Contacts of the helix formed by residues 214 - 227 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210A ARG* 2.9 18.0 + - + +
211A ILE 3.5 2.5 - - - -
213A GLU* 1.3 90.3 - - + +
215A GLU* 1.3 64.0 + - - +
216A GLU 3.2 3.3 + - - -
217A THR* 3.3 25.1 + - - +
218A ILE* 3.1 27.6 + - + +
249A PO4 3.2 36.7 + - - +
156B TRP* 3.5 44.8 - - + +
157B ASP* 5.0 9.1 + - - -
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Residues in contact with GLU 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A PRO* 2.9 31.5 - - + +
26A LYS* 3.4 20.8 - - + -
27A LEU* 3.5 15.6 - - - +
30A ARG* 3.3 33.9 - - - +
211A ILE* 2.9 40.5 + - + +
212A SER* 4.4 5.2 + - - +
213A GLU 3.8 1.6 - - - -
214A ARG* 1.3 76.4 - - - +
216A GLU* 1.3 56.9 + - - +
218A ILE* 3.9 2.0 - - - +
219A PHE* 2.9 33.1 + - - +
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Residues in contact with GLU 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ARG* 2.9 40.0 + - - +
214A ARG 3.2 0.8 - - - -
215A GLU* 1.3 75.1 - - - +
217A THR* 1.3 68.2 + - - +
219A PHE* 3.3 7.8 + - - +
220A ARG* 2.9 68.1 + - - +
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Residues in contact with THR 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A ARG* 3.3 30.7 + - - +
216A GLU* 1.3 81.4 - - - +
218A ILE* 1.3 57.3 + - - +
220A ARG* 3.5 7.2 + - - +
221A LEU* 3.2 26.2 + - + +
156B TRP* 3.3 44.4 - - + +
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Residues in contact with ILE 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A LEU* 3.7 28.3 - - + -
206A TYR* 3.8 36.6 - - + -
210A ARG* 3.4 28.9 - - + +
211A ILE* 3.7 14.8 - - + +
214A ARG* 3.1 19.1 + - + +
215A GLU* 4.1 2.7 - - - +
217A THR* 1.3 74.3 - - - +
219A PHE* 1.3 61.4 + - - +
221A LEU* 3.5 6.2 + - - +
222A GLU* 2.9 28.8 + - - +
156B TRP* 3.5 32.5 - - + -
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Residues in contact with PHE 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A LEU* 3.9 14.1 - - + +
30A ARG* 3.5 70.9 - - + +
31A LEU* 3.7 28.3 - - + -
34A SER* 4.1 12.8 - - - -
215A GLU* 2.9 19.1 + - - +
216A GLU* 3.7 11.7 - - - +
218A ILE* 1.3 77.6 - - - +
220A ARG* 1.3 60.3 + - + +
222A GLU* 3.9 1.4 - - - +
223A GLN* 2.9 59.9 + - - +
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Residues in contact with ARG 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A GLU* 2.9 51.6 + - - +
217A THR* 3.8 6.5 - - - +
218A ILE 3.3 0.2 - - - -
219A PHE* 1.3 74.8 - - + +
221A LEU* 1.3 65.5 + - - +
223A GLN* 3.3 20.4 - - - +
224A GLU* 3.2 32.9 + - - +
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Residues in contact with LEU 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A TYR* 3.6 20.2 - - + +
217A THR* 3.2 16.9 + - + +
218A ILE* 3.7 5.4 - - - +
219A PHE 3.4 0.2 - - - -
220A ARG* 1.3 76.1 - - - +
222A GLU* 1.3 58.5 + - - +
224A GLU* 3.0 18.2 + - + +
225A LEU* 2.9 55.0 + - + +
147B LEU* 4.9 7.6 - - + -
151B ILE* 4.6 9.4 - - + -
156B TRP* 4.1 23.3 - - + -
159B ILE* 5.2 0.4 - - + -
163B LEU* 4.2 34.5 - - + -
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Residues in contact with GLU 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A LEU* 4.7 5.4 - - + -
31A LEU* 3.9 25.8 - - + +
200A GLY 4.5 1.6 - - - +
202A GLY* 3.4 12.1 + - - -
203A VAL* 2.8 32.1 + - - +
204A MSE 3.0 23.2 + - - +
206A TYR* 2.7 37.8 + - + +
218A ILE* 2.9 19.6 + - + +
219A PHE* 3.9 2.7 - - - +
221A LEU* 1.3 73.2 - - - +
223A GLN* 1.3 60.6 + - - +
225A LEU* 3.8 5.5 - - - +
226A SER* 2.8 34.0 + - - -
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Residues in contact with GLN 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A LEU* 3.9 11.0 - - + +
34A SER* 4.3 13.4 + - - +
35A PHE* 5.1 2.7 - - + -
219A PHE* 2.9 46.8 + - + +
220A ARG* 3.3 23.8 - - - +
222A GLU* 1.3 76.1 - - - +
224A GLU* 1.3 60.5 + - + +
226A SER* 2.8 20.6 + - - -
227A ARG* 3.3 36.4 + - - +
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Residues in contact with GLU 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A ARG* 3.4 22.3 - - - +
221A LEU* 3.0 16.9 + - + +
223A GLN* 1.3 75.9 - - + +
225A LEU* 1.3 68.3 + - + +
227A ARG* 3.1 24.6 + - - +
228A ASP* 3.7 6.1 + - - +
163B LEU* 6.2 0.2 - - - +
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Residues in contact with LEU 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A VAL* 3.9 17.8 - - + +
204A MSE 3.6 37.5 - - + -
221A LEU* 2.9 43.5 + - + +
222A GLU* 3.8 11.0 - - - +
224A GLU* 1.3 78.7 - - + +
226A SER* 1.3 60.5 + - - +
228A ASP* 3.1 22.0 + - + +
231A ILE* 3.8 26.6 - - + +
232A ILE* 4.1 1.0 - - - +
143B PHE* 5.7 2.2 - - + -
144B TYR* 4.1 15.0 - - + +
147B LEU* 4.5 6.3 - - + -
163B LEU* 6.2 0.4 - - + -
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Residues in contact with SER 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A LEU* 5.6 1.6 - - - -
35A PHE* 3.5 29.4 - - - -
198A ILE 4.3 0.5 - - - +
199A ARG* 3.3 34.0 + - - +
200A GLY 3.2 29.2 - - - +
203A VAL* 4.1 2.2 - - - +
222A GLU* 2.8 19.9 + - - -
223A GLN 2.8 21.1 + - - -
225A LEU* 1.3 73.3 - - - +
227A ARG* 1.3 58.1 + - - +
228A ASP 3.3 0.2 - - - -
232A ILE* 3.4 5.8 - - - +
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Residues in contact with ARG 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A PHE* 4.9 2.4 - - - -
38A GLU* 3.4 21.2 + - - -
197A ASP* 6.0 1.1 - - - -
198A ILE 5.8 1.1 - - - -
199A ARG* 3.3 44.8 - - - +
223A GLN* 3.3 41.0 + - - +
224A GLU* 3.1 11.5 + - - +
225A LEU 3.1 0.8 - - - -
226A SER* 1.3 76.5 - - - +
228A ASP* 1.3 60.4 + - - +
229A ARG* 3.4 10.3 + - - +
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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