Contacts of the helix formed by residues 149 - 163 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B VAL* 3.9 3.6 - - - -
148B TRP* 1.3 108.6 - - + +
150B SER* 1.3 63.4 + - - +
151B GLU* 2.7 41.4 + - - +
152B ASP* 3.1 17.8 + - - +
153B ALA* 3.0 21.7 + - - +
180B PHE* 3.5 40.3 - - + +
199B LYS* 5.2 2.4 - - - +
201B GLU* 3.3 16.2 + - - -
239B ARG* 5.4 0.2 - - - +
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Residues in contact with SER 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B VAL* 2.7 41.9 + - - -
4B THR 3.3 14.6 + - - -
5B VAL* 3.4 10.9 + - - +
8B ALA* 3.3 17.3 - - - +
149B ASN* 1.3 72.4 - - - +
151B GLU* 1.3 63.9 + - - +
153B ALA* 3.1 10.5 + - - -
154B LYS* 3.1 12.6 + - - +
180B PHE* 3.6 20.3 - - - -
182B PHE* 3.9 5.3 - - - -
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Residues in contact with GLU 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B ASN* 2.7 19.3 + - - +
150B SER* 1.3 78.2 - - - +
152B ASP* 1.3 60.4 + - - +
154B LYS* 3.5 0.3 + - - -
155B GLY 3.2 14.7 + - - -
180B PHE* 5.3 0.6 - - + +
181B GLU 4.9 2.0 - - - +
182B PHE* 3.9 13.8 - - + -
183B PRO* 3.0 32.3 - - + +
186B ALA* 4.3 8.7 - - + -
191B PHE* 3.3 35.8 - - + -
193B ILE* 3.4 2.7 - - + +
199B LYS* 3.8 23.6 + - - -
239B ARG* 3.9 13.2 + - - -
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Residues in contact with ASP 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B PRO* 3.8 8.6 - - + +
148B TRP* 2.7 35.3 + - - +
149B ASN* 3.1 25.9 + - - +
151B GLU* 1.3 78.2 - - - +
153B ALA* 1.3 64.3 + - - +
155B GLY* 3.2 0.5 + - - -
156B LEU* 2.9 32.0 + - + +
193B ILE* 3.6 9.2 - - - -
201B GLU* 4.0 0.7 - - - +
237B ASN* 2.9 19.6 - - - +
239B ARG* 2.8 39.8 + - - +
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Residues in contact with ALA 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B VAL* 3.8 16.6 - - + -
8B ALA* 4.4 2.5 - - + -
9B ILE* 3.7 29.6 - - + +
147B PRO* 3.8 19.3 - - + -
149B ASN 3.0 9.6 + - - +
150B SER* 3.1 7.6 + - - +
152B ASP* 1.3 80.2 - - - +
154B LYS* 1.3 60.4 + - - +
156B LEU* 5.2 0.4 - - - -
157B ILE* 3.2 27.1 + - - +
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Residues in contact with LYS 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ALA* 3.3 29.8 - - + +
11B GLN* 2.9 25.7 + - + +
12B GLY* 4.2 3.1 - - - -
15B GLU* 2.8 41.7 + - - -
150B SER 3.1 13.9 + - - +
151B GLU 4.3 1.8 - - - +
153B ALA* 1.3 75.8 - - - +
155B GLY* 1.3 65.8 + - - +
157B ILE* 3.1 18.2 - - - +
158B LYS* 3.1 20.7 + - + +
182B PHE* 3.9 11.9 - - + -
186B ALA 2.9 27.0 + - - +
187B GLN* 3.3 12.3 + - - +
188B SER 3.6 4.6 + - - -
191B PHE* 4.4 5.8 - - + -
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Residues in contact with GLY 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B GLU 3.2 9.5 + - - -
152B ASP 3.7 1.8 - - - -
154B LYS* 1.3 78.4 - - - +
156B LEU* 1.3 56.5 + - - +
158B LYS* 3.3 3.3 + - - +
159B SER* 2.9 24.4 + - - -
191B PHE* 3.7 18.7 - - - -
192B LEU* 4.3 2.5 - - - -
193B ILE* 3.4 32.7 + - - -
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Residues in contact with LEU 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B VAL* 3.9 45.6 - - + +
147B PRO* 4.0 26.0 - - + -
152B ASP* 2.9 24.4 + - + +
153B ALA* 4.7 1.6 - - - +
155B GLY* 1.3 72.0 - - - +
157B ILE* 1.3 62.3 + - - +
159B SER* 3.9 3.4 - - - -
160B ALA* 3.0 30.0 + - - +
169B VAL* 5.0 2.2 - - + +
193B ILE* 3.5 33.0 - - + +
194B PRO 4.7 0.4 - - - +
195B ILE* 4.5 11.9 - - + +
239B ARG* 4.1 16.4 - - + +
240B THR* 4.7 3.6 - - - +
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Residues in contact with ILE 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ILE* 4.3 15.3 - - + +
12B GLY* 4.1 19.7 - - - -
13B MET* 4.6 7.9 - - + -
77B ILE* 5.5 1.6 - - + -
113B VAL* 4.6 8.5 - - + -
115B ARG* 3.8 29.6 - - + -
153B ALA 3.2 17.1 + - - +
154B LYS* 3.1 17.3 - - - +
156B LEU* 1.3 78.0 - - - +
158B LYS* 1.3 67.7 + - + +
160B ALA* 4.1 1.2 - - - +
161B ILE* 3.2 35.8 + - + +
169B VAL* 4.3 27.2 - - + +
171B GLU* 4.4 3.6 - - - +
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Residues in contact with LYS 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B GLY* 3.9 16.4 - - - +
15B GLU* 2.8 39.3 + - - +
16B GLU* 2.8 37.2 + - - +
154B LYS* 3.1 31.7 + - + +
155B GLY 3.8 1.3 - - - +
157B ILE* 1.3 77.3 - - - +
159B SER* 1.3 67.7 + - - +
161B ILE* 3.1 3.1 + - - +
162B ARG* 2.9 31.9 + - - +
189B LYS 3.4 24.5 + - - -
190B ASP 4.6 0.2 - - - -
191B PHE* 3.0 26.7 - - - +
192B LEU* 3.7 12.3 - - + -
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Residues in contact with SER 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B GLY 2.9 12.2 + - - -
156B LEU* 3.9 4.5 - - - -
158B LYS* 1.3 75.1 - - - +
160B ALA* 1.3 51.6 + - - +
162B ARG* 3.3 6.2 + - - +
163B ASP* 2.7 35.2 + - - +
192B LEU* 4.0 16.5 - - - +
193B ILE 2.8 36.9 + - - -
194B PRO* 4.0 5.2 - - - +
195B ILE* 4.1 15.1 + - - +
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Residues in contact with ALA 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B VAL* 3.3 14.6 - - + +
145B VAL* 5.6 0.7 - - + -
156B LEU 3.0 19.0 + - - +
157B ILE 4.1 3.4 - - - +
159B SER* 1.3 72.6 - - - +
161B ILE* 1.3 67.1 + - - +
163B ASP* 3.1 16.0 + - - +
167B VAL* 3.4 32.6 - - + +
169B VAL* 4.3 9.0 - - + -
195B ILE* 4.3 6.0 - - + +
1003B K 2.9 14.9 - - - -
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Residues in contact with ILE 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B GLY 4.7 0.4 - - - +
13B MET* 4.5 7.0 - - - -
16B GLU* 3.6 41.5 - - + +
19B ARG* 5.8 0.2 - - - +
23B VAL* 4.0 24.2 - - + -
75B ARG* 3.3 18.9 + - - +
77B ILE* 3.4 35.7 - - + -
113B VAL* 3.9 12.6 - - + -
157B ILE* 3.2 32.3 + - + +
158B LYS 3.1 5.6 + - - +
160B ALA* 1.3 74.2 - - - +
162B ARG* 1.3 62.5 + - + +
163B ASP 3.1 1.4 - - - +
1003B K 2.9 17.8 - - - -
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Residues in contact with ARG 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B GLU* 2.5 41.8 + - - +
19B ARG* 3.4 47.6 - - - +
75B ARG* 3.4 10.5 + - - +
158B LYS* 2.9 32.0 + - - +
159B SER* 3.4 5.4 - - - +
161B ILE* 1.3 79.7 - - + +
163B ASP* 1.3 60.5 + - - +
164B ASN* 3.8 5.2 + - - +
189B LYS 4.6 4.4 + - - -
190B ASP* 5.1 11.5 + - - +
192B LEU* 4.0 34.5 - - + +
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Residues in contact with ASP 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A ASP* 4.0 4.9 - - - +
75B ARG* 3.0 8.5 + - - -
143B LYS* 2.8 26.6 + - - +
159B SER 2.7 20.0 + - - +
160B ALA* 3.1 15.1 + - - +
162B ARG* 1.3 75.2 - - - +
164B ASN* 1.3 68.6 + - - +
165B ASN* 2.7 32.8 + - - +
167B VAL* 4.0 12.4 - - + +
195B ILE* 4.6 7.1 - - + +
1003B K 2.6 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