Contacts of the helix formed by residues 215 - 237 (chain A) in PDB entry 3QTC
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 PRO 215 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188A PRO* 6.4 3.8 - - + -
190A LEU* 5.5 0.2 - - + -
213A GLY 3.7 4.7 - - - +
214A LYS* 1.3 90.4 - - + +
216A PHE* 1.3 67.3 + - - +
217A ARG* 3.2 9.6 - - + +
218A GLU* 3.1 44.6 + - + +
219A LEU* 3.2 11.4 + - - +
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Residues in contact with PHE 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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190A LEU* 3.7 17.9 - - + +
194A GLN* 3.5 71.3 - - + +
197A ARG* 3.9 13.2 - - + -
198A LEU* 3.8 25.6 - - + -
214A LYS 3.9 0.6 + - - -
215A PRO* 1.3 72.4 - - - +
217A ARG* 1.3 62.0 + - + +
218A GLU 3.2 0.2 + - - -
219A LEU* 3.2 4.5 + - - +
220A GLU* 2.8 62.6 + - - +
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Residues in contact with ARG 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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215A PRO* 3.2 9.7 - - + +
216A PHE* 1.3 87.0 - - + +
218A GLU* 1.3 61.7 + - + +
220A GLU* 3.9 8.8 - - - +
221A SER* 3.1 35.1 + - - -
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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 LYS* 3.3 29.4 - - + +
215A PRO* 3.1 35.4 + - + +
217A ARG* 1.3 78.4 - - + +
219A LEU* 1.3 65.0 + - - +
221A SER* 3.4 6.2 + - - -
222A GLU* 3.1 24.6 + - - +
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Residues in contact with LEU 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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190A LEU* 4.4 15.3 - - + -
198A LEU* 4.0 29.4 - - + -
212A SER* 6.1 4.9 - - - -
214A LYS* 3.6 52.7 - - + +
215A PRO 3.2 11.2 + - - +
216A PHE 3.7 4.9 - - - +
218A GLU* 1.3 76.5 - - - +
220A GLU* 1.3 61.8 + - - +
222A GLU* 3.4 6.4 + - + +
223A LEU* 3.1 31.1 + - + +
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Residues in contact with GLU 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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197A ARG* 3.1 30.5 + - - +
198A LEU* 3.7 14.9 - - + +
201A LEU* 4.0 14.4 - - + -
216A PHE* 2.8 40.0 + - + +
217A ARG* 3.9 9.1 - - - +
219A LEU* 1.3 74.3 - - - +
221A SER* 1.3 59.9 + - - +
223A LEU* 3.3 1.0 + - - +
224A LEU* 2.8 52.5 + - + +
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Residues in contact with SER 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 ARG* 3.1 26.8 + - - -
218A GLU* 3.4 7.6 + - - -
220A GLU* 1.3 75.1 - - - +
222A GLU* 1.3 58.2 + - - +
224A LEU* 3.8 9.9 - - - +
225A SER* 3.0 30.1 + - - -
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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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214A LYS* 6.3 1.3 - - - +
218A GLU 3.1 17.2 + - - +
219A LEU* 3.7 8.3 - - + +
221A SER* 1.3 76.1 - - - +
223A LEU* 1.3 60.4 + - + +
225A SER* 3.3 9.2 + - - -
226A ARG* 2.9 76.9 + - - +
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Residues in contact with LEU 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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198A LEU* 3.6 42.8 - - + +
201A LEU* 3.8 18.2 - - + +
202A LEU* 4.0 18.2 - - + -
206A ASP* 3.9 24.7 - - - +
219A LEU* 3.1 22.4 + - + +
220A GLU 3.9 2.5 - - - +
222A GLU* 1.3 78.0 - - + +
224A LEU* 1.3 66.4 + - - +
226A ARG* 3.2 16.4 + - - +
227A ARG* 2.9 36.6 + - - +
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Residues in contact with LEU 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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197A ARG* 3.5 24.5 - - - +
201A LEU* 3.8 16.6 - - + -
220A GLU* 2.8 43.4 + - + +
221A SER* 3.8 8.3 - - - +
223A LEU* 1.3 72.3 - - - +
225A SER* 1.3 62.8 + - - +
227A ARG* 3.9 3.6 - - - +
228A LYS* 3.0 40.7 + - - +
454A LEU* 3.8 33.3 - - + +
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Residues in contact with SER 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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221A SER 3.0 18.1 + - - -
222A GLU* 3.5 9.9 - - - -
223A LEU 3.2 0.2 - - - -
224A LEU* 1.3 76.5 - - - +
226A ARG* 1.3 62.6 + - - +
228A LYS* 3.5 8.8 + - - +
229A LYS* 3.1 39.1 + - - +
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Residues in contact with ARG 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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206A ASP* 3.2 36.8 + - - +
207A GLU* 4.2 16.4 + - - +
222A GLU* 2.9 50.6 + - - +
223A LEU* 3.2 18.4 + - - +
225A SER* 1.3 78.4 - - - +
227A ARG* 1.3 71.3 + - - +
229A LYS* 3.3 8.1 + - - +
230A ASP* 2.9 31.4 + - - +
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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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201A LEU* 2.8 47.3 + - + +
202A LEU 5.3 0.4 - - - -
203A ASN* 3.5 19.0 - - - +
206A ASP* 2.7 40.6 + - - -
223A LEU* 2.9 28.5 + - - +
224A LEU 4.0 0.7 - - - +
226A ARG* 1.3 92.7 - - - +
228A LYS* 1.3 65.4 + - - +
230A ASP* 2.8 35.6 + - - +
231A LEU* 3.0 27.0 + - - +
439A ARG* 6.0 2.2 - - - +
450A ILE* 3.9 27.4 - - + +
451A SER 5.1 2.2 - - - +
454A LEU* 4.0 18.8 - - + -
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Residues in contact with LYS 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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224A LEU* 3.0 32.8 + - - +
225A SER* 3.8 7.2 - - - +
227A ARG* 1.3 76.3 - - - +
229A LYS* 1.3 58.5 + - + +
231A LEU* 3.3 5.1 + - - +
232A GLN* 2.9 49.3 + - - +
454A LEU* 3.6 44.0 + - + -
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Residues in contact with LYS 229 (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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225A SER* 3.1 28.0 + - - +
226A ARG* 3.5 10.8 - - - +
228A LYS* 1.3 74.4 - - - +
230A ASP* 1.3 60.5 + - - +
232A GLN* 2.7 33.1 + - + +
233A GLN* 2.9 31.3 + - - +
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Residues in contact with ASP 230 (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 ASN* 4.5 7.1 - - - +
226A ARG* 2.9 16.9 + - - +
227A ARG* 2.8 44.9 + - - +
229A LYS* 1.3 77.1 - - - +
231A LEU* 1.3 62.0 + - - +
233A GLN* 3.3 12.8 + - - +
234A ILE* 3.1 26.7 + - + +
450A ILE* 3.8 20.8 - - + +
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Residues in contact with LEU 231 (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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227A ARG 3.0 12.1 + - - +
228A LYS* 3.3 6.5 + - - +
230A ASP* 1.3 73.4 - - - +
232A GLN* 1.3 65.0 + - + +
234A ILE* 3.4 6.9 + - + +
235A TYR* 3.0 24.7 + - - +
447A TYR* 4.1 28.7 - - + -
450A ILE* 3.8 30.1 - - + -
451A SER 4.3 4.0 - - - +
452A THR* 5.2 7.0 - - + -
454A LEU* 3.7 30.1 - - + -
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Residues in contact with GLN 232 (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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228A LYS* 2.9 35.7 + - - +
229A LYS* 2.7 45.7 + - + +
231A LEU* 1.3 77.6 - - + +
233A GLN* 1.3 56.2 + - - +
235A TYR* 3.4 9.2 + - + +
236A ALA* 2.9 32.3 + - - +
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Residues in contact with GLN 233 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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229A LYS 2.9 16.8 + - - +
230A ASP* 3.7 12.0 - - - +
231A LEU 3.2 0.2 - - - -
232A GLN* 1.3 72.3 - - - +
234A ILE* 1.3 68.6 + - + +
236A ALA* 3.3 4.0 + - - -
237A GLU* 3.0 61.7 + - - +
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Residues in contact with ILE 234 (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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230A ASP* 3.1 11.7 + - + +
231A LEU* 3.7 7.9 - - + +
232A GLN 3.4 0.2 - - - -
233A GLN* 1.3 77.7 - - + +
235A TYR* 1.3 64.2 + - - +
237A GLU 3.3 4.2 + - - -
238A GLU* 3.4 6.0 + - + +
239A ARG* 3.0 43.7 + - - +
240A GLU 4.7 1.1 - - - +
242A TYR* 6.0 0.9 - - + +
447A TYR* 4.0 26.2 - - + +
448A ASN* 4.0 26.2 - - + +
450A ILE* 3.5 32.3 - - + -
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Residues in contact with TYR 235 (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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231A LEU 3.0 16.7 + - - +
232A GLN* 3.7 9.0 - - + +
233A GLN 3.3 0.2 - - - -
234A ILE* 1.3 78.8 - - - +
236A ALA* 1.3 58.5 + - - +
239A ARG* 2.9 46.4 + - + +
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Residues in contact with ALA 236 (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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232A GLN 2.9 17.4 + - - +
233A GLN* 3.8 5.4 - - - +
234A ILE 3.2 0.2 - - - -
235A TYR* 1.3 79.1 - - - +
237A GLU* 1.3 67.4 + - + +
239A ARG* 3.2 11.1 + - - +
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Residues in contact with GLU 237 (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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233A GLN* 3.0 48.2 + - - +
234A ILE* 3.3 0.6 + - - -
236A ALA* 1.3 85.0 - - + +
238A GLU* 1.3 64.8 + - + +
239A ARG* 3.1 26.3 + - - -
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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