Contacts of the helix formed by residues 142 - 154 (chain B) in PDB entry 2AVN
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 142 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140B VAL 3.8 0.6 + - - -
141B ASP* 1.3 74.9 - - - +
143B PHE* 1.3 69.1 + - - +
144B TYR* 3.1 12.2 + - - -
145B THR* 3.0 27.4 + - - +
146B PHE* 3.2 14.5 + - - -
181B ALA* 3.8 2.5 - - - -
182B PHE 3.9 2.5 - - - -
233B TRP* 2.8 53.8 + - - +
235B ALA 2.8 24.5 + - - +
236B ASP 3.9 9.6 + - - +
237B HIS* 4.6 0.2 - - - -
238B ILE* 3.9 14.5 - - + +
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Residues in contact with PHE 143 (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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225A LEU* 5.7 1.6 - - + -
142B ASN* 1.3 72.3 + - - +
144B TYR* 1.3 87.4 + + + +
146B PHE* 3.2 5.0 + - - +
147B LEU* 2.9 38.9 + - + +
162B PHE* 3.5 42.0 - + - -
163B LEU* 3.9 29.6 - - + -
166B GLN* 3.7 27.1 - - + -
181B ALA* 3.5 16.4 - - - +
182B PHE 3.0 20.3 + - - +
183B LYS* 3.5 32.5 - - + -
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Residues in contact with TYR 144 (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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204A MSE 3.6 29.2 - - + +
225A LEU* 4.1 10.7 - - + +
228A ASP* 3.1 24.4 + - - -
231A ILE* 3.3 40.8 - - + +
234A LYS* 4.7 10.8 - - + -
142B ASN* 3.1 14.1 + - - +
143B PHE* 1.3 101.5 - + - +
145B THR* 1.3 57.5 + - - +
147B LEU* 3.9 6.4 - - + +
148B GLN* 3.1 26.5 + - - +
183B LYS* 3.9 17.4 - - + +
184B PRO* 4.1 22.4 - - + +
233B TRP* 3.8 23.6 - + - +
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Residues in contact with THR 145 (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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234A LYS* 6.2 0.4 - - - +
142B ASN* 3.0 15.5 + - - +
144B TYR* 1.3 77.2 - - - +
146B PHE* 1.3 69.9 + - + +
148B GLN* 3.4 6.1 + - - +
149B GLN* 3.1 46.2 + - - +
234B LYS 4.5 3.3 + - - -
235B ALA 2.8 26.3 + - - -
236B ASP* 3.8 29.6 - - - +
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Residues in contact with PHE 146 (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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141B ASP* 3.4 37.9 - - + -
142B ASN 3.2 10.6 + - - +
143B PHE 3.4 7.9 - - - +
145B THR* 1.3 83.3 - - + +
147B LEU* 1.3 59.7 + - - +
149B GLN* 3.2 19.9 + - - +
150B MSE 2.8 37.8 + - + +
162B PHE* 3.5 16.6 - + + -
168B THR* 3.6 31.6 - - + -
170B VAL* 4.2 13.9 - - + -
179B SER* 3.9 16.6 - - - -
181B ALA* 3.7 16.8 - - + -
236B ASP 6.2 0.2 - - - -
237B HIS* 6.2 0.2 - + - -
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Residues in contact with LEU 147 (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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204A MSE 4.1 27.1 - - + -
221A LEU* 4.9 4.5 - - + -
225A LEU* 4.5 11.0 - - + -
143B PHE* 2.9 27.9 + - + +
144B TYR* 3.9 7.6 - - + +
146B PHE* 1.3 77.6 - - - +
148B GLN* 1.3 56.9 + - - +
150B MSE 3.3 5.1 + - + +
151B ILE* 2.9 46.3 + - + +
159B ILE* 3.8 30.7 - - + -
162B PHE* 4.0 16.5 - - + -
163B LEU* 3.8 26.2 - - + -
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Residues in contact with GLN 148 (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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204A MSE 3.5 8.1 - - - -
205A GLU* 2.7 55.2 + - - +
234A LYS* 3.2 22.7 + - - +
144B TYR 3.1 19.1 + - - +
145B THR* 3.8 6.7 - - - +
146B PHE 3.3 0.2 - - - -
147B LEU* 1.3 76.0 - - - +
149B GLN* 1.3 63.5 - - + +
151B ILE* 3.5 9.5 + - - +
152B GLU* 3.2 34.2 + - + +
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Residues in contact with GLN 149 (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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145B THR* 3.1 32.7 + - - +
146B PHE* 3.2 26.8 + - - +
148B GLN* 1.3 79.1 - - + +
150B MSE 1.3 62.9 + - + +
152B GLU* 3.2 18.0 + - - +
153B LYS* 3.4 19.8 + - + +
236B ASP* 4.8 4.9 + - - -
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Residues in contact with MSE 150 (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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210A ARG* 3.7 0.2 + - - -
146B PHE* 2.8 22.1 + - + +
147B LEU* 3.6 5.8 - - - +
149B GLN* 1.3 75.3 - - + +
151B ILE* 1.3 61.8 + - - +
153B LYS 3.0 0.2 + - - -
154B ASP* 2.8 62.7 + - - +
158B GLN* 3.4 41.5 - - + +
159B ILE* 3.7 16.5 - - + +
162B PHE* 3.6 39.0 - - + -
168B THR* 4.4 18.4 - - + +
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Residues in contact with ILE 151 (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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204A MSE 3.9 19.3 - - + -
205A GLU 3.3 22.7 - - - +
206A TYR* 3.5 42.0 - - + +
207A PRO* 3.9 5.3 - - + +
210A ARG* 2.7 32.1 + - - +
221A LEU* 4.6 4.7 - - + -
147B LEU* 2.9 40.5 + - + +
148B GLN* 3.7 8.5 - - - +
150B MSE 1.3 75.4 - - - +
152B GLU* 1.3 57.9 + - - +
156B TRP* 4.3 7.9 - - + -
159B ILE* 3.8 14.4 - - + -
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Residues in contact with GLU 152 (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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205A GLU* 3.9 13.3 - - - +
206A TYR 5.5 0.2 - - - -
207A PRO* 3.7 26.9 - - - +
210A ARG* 4.5 4.7 + - - -
148B GLN* 3.2 36.4 + - + +
149B GLN* 3.2 10.5 + - - +
150B MSE 3.1 1.0 - - - -
151B ILE* 1.3 79.1 - - - +
153B LYS* 1.3 64.3 + - + +
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Residues in contact with LYS 153 (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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210A ARG* 4.7 1.3 - - - -
149B GLN* 3.4 16.6 + - + +
150B MSE 3.0 0.8 + - - -
152B GLU* 1.3 86.9 - - + +
154B ASP* 1.3 74.8 + - - +
155B ALA 4.2 0.2 + - - -
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Residues in contact with ASP 154 (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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210A ARG* 2.7 33.9 + - - -
150B MSE 2.8 60.8 + - + +
153B LYS* 1.3 86.8 - - - +
155B ALA* 1.3 62.7 + - - +
158B GLN* 4.4 6.7 - - + +
159B ILE* 4.1 1.9 - - + +
168B THR* 5.3 1.6 + - - -
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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