Contacts of the helix formed by residues 159 - 170 (chain R) in PDB entry 3A9Q
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 R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40R LYS 3.4 11.9 - - - +
41R TYR* 3.4 13.7 - - - -
42R VAL 4.9 0.2 + - - -
45R SER* 4.1 14.4 + - - +
105R ARG* 2.9 44.0 + - - -
154R ALA* 2.8 19.4 + - + +
155R THR* 5.8 0.2 - - - -
157R ASN* 3.3 4.3 + - + +
158R GLY* 1.3 69.3 - - - +
160R VAL* 1.3 62.8 + - - +
161R GLN* 3.4 3.8 + - - +
162R LEU* 3.0 20.7 + - + +
163R ALA* 3.1 23.0 + - - +
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Residues in contact with VAL 160 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158R GLY 3.2 10.9 + - - +
159R ASP* 1.3 72.9 + - - +
161R GLN* 1.3 62.1 + - - +
163R ALA* 3.4 6.0 + - - +
164R ASP* 3.1 20.4 + - - +
148S LEU* 4.5 14.7 - - + +
151S HIS* 3.3 46.0 - - + +
167S GLU* 3.9 9.0 - - + +
171S LEU* 3.5 22.9 - - + -
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Residues in contact with GLN 161 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101R TYR* 2.5 40.4 + - - -
105R ARG* 3.9 8.9 + - - +
159R ASP* 3.4 2.6 + - - +
160R VAL* 1.3 78.0 - - - +
162R LEU* 1.3 60.4 + - - +
164R ASP* 3.3 12.4 + - + +
165R PHE* 2.9 34.3 + - - +
148S LEU* 5.5 3.7 - - + +
171S LEU* 3.7 37.9 - - + +
172S GLY* 3.6 18.7 - - - +
175S VAL* 3.8 22.5 - - + +
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Residues in contact with LEU 162 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41R TYR* 4.4 3.8 - - + -
45R SER* 3.7 32.5 - - - +
49R VAL* 4.1 22.9 - - + -
101R TYR* 3.3 33.0 + - + +
105R ARG* 4.0 2.0 - - - +
150R LEU* 4.5 8.7 - - + -
153R VAL* 5.9 0.4 - - + -
154R ALA* 3.6 20.9 - - + +
159R ASP* 3.0 24.1 + - + +
161R GLN* 1.3 75.4 - - - +
163R ALA* 1.3 65.7 + - - +
165R PHE* 3.3 4.5 + - + +
166R VAL* 3.0 36.7 + - + +
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Residues in contact with ALA 163 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151R HIS* 3.4 25.3 - - + +
154R ALA* 3.7 14.7 - - + +
155R THR* 4.1 13.2 - - + +
159R ASP 3.1 17.0 + - - +
160R VAL* 3.7 6.1 - - - +
161R GLN 3.3 0.2 - - - -
162R LEU* 1.3 77.0 - - - +
164R ASP* 1.3 64.4 + - - +
166R VAL* 3.3 1.3 + - - -
167R GLU* 3.0 30.0 + - - +
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Residues in contact with ASP 164 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214C CA 4.1 1.4 - - - -
160R VAL 3.1 13.9 + - - +
161R GLN* 3.6 18.4 + - + +
162R LEU 3.2 0.2 - - - -
163R ALA* 1.3 74.7 - - - +
165R PHE* 1.3 58.8 + - - +
167R GLU* 3.3 6.8 + - - +
168R THR* 2.7 42.0 + - - +
213R CA 2.6 27.2 - - - -
167S GLU* 3.4 51.1 - - + +
168S THR* 4.4 4.8 + - - -
172S GLY* 6.0 0.3 - - - -
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Residues in contact with PHE 165 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97R LYS* 4.0 19.1 - - + -
98R LEU* 3.8 21.1 - - + -
101R TYR* 3.5 62.4 - + + -
104R LYS* 6.3 0.9 - - - -
161R GLN* 2.9 24.3 + - - +
162R LEU* 3.6 5.4 - - + +
164R ASP* 1.3 77.1 + - - +
166R VAL* 1.3 70.0 + - + +
168R THR* 4.7 2.7 - - - -
169R GLU* 2.8 62.4 + - + +
170R TYR* 3.8 21.1 - + - -
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Residues in contact with VAL 166 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147R LEU* 3.8 31.0 - - + +
150R LEU* 3.7 31.2 - - + -
151R HIS* 4.2 14.4 - - + +
162R LEU* 3.0 29.4 + - + +
163R ALA* 3.7 5.2 - - - +
164R ASP 3.3 0.2 - - - -
165R PHE* 1.3 83.3 - - + +
167R GLU* 1.3 62.8 + - - +
170R TYR* 3.0 25.1 + - + +
171R LEU* 3.2 21.9 + - + -
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Residues in contact with GLU 167 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160C VAL* 4.0 9.1 - - + +
164C ASP* 3.4 33.7 - - + +
214C CA 2.7 27.0 - - - -
151R HIS* 2.8 37.6 + - + +
163R ALA* 3.0 18.7 + - - +
164R ASP* 3.7 6.0 + - - +
166R VAL* 1.3 78.1 - - - +
168R THR* 1.3 65.2 + - - +
171R LEU* 3.4 32.0 + - + +
172R GLY 3.8 4.2 + - - -
213R CA 4.1 2.0 - - - -
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Residues in contact with THR 168 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164C ASP* 4.9 3.1 - - - -
164R ASP* 2.7 29.5 + - - +
165R PHE* 4.1 2.2 - - - -
167R GLU* 1.3 76.4 - - - +
169R GLU* 1.3 78.0 + - - +
170R TYR 5.3 0.2 - - - -
171R LEU 5.2 0.2 + - - -
172R GLY* 5.3 2.1 + - - -
213R CA 2.6 26.6 - - - -
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Residues in contact with GLU 169 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94R HIS* 6.1 0.5 - - - -
97R LYS* 2.7 44.6 + - + +
165R PHE* 2.8 44.7 + - + +
168R THR* 1.3 91.0 - - - +
170R TYR* 1.3 78.9 + - + +
173R ALA* 4.5 10.7 - - - +
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Residues in contact with TYR 170 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56R GLU* 4.2 6.1 - - - -
94R HIS* 2.7 55.1 + + + -
97R LYS* 3.4 13.8 - - + +
98R LEU* 3.2 30.8 + - + +
147R LEU* 3.7 35.4 - - + +
165R PHE* 3.8 28.5 - + - -
166R VAL* 3.0 22.8 + - + +
168R THR 3.5 0.2 - - - -
169R GLU* 1.3 94.1 - - + +
171R LEU* 1.3 60.6 + - - +
172R GLY 3.4 1.6 - - - -
173R ALA* 3.4 5.4 + - - +
174R 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