Contacts of the helix formed by residues 149 - 163 (chain R) 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 R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5R VAL* 3.8 3.4 - - - -
148R TRP* 1.3 108.5 - - + +
150R SER* 1.3 62.8 + - - +
151R GLU* 2.8 27.0 + - - +
152R ASP* 3.0 17.4 + - - +
153R ALA* 3.3 19.6 + - - +
180R PHE* 3.5 40.6 - - + +
199R LYS* 5.2 2.6 - - - +
201R GLU* 3.2 18.0 + - - -
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Residues in contact with SER 150 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3R VAL* 2.8 43.2 + - - -
4R THR 3.2 15.6 - - - -
5R VAL* 3.2 8.8 + - - +
8R ALA* 3.3 16.6 - - - +
149R ASN* 1.3 72.5 + - - +
151R GLU* 1.3 69.0 + - - +
153R ALA* 3.1 10.0 + - - -
154R LYS* 3.1 10.9 + - - +
180R PHE* 3.4 21.1 - - - -
182R PHE* 4.0 3.6 - - - -
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Residues in contact with GLU 151 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149R ASN* 2.8 16.9 + - - +
150R SER* 1.3 78.1 - - - +
152R ASP* 1.3 64.3 + - - +
154R LYS* 3.3 0.3 + - - -
155R GLY 3.3 15.4 + - - -
180R PHE* 5.2 1.2 - - + +
181R GLU 4.5 2.1 - - - +
182R PHE* 3.7 14.0 - - + -
183R PRO* 2.8 34.2 - - - +
185R GLU* 6.4 0.2 - - - -
186R ALA* 4.1 10.8 - - + -
191R PHE* 3.5 33.8 - - + -
193R ILE* 3.5 2.5 - - + +
199R LYS* 4.3 21.7 + - - -
239R ARG* 4.5 7.4 + - - -
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Residues in contact with ASP 152 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147R PRO* 3.7 7.7 - - + +
148R TRP* 2.8 31.9 + - - +
149R ASN* 3.0 28.1 + - - +
151R GLU* 1.3 75.6 - - - +
153R ALA* 1.3 59.1 + - - +
156R LEU* 2.9 38.3 + - + +
193R ILE* 3.6 9.2 - - - +
201R GLU* 4.1 0.9 - - - +
237R ASN* 2.8 23.6 + - - +
239R ARG* 2.9 35.8 + - - -
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Residues in contact with ALA 153 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5R VAL* 3.7 22.4 - - + +
8R ALA* 4.7 0.2 - - + -
9R ILE* 3.7 28.0 - - + +
147R PRO* 3.8 21.1 - - + -
149R ASN 3.3 4.0 + - - +
150R SER* 3.1 8.9 + - - +
152R ASP* 1.3 80.5 - - - +
154R LYS* 1.3 60.8 + - - +
156R LEU* 5.0 0.4 - - - -
157R ILE* 3.2 27.3 + - - +
169R VAL* 6.1 0.2 - - - +
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Residues in contact with LYS 154 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8R ALA* 3.4 29.3 - - + +
11R GLN* 2.8 27.5 + - + +
12R GLY* 4.4 3.6 - - - +
15R GLU* 2.8 43.6 + - - -
150R SER 3.1 14.5 + - - +
151R GLU 4.1 2.2 - - - +
152R ASP 3.2 0.2 - - - -
153R ALA* 1.3 77.7 - - - +
155R GLY* 1.3 63.4 + - - +
157R ILE* 3.4 3.6 - - - +
158R LYS* 3.1 33.8 + - + +
182R PHE* 3.9 14.4 - - + -
186R ALA 3.3 20.2 + - - +
187R GLN* 3.3 14.6 + - - +
188R SER 4.1 4.3 - - - -
191R PHE* 4.4 6.1 - - + -
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Residues in contact with GLY 155 (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 GLU 3.3 8.7 + - - -
152R ASP 3.9 0.2 - - - -
154R LYS* 1.3 76.7 - - - +
156R LEU* 1.3 59.2 + - - +
158R LYS* 3.2 2.3 + - - +
159R SER* 2.8 30.3 + - - -
191R PHE* 3.8 16.9 - - - -
192R LEU* 4.3 3.1 - - - -
193R ILE* 3.5 30.9 + - - -
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Residues in contact with LEU 156 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145R VAL* 4.0 35.3 - - + +
147R PRO* 3.8 29.4 - - + -
152R ASP* 2.9 26.7 + - + +
153R ALA* 4.7 2.0 - - - +
155R GLY* 1.3 75.3 - - - +
157R ILE* 1.3 63.4 + - - +
159R SER* 3.9 3.3 - - - -
160R ALA* 3.1 25.1 + - - +
169R VAL* 5.0 3.1 - - + +
193R ILE* 3.7 31.2 - - + +
194R PRO 4.7 2.7 - - - +
195R ILE* 4.4 8.7 - - + +
239R ARG* 4.1 23.8 - - + +
240R THR* 4.7 4.9 - - - +
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Residues in contact with ILE 157 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9R ILE* 4.5 15.3 - - + +
12R GLY* 4.2 21.8 - - - -
13R MET* 4.6 9.2 - - + -
77R ILE* 5.2 2.0 - - + -
113R VAL* 4.3 11.0 - - + -
115R ARG* 3.8 29.4 - - - +
153R ALA 3.2 20.4 + - - +
154R LYS* 3.4 8.7 - - - +
156R LEU* 1.3 80.5 - - - +
158R LYS* 1.3 64.0 + - - +
160R ALA* 4.0 1.4 - - - +
161R ILE* 3.2 35.8 + - + +
169R VAL* 3.9 30.1 - - + +
171R GLU* 4.7 1.8 - - - +
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Residues in contact with LYS 158 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12R GLY* 4.0 13.8 + - - +
15R GLU* 2.8 42.1 + - - +
16R GLU* 2.8 36.0 + - - +
154R LYS* 3.1 33.2 + - + +
155R GLY 3.7 2.0 - - - +
157R ILE* 1.3 73.6 - - - +
159R SER* 1.3 65.8 + - - +
160R ALA 3.2 0.2 + - - -
161R ILE* 3.3 2.4 + - - +
162R ARG* 2.9 29.9 + - - +
189R LYS 3.3 22.1 + - - -
191R PHE 3.1 24.7 - - - +
192R LEU* 3.6 15.3 - - + -
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Residues in contact with SER 159 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155R GLY 2.8 14.6 + - - -
156R LEU* 3.9 4.5 - - - -
158R LYS* 1.3 72.1 - - - +
160R ALA* 1.3 53.0 + - - +
162R ARG* 3.3 5.7 - - - +
163R ASP* 2.5 36.5 + - - +
192R LEU* 4.1 13.4 - - - +
193R ILE 2.8 36.5 + - - -
194R PRO* 4.0 5.2 - - - +
195R ILE* 4.0 18.7 - - - +
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Residues in contact with ALA 160 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113R VAL* 3.1 20.7 - - + +
145R VAL* 5.8 0.4 - - + -
156R LEU 3.1 18.7 + - - +
157R ILE 4.0 3.6 - - - +
159R SER* 1.3 73.9 - - - +
161R ILE* 1.3 57.2 + - - +
163R ASP* 3.1 8.6 + - - +
167R VAL* 3.6 37.7 - - + +
169R VAL* 4.3 5.8 - - + -
195R ILE* 4.3 3.5 - - + +
1001R K 2.7 27.2 - - - -
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Residues in contact with ILE 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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12R GLY 4.8 0.2 - - - +
13R MET* 4.5 7.0 - - - -
16R GLU* 3.5 39.3 - - + +
19R ARG* 5.7 0.9 - - - +
23R VAL* 3.8 28.9 - - + -
75R ARG* 3.2 19.1 + - + +
77R ILE* 3.3 35.7 - - + -
113R VAL* 4.0 11.0 - - + -
157R ILE* 3.2 28.2 + - + +
158R LYS 3.3 4.1 + - - +
160R ALA* 1.3 75.7 - - - +
162R ARG* 1.3 65.2 + - - +
163R ASP 3.1 10.2 - - - +
1001R K 3.2 4.8 - - - -
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Residues in contact with ARG 162 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16R GLU* 2.4 48.9 + - - -
19R ARG* 3.4 45.6 - - - +
75R ARG* 3.6 8.8 + - - +
158R LYS* 2.9 23.8 + - - +
159R SER* 3.3 6.1 - - - +
161R ILE* 1.3 79.9 - - - +
163R ASP* 1.3 61.4 + - - +
164R ASN* 4.4 3.8 + - - +
189R LYS 4.4 10.5 + - - -
190R ASP* 4.7 9.9 + - - +
192R LEU* 3.6 38.5 - - + +
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Residues in contact with ASP 163 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343Q ASP* 3.8 5.8 - - - +
75R ARG* 2.9 13.5 + - - -
143R LYS* 2.7 29.4 + - - +
159R SER 2.5 21.0 + - - +
160R ALA* 3.1 9.5 + - - +
162R ARG* 1.3 73.7 - - - +
164R ASN* 1.3 58.7 + - - +
165R ASN* 2.6 46.7 + - - +
167R VAL* 4.1 16.3 - - + +
195R ILE* 4.7 7.8 - - + +
1001R K 2.7 21.4 - - - -
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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
------------------------------------------------------------
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