Contacts of the helix formed by residues 206 - 221 (chain A) in PDB entry 2AXV
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 206 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A TYR* 5.0 7.9 - - + -
201A SER* 2.9 19.8 + - - +
204A ASN* 3.1 11.7 - - + +
205A ARG* 1.3 71.9 - - - +
207A LEU* 1.3 58.3 + - - +
208A LYS* 3.2 8.0 + - - +
209A GLU* 2.9 40.3 + - + +
210A ALA* 2.9 23.0 + - - +
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Residues in contact with LEU 207 (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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202A ILE* 5.2 3.8 - - + -
205A ARG* 3.1 34.4 + - - +
206A ASN* 1.3 74.3 - - - +
208A LYS* 1.3 61.2 + - - +
210A ALA* 3.8 7.2 - - + -
211A GLN* 3.0 23.4 + - - +
243A TYR* 3.3 28.8 + - + +
246A LEU* 4.0 29.6 - - + +
247A THR* 3.6 33.9 - - + +
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Residues in contact with LYS 208 (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 ASN* 3.2 5.9 + - - +
207A LEU* 1.3 78.6 - - + +
209A GLU* 1.3 71.3 + - - +
211A GLN* 3.3 12.2 + - + +
212A TYR* 3.1 20.3 + - - +
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Residues in contact with GLU 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A TYR* 2.8 35.1 + - + +
169A SER* 4.5 2.3 - - - -
173A LYS* 2.9 33.0 + - - -
201A SER* 3.3 17.9 - - - +
206A ASN* 2.9 32.8 + - - +
208A LYS* 1.3 79.0 - - + +
210A ALA* 1.3 67.7 + - - +
212A TYR* 3.0 8.0 + - - +
213A TYR* 3.0 26.2 + - + -
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Residues in contact with ALA 210 (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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198A LEU* 3.4 9.9 - - + +
201A SER* 3.4 15.6 - - - -
202A ILE* 3.9 26.9 - - + +
206A ASN 2.9 19.3 + - - +
207A LEU* 3.6 11.2 - - + +
209A GLU* 1.3 78.9 - - - +
211A GLN* 1.3 64.6 + - - +
213A TYR 3.1 0.7 + - - -
214A ILE* 3.0 25.9 + - - +
243A TYR* 4.0 6.5 - - + -
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Residues in contact with GLN 211 (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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207A LEU 3.0 19.2 + - - +
208A LYS* 3.5 10.1 - - - +
210A ALA* 1.3 75.7 - - - +
212A TYR* 1.3 64.0 + - - +
214A ILE* 3.3 13.3 + - - +
215A ASN* 2.9 47.1 + - - +
243A TYR* 3.3 26.1 + - - +
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Residues in contact with TYR 212 (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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172A ILE* 5.0 1.8 - - + -
173A LYS* 3.5 61.1 + - + +
176A TYR* 3.8 16.7 + + + +
208A LYS 3.1 12.5 + - - +
209A GLU* 3.0 13.2 + - - +
211A GLN* 1.3 78.3 - - - +
213A TYR* 1.3 100.9 + + - +
215A ASN* 3.1 10.3 + - + +
216A GLN* 2.9 55.8 + - + +
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Residues in contact with TYR 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A TYR* 2.8 38.0 + + - -
169A SER* 4.8 0.5 - - - -
172A ILE* 3.6 28.4 - - + +
173A LYS* 4.1 6.6 - - - -
194A LEU* 4.1 23.9 - - + +
197A ALA* 3.2 35.4 - - + -
198A LEU* 3.7 21.1 - - + +
201A SER* 3.3 19.5 - - - -
209A GLU* 3.0 20.9 + - + -
210A ALA 3.7 4.7 - - - +
212A TYR* 1.3 105.8 - + - +
214A ILE* 1.3 61.5 + - - +
216A GLN* 3.2 4.7 + - - +
217A PHE* 2.9 24.6 + - - +
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Residues in contact with ILE 214 (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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198A LEU* 3.6 27.8 - - + -
210A ALA 3.0 21.6 + - - +
211A GLN* 3.5 10.3 - - - +
213A TYR* 1.3 74.3 - - - +
215A ASN* 1.3 62.0 + - - +
217A PHE* 3.4 6.1 + - - +
218A GLU* 3.0 39.3 + - + +
236A ILE* 5.3 2.0 - - + -
239A LEU 5.1 0.2 - - - +
240A LYS* 3.6 44.6 - - + +
243A TYR* 4.1 30.7 - - + -
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Residues in contact with ASN 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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211A GLN* 2.9 44.9 + - - +
212A TYR* 3.1 8.1 + - - +
214A ILE* 1.3 78.8 - - - +
216A GLN* 1.3 64.7 + - - +
218A GLU* 3.1 9.9 + - - +
219A HIS* 2.8 31.9 + - - +
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Residues in contact with GLN 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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176A TYR* 3.4 22.0 - - + +
177A PRO* 3.1 41.8 - - - +
178A ILE 4.4 0.8 - - - +
194A LEU* 3.9 18.2 - - + -
212A TYR* 2.9 48.8 + - + +
213A TYR 3.2 8.5 + - - +
215A ASN* 1.3 79.0 - - - +
217A PHE* 1.3 60.6 + - - +
219A HIS* 3.3 8.6 + - - +
220A LEU* 3.2 27.2 + - - +
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Residues in contact with PHE 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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191A GLN* 4.1 26.5 - - + -
194A LEU* 4.3 12.7 - - + +
198A LEU* 6.2 0.2 - - + -
213A TYR 2.9 16.5 + - - +
214A ILE* 3.6 4.9 - - - +
216A GLN* 1.3 74.3 - - - +
218A GLU* 1.3 63.6 + - - +
220A LEU* 2.9 41.4 + - + +
221A LYS* 3.3 39.5 + - - +
228A ILE* 3.7 24.2 - - + -
232A TYR* 4.3 2.7 - - + -
233A ASP* 3.8 22.4 - - - -
236A ILE* 3.4 48.2 - - + -
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Residues in contact with GLU 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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214A ILE* 3.0 25.3 + - + +
215A ASN* 3.5 13.5 - - - +
217A PHE* 1.3 80.9 - - - +
219A HIS* 1.3 61.5 + - - +
221A LYS* 3.3 52.8 + - - +
222A THR* 3.8 8.8 - - - +
236A ILE* 5.3 1.4 - - - +
237A ASN* 4.9 1.4 + - - -
240A LYS* 3.0 35.6 + - - +
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Residues in contact with HIS 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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177A PRO* 3.7 29.1 - - + +
178A ILE 3.0 30.0 + - - -
179A VAL* 4.9 6.3 - - + +
215A ASN 2.8 17.1 + - - +
216A GLN* 3.3 12.8 + - - +
218A GLU* 1.3 77.0 - - - +
220A LEU* 1.3 67.4 + - + +
222A THR* 2.8 37.4 + - - +
223A ILE* 3.8 4.1 + - + +
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Residues in contact with LEU 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A TYR* 5.0 1.3 - - + -
178A ILE* 3.8 35.4 - - + +
190A ILE* 4.4 13.5 - - + -
191A GLN* 3.7 31.0 - - + -
194A LEU* 3.9 21.3 - - + -
216A GLN* 3.2 16.6 + - - +
217A PHE* 2.9 16.8 + - + +
219A HIS* 1.3 81.9 - - + +
221A LYS* 1.3 56.9 + - - +
223A ILE* 2.8 36.1 + - + +
226A ILE* 3.3 12.8 - - + +
228A ILE* 4.0 11.0 - - + -
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Residues in contact with LYS 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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217A PHE* 3.3 37.2 - - - +
218A GLU* 3.3 43.7 + - - +
219A HIS 3.1 0.6 - - - -
220A LEU* 1.3 75.4 - - - +
222A THR* 1.3 60.0 + - + +
223A ILE 3.6 2.1 + - - +
226A ILE* 4.1 13.3 - - - +
228A ILE* 4.1 18.6 - - + -
233A ASP* 2.9 34.1 + - - +
237A ASN* 4.2 5.5 - - - +
240A LYS* 5.4 0.4 - - - +
231B TYR* 5.0 0.4 - - - -
267B ILE 4.6 4.0 + - - -
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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