Contacts of the helix formed by residues 215 - 228 (chain A) in PDB entry 3QN3
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 THR 215 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213A ASN* 3.1 15.9 + - - -
214A ASN* 1.3 81.4 - - + +
216A GLU* 1.3 65.3 + - - +
217A PRO 3.2 2.2 - - - -
218A ILE* 2.9 8.3 + - + +
219A ASP* 2.9 28.6 + - - -
266A ARG* 3.9 19.0 + - - +
270A LEU* 3.7 29.8 - - + -
273A LYS* 6.0 0.7 - - + -
274A TYR* 3.7 19.7 - - + +
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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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211A LEU* 3.2 27.8 - - + +
212A ALA* 2.7 43.8 + - - +
213A ASN* 2.8 18.0 + - - +
215A THR* 1.3 77.2 + - - +
217A PRO* 1.3 69.6 - - + +
219A ASP* 3.2 11.4 + - + +
220A LEU* 3.0 23.7 + - - +
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Residues in contact with PRO 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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149A ILE* 3.8 19.6 - - + +
159A VAL* 4.2 7.4 - - + -
164A PHE* 3.6 40.6 - - + -
211A LEU* 3.8 19.0 - - + -
213A ASN 3.1 24.5 - - - +
214A ASN 3.5 3.8 - - - -
215A THR 3.4 3.6 - - - -
216A GLU* 1.3 94.0 - - + +
218A ILE* 1.3 60.5 + - - +
220A LEU* 3.3 3.3 + - + +
221A LEU* 3.1 25.3 + - - +
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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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161A PHE* 5.5 1.3 - - + -
164A PHE* 4.1 14.4 - - + -
214A ASN 3.8 18.2 - - - +
215A THR* 2.9 9.8 + - - +
217A PRO* 1.3 73.9 - - - +
219A ASP* 1.3 66.1 + - - +
221A LEU* 3.1 9.9 + - - +
222A MET* 2.9 26.2 + - + +
236A ILE* 4.5 16.6 - - + -
238A LEU* 4.4 14.1 - - + -
270A LEU* 4.7 9.0 - - + -
274A TYR* 3.6 46.7 - - + -
276A ILE* 4.0 23.8 - - + -
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Residues in contact with ASP 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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215A THR* 2.9 20.8 + - - +
216A GLU* 3.6 13.4 + - + +
218A ILE* 1.3 74.9 - - - +
220A LEU* 1.3 57.7 + - - +
222A MET* 3.3 9.0 + - - +
223A THR* 3.0 32.9 + - - +
273A LYS* 4.7 2.8 + - - -
274A TYR* 2.7 33.8 + - - -
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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
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149A ILE* 3.9 12.8 - - + -
188A LEU* 3.4 30.3 - - + -
191A GLU* 4.6 14.4 - - + +
192A LEU* 4.1 20.9 - - + -
209A PRO* 5.4 0.2 - - + -
211A LEU* 4.7 15.7 - - + -
216A GLU 3.0 12.3 + - - +
217A PRO 3.5 9.6 - - - +
219A ASP* 1.3 74.4 - - - +
221A LEU* 1.3 66.4 + - - +
223A THR* 3.3 10.5 + - + +
224A CYS* 3.0 37.6 + - - -
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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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148A ILE* 3.5 35.9 - - + -
149A ILE* 3.8 18.8 - - + -
164A PHE* 4.1 23.3 - - + -
165A MET 4.0 8.1 - - - +
166A ILE* 3.7 16.2 - - + -
184A ILE* 4.9 1.1 - - + +
188A LEU* 4.6 4.0 - - + -
217A PRO 3.1 17.1 + - - +
218A ILE* 3.1 8.3 + - - +
220A LEU* 1.3 74.7 - - - +
222A MET* 1.3 52.6 + - - +
224A CYS* 3.2 6.7 + - + +
225A ILE* 2.8 40.9 + - - +
236A ILE* 3.5 30.3 - - + -
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Residues in contact with MET 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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218A ILE* 2.9 28.3 + - + +
219A ASP* 3.5 10.5 - - - +
221A LEU* 1.3 73.9 - - - +
223A THR* 1.3 64.8 + - - +
225A ILE* 3.5 16.3 + - + +
226A LYS* 3.1 24.4 + - - +
231A GLU* 5.8 8.1 - - + -
232A ASN 6.3 0.4 - - - +
234A VAL 5.9 0.7 - - - +
236A ILE* 4.2 15.0 - - - -
274A TYR* 4.3 11.0 - - + -
275A PRO* 3.7 37.7 - - + -
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Residues in contact with THR 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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191A GLU* 4.5 7.2 - - - +
219A ASP* 3.0 15.2 + - - +
220A LEU* 3.6 15.1 - - + -
222A MET* 1.3 75.9 - - - +
224A CYS* 1.3 62.9 + - - +
226A LYS* 3.3 5.7 + - - +
227A LYS* 2.9 55.9 + - + +
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Residues in contact with CYS 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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184A ILE* 3.9 20.8 - - + +
187A ILE* 4.0 18.6 - - + +
188A LEU* 3.6 42.8 - - + -
191A GLU* 4.1 8.7 - - - -
220A LEU* 3.0 28.7 + - - +
221A LEU* 3.7 5.8 - - + +
223A THR* 1.3 76.4 - - - +
225A ILE* 1.3 64.2 + - - +
227A LYS* 3.9 1.0 - - - +
228A ALA* 3.0 25.5 + - - +
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Residues in contact with ILE 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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166A ILE* 4.2 6.1 - - + -
184A ILE* 4.1 18.4 - - + -
221A LEU 2.8 30.6 + - - +
222A MET* 3.8 17.9 - - + +
223A THR 3.3 0.2 - - - -
224A CYS* 1.3 73.6 - - - +
226A LYS* 1.3 62.1 + - - +
228A ALA* 3.3 3.3 + - - +
229A GLY 3.3 3.3 + - - -
230A TYR* 3.1 51.3 + - + +
231A GLU* 3.7 7.0 - - - +
232A ASN 4.9 0.7 - - - +
234A VAL* 3.8 46.0 - - + +
236A ILE* 4.1 19.7 - - + -
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Residues in contact with LYS 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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222A MET 3.1 16.5 + - - +
223A THR* 3.8 4.7 - - - +
225A ILE* 1.3 74.2 - - - +
227A LYS* 1.3 67.3 + - + +
229A GLY* 2.9 15.4 + - - -
231A GLU* 3.5 50.0 + - + +
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Residues in contact with LYS 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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187A ILE* 4.1 20.7 - - + +
191A GLU* 3.0 40.4 + - + +
223A THR* 2.9 32.8 + - + +
224A CYS 4.0 3.4 - - - +
226A LYS* 1.3 77.2 - - + +
228A ALA* 1.3 60.3 + - - +
229A GLY 3.4 0.7 + - - -
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Residues in contact with ALA 228 (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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183A GLU* 4.6 4.9 - - + +
184A ILE* 3.4 28.7 - - + +
187A ILE* 3.5 21.3 - - + +
224A CYS 3.0 18.8 + - - +
225A ILE 3.6 2.9 - - - +
226A LYS 3.2 0.2 - - - -
227A LYS* 1.3 75.2 - - - +
229A GLY* 1.3 58.9 + - - +
230A TYR* 3.5 21.3 - - + -
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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