Contacts of the helix formed by residues 160 - 169 (chain Q) 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 Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153K ARG* 3.2 42.5 + - - +
158Q GLU 3.2 8.4 + - - -
159Q ASN* 1.3 71.2 + - - +
161Q MET* 1.3 64.2 + - - +
163Q GLU* 3.3 6.2 + - - -
164Q TYR* 3.1 18.7 + - - +
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Residues in contact with MET 161 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153K ARG 3.6 3.8 + - - -
154K LEU* 4.0 26.7 - - + -
159K ASN* 3.8 24.0 - - - +
161K MET* 3.6 29.6 - - + +
162K GLY* 4.4 3.6 - - - -
165K LEU* 3.9 27.1 - - + -
159Q ASN* 3.4 9.9 + - - +
160Q GLY* 1.3 73.8 - - - +
162Q GLY* 1.3 64.6 + - - +
164Q TYR* 3.4 1.9 + - - +
165Q LEU* 3.1 25.8 + - + +
161X MET* 3.6 34.1 - - + +
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Residues in contact with GLY 162 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154Q LEU* 3.3 36.5 - - - +
156Q LEU* 3.9 5.6 - - - -
159Q ASN* 3.3 23.8 + - - +
160Q GLY 3.2 0.4 - - - -
161Q MET* 1.3 79.8 - - - +
163Q GLU* 1.3 61.1 + - - +
165Q LEU* 3.5 1.9 + - - +
166Q PHE* 3.1 18.0 + - - +
161X MET* 4.4 3.4 - - - -
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Residues in contact with GLU 163 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153K ARG* 3.4 22.3 + - - +
44Q LEU* 3.9 18.5 - - + +
47Q VAL* 5.8 0.3 - - - +
91Q ASN* 3.5 13.2 - - - +
92Q THR* 2.8 46.4 + - + +
156Q LEU* 3.5 27.9 - - + +
159Q ASN 3.3 9.5 + - - +
160Q GLY* 3.3 10.1 + - - +
162Q GLY* 1.3 73.9 - - - +
164Q TYR* 1.3 65.4 - - - +
166Q PHE* 3.3 6.2 + - - +
167Q ASP* 3.2 20.3 + - - +
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Residues in contact with TYR 164 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150K ASN* 3.1 28.5 - - + -
153K ARG* 4.1 9.3 - - - +
154K LEU* 3.9 42.2 - - + -
165K LEU* 4.4 8.7 - - + -
166K PHE* 3.6 8.4 - - - -
169K HIS* 3.0 38.4 - + + +
170K SER* 2.9 31.2 + - - -
44Q LEU* 4.6 2.7 - - - -
160Q GLY 3.1 13.4 + - - +
161Q MET 3.6 7.0 - - - +
163Q GLU* 1.3 77.1 - - - +
165Q LEU* 1.3 71.7 + - + +
167Q ASP* 3.3 4.3 + - - -
168Q LYS* 3.1 54.3 + - + +
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Residues in contact with LEU 165 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165K LEU* 4.1 26.7 - - + -
169K HIS* 4.5 12.6 - - + +
154Q LEU* 4.9 2.9 - - + -
161Q MET* 3.1 25.3 + - + +
162Q GLY* 3.8 5.2 - - - +
163Q GLU 3.3 0.2 - - - -
164Q TYR* 1.3 82.5 - - + +
166Q PHE* 1.3 66.0 + - - +
168Q LYS* 3.1 3.4 + - + +
169Q HIS* 3.0 46.4 + - + +
161X MET* 4.0 27.4 - - + -
164X TYR* 4.1 12.1 - - + -
165X LEU* 4.0 27.1 - - + -
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Residues in contact with PHE 166 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47Q VAL* 4.3 7.0 - - + -
92Q THR* 3.8 23.6 - - + -
96Q MET* 4.3 5.4 - - + -
147Q PHE* 3.6 45.5 - + + -
150Q ASN* 4.6 2.9 - - + -
151Q LEU* 3.5 34.8 - - + -
154Q LEU* 3.8 14.1 - - + +
162Q GLY 3.1 13.6 + - - +
163Q GLU 3.5 9.6 - - - +
165Q LEU* 1.3 77.3 - - - +
167Q ASP* 1.3 64.1 + - - +
170Q SER* 3.0 47.7 + - - -
171Q VAL* 3.8 20.8 + - + +
164X TYR* 3.5 9.9 - + - -
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Residues in contact with ASP 167 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44Q LEU* 3.3 28.3 - - + +
45Q HIS* 4.4 2.3 + - - +
46Q ASN* 3.0 66.0 + - - +
47Q VAL* 3.1 22.8 + - + +
163Q GLU 3.2 8.4 + - - +
164Q TYR 3.4 9.9 - - - +
165Q LEU 3.2 0.2 - - - -
166Q PHE* 1.3 81.5 - - - +
168Q LYS* 1.3 81.2 + - - +
169Q HIS 3.6 0.2 + - - -
171Q VAL* 4.4 7.2 + - - +
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Residues in contact with LYS 168 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150K ASN* 4.9 2.2 + - - -
169K HIS* 3.8 49.0 + - + +
170K SER* 4.5 4.0 - - - +
44Q LEU* 5.0 1.0 - - - +
46Q ASN* 4.4 8.7 - - - +
164Q TYR* 3.1 58.9 + - + +
165Q LEU* 3.1 8.5 + - + +
167Q ASP* 1.3 104.7 + - - +
169Q HIS* 1.3 65.9 + - + +
171Q VAL 5.3 1.6 - - - -
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Residues in contact with HIS 169 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169K HIS* 4.0 25.6 + + - -
165Q LEU* 3.0 34.5 + - + +
166Q PHE 3.4 0.2 + - - -
168Q LYS* 1.3 84.6 + - + +
170Q SER* 1.3 63.0 + - - +
171Q VAL 3.5 2.8 - - - -
164X TYR* 3.1 26.9 - + + +
165X LEU* 4.6 5.2 - - + +
168X LYS* 3.8 35.2 - - + +
169X HIS* 4.0 27.1 + + - -
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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