Contacts of the helix formed by residues 160 - 169 (chain P) 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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153L ARG* 3.3 42.5 + - - +
158P GLU 3.2 8.0 + - - -
159P ASN* 1.3 71.8 + - - +
161P MET* 1.3 63.3 + - - +
163P GLU* 3.3 6.4 + - - -
164P TYR* 3.1 18.9 + - - +
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Residues in contact with MET 161 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153L ARG 3.6 3.8 + - - -
154L LEU* 4.1 24.7 - - + +
159L ASN* 3.7 26.5 - - - +
161L MET* 3.6 29.6 - - + +
162L GLY* 4.4 3.8 - - - -
165L LEU* 4.0 24.5 - - + -
159P ASN* 3.4 11.0 + - - +
160P GLY* 1.3 73.2 - - - +
162P GLY* 1.3 65.6 + - - +
164P TYR* 3.4 1.9 + - - +
165P LEU* 3.1 24.9 + - + +
161W MET* 3.6 34.1 - - + +
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Residues in contact with GLY 162 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154P LEU* 3.3 35.2 - - - +
156P LEU* 3.9 6.1 - - - -
159P ASN* 3.3 24.6 + - - +
160P GLY 3.2 0.8 - - - -
161P MET* 1.3 80.0 - - - +
163P GLU* 1.3 60.6 + - - +
165P LEU* 3.5 1.5 + - - +
166P PHE 3.1 17.8 + - - -
161W MET* 4.4 3.6 - - - -
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Residues in contact with GLU 163 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153L ARG* 3.4 21.4 + - - +
44P LEU* 3.9 18.7 - - + +
91P ASN* 3.5 12.5 - - - +
92P THR* 2.8 45.8 + - - +
156P LEU* 3.5 28.4 - - + +
159P ASN 3.3 9.5 + - - +
160P GLY* 3.3 10.1 + - - +
162P GLY* 1.3 74.5 - - - +
164P TYR* 1.3 64.5 + - - +
166P PHE* 3.3 6.6 + - - +
167P ASP* 3.2 20.4 + - - +
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Residues in contact with TYR 164 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150L ASN* 3.1 28.9 - - + -
153L ARG* 4.0 9.5 - - - +
154L LEU* 3.7 42.6 - - + -
165L LEU* 4.4 8.5 - - + -
166L PHE* 3.5 9.4 - + - -
169L HIS* 3.1 30.1 - + + +
170L SER* 2.9 30.6 + - - -
44P LEU* 4.6 2.5 - - - -
160P GLY 3.1 13.3 + - - +
161P MET 3.6 7.4 - - - +
163P GLU* 1.3 77.2 - - - +
165P LEU* 1.3 71.6 + - + +
167P ASP* 3.3 4.3 + - - +
168P LYS* 3.1 59.6 + - + +
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Residues in contact with LEU 165 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165L LEU* 4.0 31.0 - - + -
169L HIS* 4.7 7.0 - - + +
154P LEU* 4.9 3.4 - - + -
161P MET* 3.1 27.4 + - + +
162P GLY* 3.8 5.2 - - - +
163P GLU 3.3 0.2 - - - -
164P TYR* 1.3 81.7 - - + +
166P PHE* 1.3 63.7 + - - +
168P LYS* 3.1 3.3 + - + +
169P HIS* 3.0 50.4 + - + +
161W MET* 3.9 27.4 - - + -
164W TYR* 4.2 8.7 - - + -
165W LEU* 4.0 26.5 - - + -
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Residues in contact with PHE 166 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47P VAL* 4.3 5.8 - - + -
92P THR* 3.8 24.0 - - + -
96P MET* 4.3 5.6 - - + -
147P PHE* 3.6 44.9 - + + -
150P ASN* 4.6 2.7 - - + -
151P LEU* 3.5 35.4 - - + -
154P LEU* 3.8 15.0 - - + +
162P GLY 3.1 14.6 + - - +
163P GLU 3.5 9.6 - - - +
164P TYR 3.3 0.2 - - - -
165P LEU* 1.3 75.3 - - - +
167P ASP* 1.3 64.2 + - - +
170P SER* 3.0 48.8 + - - -
171P VAL* 3.8 20.8 + - + -
164W TYR* 3.5 10.1 + + - -
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Residues in contact with ASP 167 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43P ALA 5.5 0.3 - - - +
44P LEU* 3.3 28.3 - - + +
45P HIS* 4.4 2.1 + - - +
46P ASN* 2.9 66.8 + - - +
47P VAL* 3.1 23.3 + - + -
163P GLU 3.2 9.1 + - - +
164P TYR 3.4 10.3 - - - +
166P PHE* 1.3 81.7 - - - +
168P LYS* 1.3 81.8 + - - +
171P VAL* 4.4 7.9 + - - +
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Residues in contact with LYS 168 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150L ASN* 4.8 3.0 + - - -
169L HIS* 3.9 50.2 + - + +
170L SER* 4.5 4.3 - - - +
44P LEU* 5.0 0.6 - - - +
46P ASN* 4.4 9.0 - - - +
164P TYR* 3.1 59.0 + - + +
165P LEU* 3.1 8.9 + - + +
167P ASP* 1.3 105.8 + - - +
169P HIS* 1.3 66.2 + - + +
171P VAL 5.3 1.8 - - - -
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Residues in contact with HIS 169 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169L HIS* 4.1 25.1 + + - -
165P LEU* 3.0 36.2 + - + +
166P PHE 3.4 0.2 + - - -
167P ASP 3.4 0.4 - - - -
168P LYS* 1.3 84.3 + - + +
170P SER* 1.3 60.9 + - - +
171P VAL 3.5 3.5 - - - -
164W TYR* 3.1 27.4 - + + +
165W LEU* 4.6 4.4 - - + +
168W LYS* 3.8 33.9 - - + +
169W HIS* 4.0 28.8 + + - -
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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