Contacts of the helix formed by residues 149 - 163 (chain V) in PDB entry 3EXG
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 ASN 149 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5V VAL* 3.8 5.4 - - - -
148V TRP* 1.3 98.7 - - + +
150V SER* 1.3 63.1 + - - +
151V GLU* 2.9 19.5 + - - +
152V ASP* 2.8 39.5 + - - -
153V ALA* 2.8 20.5 + - - +
180V PHE* 3.6 38.4 - - + -
199V LYS* 5.8 0.2 - - - +
201V GLU* 3.5 8.3 + - - -
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Residues in contact with SER 150 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3V VAL* 2.6 36.3 + - - +
4V THR 3.4 2.3 - - - -
5V VAL* 3.3 23.3 + - - +
8V ALA* 3.6 19.1 - - - +
149V ASN* 1.3 72.2 - - - +
151V GLU* 1.3 66.3 + - - -
153V ALA* 3.1 3.1 + - - +
154V LYS* 2.9 23.4 + - - +
180V PHE* 3.8 15.4 - - - -
182V PHE* 3.8 8.5 - - - -
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Residues in contact with GLU 151 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149V ASN* 2.9 18.6 + - - +
150V SER* 1.3 75.2 - - - +
152V ASP* 1.3 63.6 + - - +
154V LYS* 4.2 0.2 - - - -
155V GLY 3.1 18.5 + - - -
180V PHE* 5.5 0.6 - - - +
181V GLU 5.9 0.9 - - - +
182V PHE* 3.6 15.6 - - + -
183V PRO* 3.2 34.9 - - + +
186V ALA* 4.8 1.6 - - - +
191V PHE* 3.3 32.8 - - + -
193V ILE* 3.5 8.9 - - + +
199V LYS* 3.2 27.7 + - - -
239V ARG* 4.7 0.3 + - - -
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Residues in contact with ASP 152 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147V PRO* 3.8 18.8 - - + -
148V TRP* 3.4 6.2 + - - +
149V ASN* 2.8 49.9 + - - +
151V GLU* 1.3 75.2 - - - +
153V ALA* 1.3 64.8 + - - +
155V GLY* 3.7 0.2 - - - -
156V LEU* 2.9 31.9 + - + +
193V ILE* 3.7 8.5 - - - -
201V GLU* 4.0 2.8 - - - +
237V ASN* 3.0 22.6 - - - +
239V ARG* 3.2 31.3 + - + +
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Residues in contact with ALA 153 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5V VAL* 3.8 28.3 - - + +
8V ALA* 4.7 0.7 - - + -
9V ILE* 3.9 17.4 - - + +
147V PRO* 3.6 21.4 - - + +
148V TRP 5.8 0.2 - - - -
149V ASN 2.8 16.1 + - - +
150V SER* 3.5 8.3 - - - +
152V ASP* 1.3 72.4 - - - +
154V LYS* 1.3 62.3 + - - +
156V LEU* 4.4 0.6 - - - +
157V ILE* 3.1 28.3 + - - +
169V VAL* 5.9 0.9 - - - +
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Residues in contact with LYS 154 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8V ALA* 3.2 30.6 + - + +
11V GLN* 3.2 18.1 + - + -
12V GLY 3.8 7.9 - - - +
15V GLU* 2.9 41.0 + - - -
150V SER 2.9 16.4 + - - +
151V GLU 4.4 1.1 - - - +
153V ALA* 1.3 75.1 - - - +
155V GLY* 1.3 62.8 + - - +
157V ILE* 3.2 16.6 - - - +
158V LYS* 3.3 22.1 + - + +
182V PHE* 3.7 19.3 - - + -
186V ALA 3.0 23.8 + - - +
187V GLN* 3.4 9.7 + - - +
188V SER 3.4 5.0 + - - -
191V PHE* 4.6 6.1 - - + -
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Residues in contact with GLY 155 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151V GLU 3.1 10.7 + - - -
154V LYS* 1.3 78.3 - - - +
156V LEU* 1.3 55.7 + - - +
158V LYS* 3.2 3.5 + - - +
159V SER* 2.9 25.5 + - - -
191V PHE* 3.7 19.8 - - - -
192V LEU* 4.2 0.3 - - - -
193V ILE* 3.5 36.0 + - - -
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Residues in contact with LEU 156 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145V VAL* 4.1 29.8 - - + +
147V PRO* 4.1 23.1 - - + -
152V ASP* 2.9 24.1 + - - +
153V ALA 4.4 0.7 - - - +
155V GLY* 1.3 68.4 - - - -
157V ILE* 1.3 60.5 + - - +
159V SER* 3.4 3.0 + - - -
160V ALA* 2.9 30.6 + - - +
169V VAL* 5.0 2.6 - - + +
193V ILE* 3.4 38.8 - - + +
194V PRO 4.9 0.7 - - - +
195V ILE* 4.8 12.2 - - + +
239V ARG* 4.0 40.8 - - + +
240V THR* 5.2 0.9 - - - +
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Residues in contact with ILE 157 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9V ILE* 4.5 15.5 - - + +
12V GLY* 4.3 12.1 - - - -
13V MET* 4.6 10.5 - - + -
77V ILE* 5.5 0.9 - - + -
113V VAL* 4.4 8.5 - - + -
115V ARG* 3.6 32.3 - - + -
153V ALA 3.1 17.8 + - - +
154V LYS* 3.2 17.9 - - - +
156V LEU* 1.3 79.0 - - - +
158V LYS* 1.3 70.3 + - + +
160V ALA* 3.5 1.5 + - + -
161V ILE* 3.1 40.0 + - + +
169V VAL* 4.0 29.0 - - + +
171V GLU* 4.9 1.6 - - - +
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Residues in contact with LYS 158 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12V GLY* 3.7 18.4 - - - +
15V GLU* 2.8 40.1 + - - +
16V GLU* 2.7 34.1 + - + +
154V LYS* 3.3 28.9 - - + +
155V GLY 3.2 3.3 + - - +
157V ILE* 1.3 80.2 - - - +
159V SER* 1.3 66.4 + - - +
160V ALA 2.9 1.7 + - - -
161V ILE* 3.0 5.2 + - - +
162V ARG* 3.0 26.7 + - - +
189V LYS 3.3 23.5 + - - -
191V PHE 3.2 22.2 - - - +
192V LEU* 3.7 14.4 - - + -
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Residues in contact with SER 159 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155V GLY 2.9 10.4 + - - -
156V LEU 3.7 4.7 - - - -
158V LYS* 1.3 75.7 - - - +
160V ALA* 1.3 54.8 - - - -
162V ARG* 3.8 6.7 - - - +
163V ASP* 3.1 27.4 + - - +
192V LEU* 3.9 18.5 - - - +
193V ILE 3.0 30.8 + - - -
194V PRO* 4.1 5.5 - - - +
195V ILE* 3.8 20.1 + - - +
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Residues in contact with ALA 160 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113V VAL* 3.2 21.6 - - + +
145V VAL* 5.4 0.2 - - + -
156V LEU 2.9 20.6 + - - +
157V ILE* 3.7 6.1 - - - +
158V LYS 2.9 0.4 + - - -
159V SER* 1.3 71.2 - - - +
161V ILE* 1.3 63.1 + - - +
162V ARG 3.4 0.2 + - - -
163V ASP* 3.5 9.7 + - - +
167V VAL* 4.0 18.4 - - + +
169V VAL* 3.9 22.4 - - + -
195V ILE* 4.2 3.1 - - + +
1004V K 2.8 19.6 - - - -
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Residues in contact with ILE 161 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13V MET* 4.7 7.4 - - - -
16V GLU* 3.7 34.8 - - + +
19V ARG* 5.9 1.3 - - - +
23V VAL* 4.0 30.3 - - + -
75V ARG* 3.4 18.2 + - + +
77V ILE* 3.7 30.7 - - + -
113V VAL* 4.1 8.5 - - + -
157V ILE* 3.1 30.7 - - + +
158V LYS 3.0 5.3 + - - +
160V ALA* 1.3 74.5 - - - +
162V ARG* 1.3 65.7 + - - +
163V ASP 3.0 10.7 - - - +
1004V K 3.1 8.8 - - - -
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Residues in contact with ARG 162 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16V GLU* 2.4 49.0 + - - +
19V ARG* 3.6 46.8 - - - +
75V ARG* 3.3 11.8 + - - +
158V LYS* 3.0 25.7 + - - +
159V SER* 4.1 6.7 - - - +
160V ALA 3.2 0.2 - - - -
161V ILE* 1.3 79.7 - - + +
163V ASP* 1.3 62.4 + - - +
164V ASN* 4.4 4.3 + - - -
189V LYS 4.4 5.3 + - - -
190V ASP* 4.8 12.9 + - - +
192V LEU* 4.0 34.0 - - + +
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Residues in contact with ASP 163 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343U ASP* 4.3 3.6 - - - +
75V ARG* 3.0 17.0 + - - -
111V PRO* 4.4 0.2 - - - +
143V LYS* 2.6 39.5 + - - +
159V SER 3.1 18.6 + - - +
160V ALA 3.5 9.9 - - - +
161V ILE 3.0 6.3 - - - +
162V ARG* 1.3 76.7 - - - +
164V ASN* 1.3 60.9 + - - +
165V ASN* 2.6 45.9 + - - +
167V VAL* 4.2 7.2 - - + -
195V ILE* 4.3 5.4 - - + +
1004V K 3.0 8.4 - - - -
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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
------------------------------------------------------------
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