
161T MET* 3.6 34.5 - - + +
159U ASN* 3.4 11.2 + - - +
160U GLY* 1.3 73.9 - - - +
162U GLY* 1.3 64.9 + - - +
164U TYR* 3.4 2.1 + - - +
165U LEU* 3.1 25.1 + - + +
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Residues in contact with GLY 162 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161T MET* 4.4 3.1 - - - -
154U LEU* 3.3 35.9 - - - +
156U LEU* 3.9 5.6 - - - -
159U ASN* 3.3 23.7 + - - +
160U GLY 3.2 0.6 - - - -
161U MET* 1.3 77.7 - - - +
163U GLU* 1.3 61.7 + - - +
165U LEU* 3.5 2.2 + - - +
166U PHE 3.1 17.0 + - - -
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Residues in contact with GLU 163 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153N ARG* 3.5 21.0 + - - +
44U LEU* 3.9 18.9 - - + +
91U ASN* 3.5 12.9 - - - +
92U THR* 2.8 46.4 + - + +
156U LEU* 3.5 28.8 - - + +
159U ASN 3.3 9.4 + - - +
160U GLY* 3.3 10.7 + - - +
162U GLY* 1.3 74.8 - - - +
164U TYR* 1.3 64.2 + - - +
166U PHE* 3.3 6.4 + - - +
167U ASP* 3.2 20.4 + - - +
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Residues in contact with TYR 164 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150N ASN* 3.1 28.9 - - + -
153N ARG* 4.0 8.7 - - - +
154N LEU* 3.7 42.2 - - + -
165N LEU* 4.4 8.1 - - + -
166N PHE* 3.5 8.8 - - - -
169N HIS* 3.1 30.8 - + + +
170N SER* 3.0 29.7 + - - -
44U LEU* 4.6 2.9 - - - -
160U GLY 3.1 13.3 + - - +
161U MET 3.6 6.7 - - - +
163U GLU* 1.3 77.2 - - - +
165U LEU* 1.3 71.5 + - + +
167U ASP* 3.3 3.9 + - - +
168U LYS* 3.1 61.7 + - + +
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Residues in contact with LEU 165 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165N LEU* 4.0 31.2 - - + -
169N HIS* 4.7 6.7 - - - +
161T MET* 3.9 27.6 - - + -
164T TYR* 4.1 11.7 - - + -
165T LEU* 3.9 27.1 - - + -
154U LEU* 4.9 2.9 - - + -
161U MET* 3.1 24.9 + - + +
162U GLY* 3.8 6.1 - - - +
163U GLU 3.3 0.2 - - - -
164U TYR* 1.3 84.2 - - + +
166U PHE* 1.3 65.9 + - - +
168U LYS* 3.1 3.6 + - + +
169U HIS* 3.0 46.1 + - + +
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Residues in contact with PHE 166 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164T TYR* 3.5 10.5 + + - -
47U VAL* 4.3 7.0 - - + -
92U THR* 3.8 23.6 - - + -
96U MET* 4.3 6.5 - - + -
147U PHE* 3.6 45.5 - + + -
150U ASN* 4.6 2.7 - - + -
151U LEU* 3.5 33.2 - - + -
154U LEU* 3.8 13.6 - - + +
162U GLY 3.1 15.1 + - - +
163U GLU 3.5 8.7 - - - +
164U TYR 3.3 0.2 - - - -
165U LEU* 1.3 75.7 - - - +
167U ASP* 1.3 64.5 + - - +
170U SER* 3.0 49.4 + - - -
171U VAL* 3.8 20.5 + - + +
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Residues in contact with ASP 167 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44U LEU* 3.3 28.8 - - + +
45U HIS* 4.4 2.4 + - - +
46U ASN* 3.0 66.7 + - - +
47U VAL* 3.1 22.9 + - + -
163U GLU 3.2 8.5 + - - +
164U TYR 3.4 10.1 - - - +
165U LEU 3.2 0.2 - - - -
166U PHE* 1.3 82.2 - - - +
168U LYS* 1.3 80.0 + - - +
169U HIS 3.6 0.2 + - - -
171U VAL* 4.4 7.8 + - - +
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Residues in contact with LYS 168 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150N ASN* 4.8 2.4 + - - -
169N HIS* 3.9 48.7 + - + +
170N SER* 4.5 4.0 - - - +
44U LEU* 5.0 1.0 - - - +
46U ASN* 4.4 8.5 - - - +
164U TYR* 3.1 60.2 + - + +
165U LEU* 3.1 8.1 + - + +
167U ASP* 1.3 104.7 + - - +
169U HIS* 1.3 67.0 + - + +
171U VAL 5.3 1.8 - - - -
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Residues in contact with HIS 169 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169N HIS* 4.1 21.5 + + - -
164T TYR* 3.1 27.6 - + + +
165T LEU* 4.6 4.3 - - + +
168T LYS* 3.8 35.6 + - + +
169T HIS* 4.0 28.4 + + - -
165U LEU* 3.0 36.5 + - + +
166U PHE 3.4 0.4 + - - -
168U LYS* 1.3 85.1 + - + +
170U SER* 1.3 62.1 + - - +
171U VAL 3.5 3.0 - - - -
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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