Contacts of the helix formed by residues 214 - 227 (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 ARG 214 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154A ASP* 5.0 5.9 + - - -
156A TRP* 3.0 66.1 - - - +
157A ASP* 5.5 3.0 + - - -
210B ARG* 2.9 19.9 + - - +
211B ILE 3.7 2.5 - - - -
213B GLU* 1.3 87.5 - - + +
215B GLU* 1.3 59.5 + - - +
216B GLU 3.4 2.9 + - - -
217B THR* 3.5 18.1 + - - +
218B ILE* 2.9 33.0 + - + +
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Residues in contact with GLU 215 (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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26B LYS* 5.2 1.5 - - + +
27B LEU* 4.1 20.4 + - + +
30B ARG* 2.8 43.3 + - - +
211B ILE* 3.1 28.3 - - + +
212B SER* 4.1 8.7 + - - +
213B GLU 3.7 1.8 + - - -
214B ARG* 1.3 76.8 - - - +
216B GLU* 1.3 55.7 + - - +
218B ILE* 3.7 3.0 - - - +
219B PHE* 2.8 35.9 + - - +
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Residues in contact with GLU 216 (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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30B ARG* 3.0 34.0 + - - +
214B ARG 3.4 0.4 - - - -
215B GLU* 1.3 77.4 + - - +
217B THR* 1.3 67.9 + - - +
219B PHE* 3.2 3.5 + - - +
220B ARG* 2.8 67.4 + - + +
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Residues in contact with THR 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A TRP* 3.8 31.9 - - + -
214B ARG* 3.6 22.3 + - + +
216B GLU* 1.3 78.9 - - - +
218B ILE* 1.3 59.9 - - - +
220B ARG* 3.9 4.6 - - - +
221B LEU* 3.1 23.5 + - + +
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Residues in contact with ILE 218 (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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156A TRP* 3.7 30.7 - - + -
27B LEU* 3.7 20.6 - - + -
206B TYR* 3.5 46.4 - - + -
210B ARG* 3.8 9.4 - - + +
211B ILE* 3.7 32.3 - - + +
214B ARG* 2.9 24.1 + - + +
215B GLU* 4.0 4.0 - - - +
217B THR* 1.3 68.8 - - - +
219B PHE* 1.3 68.4 + - - +
221B LEU* 3.3 5.8 + - - +
222B GLU* 3.0 21.9 + - + +
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Residues in contact with PHE 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B LEU* 3.6 17.5 - - + +
30B ARG* 3.5 65.3 - - + +
31B LEU* 3.7 29.6 - - + -
34B SER* 4.1 10.1 - - - -
215B GLU* 2.8 23.5 + - - +
216B GLU* 3.6 3.1 - - - +
218B ILE* 1.3 73.3 - - - +
220B ARG* 1.3 91.3 + - - +
222B GLU* 3.3 3.0 + - - +
223B GLN* 2.8 52.4 + - - +
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Residues in contact with ARG 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ARG* 3.9 9.3 - - - +
216B GLU* 2.8 50.5 + - + +
217B THR* 3.9 4.5 - - - +
219B PHE* 1.3 82.6 - - - +
221B LEU* 1.3 65.4 + - - +
223B GLN* 3.1 35.6 + - - +
224B GLU* 3.2 32.8 + - - +
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Residues in contact with LEU 221 (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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147A LEU* 4.7 9.2 - - + -
151A ILE* 4.2 18.6 - - + -
156A TRP* 4.6 14.6 - - + -
159A ILE* 5.0 3.8 - - + -
163A LEU* 4.1 35.4 - - + -
206B TYR* 3.7 20.6 - - + +
217B THR* 3.1 18.5 + - + +
218B ILE* 3.7 4.7 - - - +
220B ARG* 1.3 74.5 - - - +
222B GLU* 1.3 59.4 + - - +
224B GLU* 3.2 18.2 + - - +
225B LEU* 2.9 51.2 + - + +
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Residues in contact with GLU 222 (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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27B LEU* 4.7 4.3 - - + -
31B LEU* 3.9 24.0 - - + +
200B GLY 4.7 1.0 - - - +
202B GLY* 3.5 11.1 + - - -
203B VAL* 2.7 35.1 + - - +
204B MSE 3.0 23.6 + - - +
206B TYR* 2.6 37.9 + - + +
218B ILE* 3.0 20.1 + - + +
219B PHE* 3.7 4.9 - - - +
221B LEU* 1.3 73.0 - - - +
223B GLN* 1.3 60.4 + - - +
225B LEU* 3.9 3.9 - - - +
226B SER* 2.9 32.9 + - - -
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Residues in contact with GLN 223 (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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31B LEU* 4.0 10.1 - - + +
34B SER* 3.9 16.6 + - - +
35B PHE* 5.0 3.4 - - + -
219B PHE* 2.8 41.6 + - + +
220B ARG* 3.1 41.1 + - - +
221B LEU 3.2 0.4 - - - -
222B GLU* 1.3 77.8 - - - +
224B GLU* 1.3 59.5 + - + +
226B SER* 2.8 21.2 + - - -
227B ARG* 3.4 36.7 + - - +
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Residues in contact with GLU 224 (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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163A LEU* 5.2 9.5 - - - +
220B ARG* 3.2 19.1 + - - +
221B LEU* 3.2 19.7 + - + +
223B GLN* 1.3 75.0 - - - +
225B LEU* 1.3 65.5 + - + +
227B ARG* 3.2 23.4 + - - +
228B ASP* 3.7 6.1 + - - +
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Residues in contact with LEU 225 (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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143A PHE* 5.4 2.7 - - + -
144A TYR* 4.4 19.3 - - + -
147A LEU* 4.5 9.0 - - + -
163A LEU* 6.1 0.9 - - + -
203B VAL* 4.0 19.0 - - + +
204B MSE 3.7 48.5 - - + -
221B LEU* 2.9 38.9 + - + +
222B GLU* 3.4 13.9 + - - +
224B GLU* 1.3 78.7 - - + +
226B SER* 1.3 57.7 + - - +
228B ASP* 3.0 28.3 + - - +
231B ILE* 3.7 11.0 - - + +
232B ILE* 3.9 2.3 - - - +
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Residues in contact with SER 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU* 5.4 1.8 - - - -
35B PHE* 3.4 29.4 - - - -
198B ILE 4.3 1.4 - - - +
199B ARG* 3.2 35.2 + - - +
200B GLY 3.2 29.8 + - - +
203B VAL* 4.4 0.8 - - - +
222B GLU 2.9 14.9 + - - -
223B GLN 2.8 19.2 + - - -
225B LEU* 1.3 76.0 - - - +
227B ARG* 1.3 57.6 + - - +
228B ASP 3.3 1.1 + - - -
232B ILE* 3.6 4.8 - - - +
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Residues in contact with ARG 227 (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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34B SER* 5.8 0.2 + - - -
35B PHE* 4.9 2.0 - - - -
38B GLU* 3.1 39.8 + - - -
198B ILE 5.9 0.7 - - - -
199B ARG* 3.4 26.9 - - - +
223B GLN* 3.4 40.6 + - - +
224B GLU* 3.2 12.1 + - - +
225B LEU 3.1 1.0 - - - -
226B SER* 1.3 76.2 + - - +
228B ASP* 1.3 59.0 + - - +
229B ARG* 3.6 8.2 + - - +
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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