Contacts of the helix formed by residues 159 - 170 (chain Q) in PDB entry 3A68
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 ASP 159 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40Q LYS 3.5 9.2 - - - +
41Q TYR* 3.3 17.5 - - - -
42Q VAL 5.0 0.2 + - - -
45Q SER* 4.3 10.6 + - - +
105Q ARG* 2.8 45.9 + - - -
154Q ALA* 2.9 19.0 + - - +
155Q THR* 5.7 0.4 - - - -
157Q ASN* 3.1 5.0 - - + +
158Q GLY* 1.3 75.5 - - - +
160Q VAL* 1.3 61.2 + - - +
161Q GLN* 3.5 3.1 + - - +
162Q LEU* 3.0 19.5 + - + +
163Q ALA* 3.0 22.1 + - - +
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Residues in contact with VAL 160 (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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148N LEU* 4.3 13.4 - - + +
151N HIS* 3.3 47.1 - - + +
167N GLU* 3.7 10.3 - - + +
171N LEU* 3.5 24.0 - - + -
158Q GLY* 3.0 13.9 + - - +
159Q ASP* 1.3 72.2 + - - +
161Q GLN* 1.3 59.7 + - - +
163Q ALA* 3.4 6.7 + - - +
164Q ASP* 2.9 27.0 + - - +
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Residues in contact with GLN 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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148N LEU* 5.3 4.1 - - + +
171N LEU* 3.6 39.2 - - + +
172N GLY* 3.7 16.5 - - - +
175N VAL* 3.5 25.4 - - + +
101Q TYR* 2.4 40.0 + - - -
105Q ARG* 3.8 9.0 + - - +
159Q ASP* 3.2 2.2 + - - +
160Q VAL* 1.3 81.8 - - - +
162Q LEU* 1.3 56.9 + - - +
164Q ASP* 3.4 10.2 + - + +
165Q PHE* 2.9 32.8 + - - +
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Residues in contact with LEU 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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41Q TYR* 4.4 4.0 - - + -
45Q SER* 4.0 27.6 - - - -
49Q VAL* 3.9 23.8 - - + -
98Q LEU* 5.7 0.7 - - + -
101Q TYR* 3.2 36.8 + - + +
105Q ARG* 4.0 1.6 - - - +
150Q LEU* 4.4 11.2 - - + -
154Q ALA* 3.6 22.4 - - + +
159Q ASP* 3.0 22.6 + - - +
161Q GLN* 1.3 73.7 - - - +
163Q ALA* 1.3 66.0 + - - +
165Q PHE* 3.2 4.8 + - + +
166Q VAL* 2.9 43.3 + - + +
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Residues in contact with ALA 163 (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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151Q HIS* 3.6 24.6 - - + +
154Q ALA* 3.7 11.6 - - + +
155Q THR* 3.9 16.2 - - - +
159Q ASP 3.0 18.0 + - - +
160Q VAL* 3.7 6.1 - - - +
162Q LEU* 1.3 76.6 - - - +
164Q ASP* 1.3 57.9 + - - +
166Q VAL* 3.3 2.7 + - - +
167Q GLU* 3.0 36.9 + - - +
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Residues in contact with ASP 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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167N GLU* 3.3 42.6 - - + +
168N THR* 4.4 6.0 + - - -
171N LEU* 6.3 0.2 - - + -
172N GLY* 5.6 0.9 + - - -
160Q VAL 2.9 18.1 + - - +
161Q GLN* 3.7 11.1 + - + +
163Q ALA* 1.3 74.9 - - - +
165Q PHE* 1.3 59.4 + - - +
167Q GLU* 3.3 7.8 + - - -
168Q THR* 2.8 47.4 + - - -
363Q CA 2.6 26.6 - - - -
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Residues in contact with PHE 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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97Q LYS* 4.0 20.6 - - + -
98Q LEU* 3.8 13.5 - - + -
101Q TYR* 3.6 58.3 - + + -
104Q LYS* 6.2 2.7 - - - -
161Q GLN* 2.9 26.1 + - - +
162Q LEU* 3.2 10.3 + - + +
164Q ASP* 1.3 76.5 - - - +
166Q VAL* 1.3 61.5 + - + +
168Q THR* 4.8 2.9 - - - -
169Q GLU* 2.8 59.4 + - + +
170Q TYR* 3.6 27.6 - + - -
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Residues in contact with VAL 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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98Q LEU* 5.6 0.2 - - + -
147Q LEU* 4.0 20.9 - - + +
150Q LEU* 3.6 30.3 - - + -
151Q HIS* 4.3 13.0 - - + +
162Q LEU* 2.9 30.2 + - + +
163Q ALA* 3.7 6.1 - - - +
165Q PHE* 1.3 82.6 - - + +
167Q GLU* 1.3 62.9 + - - +
170Q TYR* 3.0 33.0 + - + +
171Q LEU* 3.0 30.6 + - + -
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Residues in contact with GLU 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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160J VAL* 4.1 6.7 - - + +
161J GLN* 5.8 0.2 + - - -
164J ASP* 3.5 33.7 - - + +
167J GLU* 5.7 0.4 - - - -
167N GLU* 3.8 3.5 - - - +
361N CA 4.3 0.5 - - - -
151Q HIS* 2.7 31.6 + - + +
163Q ALA* 3.0 20.4 + - - +
164Q ASP* 3.3 11.4 + - - +
166Q VAL* 1.3 79.9 - - - +
168Q THR* 1.3 63.2 + - - +
171Q LEU* 3.5 28.0 + - + +
172Q GLY* 3.8 9.9 + - - -
363Q CA 2.5 28.8 - - - -
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Residues in contact with THR 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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164J ASP* 4.9 4.3 + - - -
164Q ASP* 2.8 34.5 + - - -
165Q PHE* 4.2 2.2 - - - -
167Q GLU* 1.3 78.6 - - - +
169Q GLU* 1.3 78.0 + - - +
173Q GLU* 3.5 1.7 - - - +
215Q CA 2.6 27.0 - - - -
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Residues in contact with GLU 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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94Q HIS* 5.7 2.9 + - - -
97Q LYS* 2.7 37.0 + - + +
165Q PHE* 2.8 41.1 + - + +
168Q THR* 1.3 96.0 - - - +
170Q TYR* 1.3 81.4 + - + +
173Q GLU* 3.3 22.9 - - - +
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Residues in contact with TYR 170 (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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56Q GLU* 4.2 6.5 - - - -
94Q HIS* 2.7 55.5 + + + -
97Q LYS* 3.3 21.2 - - + +
98Q LEU* 3.3 24.2 + - + +
147Q LEU* 3.8 34.2 - - + +
165Q PHE* 3.6 33.9 - + - -
166Q VAL* 3.0 19.1 + - + +
168Q THR 3.6 0.4 - - - -
169Q GLU* 1.3 95.2 - - + +
171Q LEU* 1.3 58.7 + - - +
172Q GLY 3.5 2.2 - - - -
173Q GLU* 3.4 5.7 + - - +
174Q GLN* 2.9 32.0 + - - +
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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