Contacts of the helix formed by residues 223 - 236 (chain A) in PDB entry 2QLU
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 ASP 223 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201A PHE* 3.4 55.1 - - + +
219A PHE* 3.9 7.9 - - + -
220A PRO* 2.9 36.0 + - - +
222A GLN* 1.3 88.4 + - - +
224A LYS* 1.3 64.4 + - - +
225A GLN 3.0 3.8 - - - +
226A SER* 3.0 15.9 + - - +
227A TRP* 3.2 8.5 + - - +
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Residues in contact with LYS 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 PRO 3.9 1.0 + - - -
221A LEU* 3.4 21.8 + - + +
222A GLN 3.3 3.4 - - - -
223A ASP* 1.3 76.3 - - - +
225A GLN* 1.3 71.7 + - + +
227A TRP* 3.1 19.1 + - + +
228A GLN* 2.8 29.9 + - + +
252A LYS* 3.5 38.1 - - - +
261A LEU* 3.7 26.5 - - + -
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Residues in contact with GLN 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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222A GLN 4.9 1.9 + - - +
223A ASP* 3.0 1.6 - - - +
224A LYS* 1.3 96.6 - - + +
226A SER* 1.3 57.4 + - - +
228A GLN* 3.6 26.2 - - - +
229A SER* 2.8 35.0 + - - +
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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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201A PHE* 3.4 47.7 - - - +
219A PHE* 4.0 8.4 - - - -
223A ASP* 3.0 12.7 + - - +
225A GLN* 1.3 77.6 - - - +
227A TRP* 1.3 59.1 + - - +
229A SER* 3.8 5.7 - - - -
230A GLU* 3.0 29.3 + - - +
341A GLY* 4.1 10.9 + - - -
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Residues in contact with TRP 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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219A PHE* 3.7 36.1 - + + -
223A ASP 3.2 6.1 + - - +
224A LYS* 3.1 22.5 + - + +
226A SER* 1.3 75.8 - - - +
228A GLN* 1.3 89.9 + - - +
230A GLU* 3.9 0.8 - - - -
231A ARG* 3.0 47.6 + - - +
250A ALA* 3.9 24.7 - - + +
251A GLU 4.1 17.5 - - - -
252A LYS* 3.9 26.0 - - + -
261A LEU* 3.6 38.4 - - + -
262A TRP 2.8 27.9 + - - +
263A LEU* 3.8 16.0 - - + +
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Residues in contact with GLN 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 LYS* 2.8 18.8 + - + +
225A GLN* 3.6 26.0 - - - +
227A TRP* 1.3 88.2 - - + +
229A SER* 1.3 65.3 + - - +
231A ARG* 2.8 41.3 + - - +
232A GLU* 2.9 64.5 + - - +
252A LYS* 5.9 0.2 - - - -
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Residues in contact with SER 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 GLN* 2.8 26.0 + - - +
226A SER* 3.8 3.0 - - - -
228A GLN* 1.3 77.9 - - - +
230A GLU* 1.3 63.7 + - - -
232A GLU* 3.2 7.7 + - - +
233A ILE* 3.0 26.9 + - - +
340A PHE 4.6 2.7 - - - -
341A GLY 3.5 23.3 + - - -
343A ALA 5.8 2.9 - - - -
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Residues in contact with GLU 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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217A LYS* 3.5 22.8 + - - +
219A PHE* 3.8 11.4 - - - -
226A SER 3.0 15.8 + - - +
227A TRP* 4.1 3.6 - - - +
229A SER* 1.3 79.2 - - - +
231A ARG* 1.3 60.6 + - - +
233A ILE* 3.5 2.6 + - - +
234A PHE* 3.1 54.1 + - + -
245A LEU* 5.8 0.3 - - - +
263A LEU* 3.9 17.5 - - + +
339A ASP* 3.5 8.1 + - - +
340A PHE* 3.0 37.8 + - + -
341A GLY* 3.8 12.1 + - - -
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Residues in contact with ARG 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 TRP* 3.0 48.4 + - - +
228A GLN* 2.8 56.0 + - - +
230A GLU* 1.3 75.7 - - - +
232A GLU* 1.3 59.0 + - + +
234A PHE* 3.4 7.0 + - - +
235A SER* 2.5 40.0 + - - +
247A PHE* 4.5 6.9 - - + -
250A ALA* 3.9 25.6 + - + +
252A LYS* 5.5 3.2 - - - +
263A LEU* 4.1 8.9 - - + +
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Residues in contact with GLU 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 GLN* 2.9 53.5 + - - +
229A SER* 3.8 6.1 - - - +
231A ARG* 1.3 72.3 - - + +
233A ILE* 1.3 68.8 + - + +
235A SER* 3.2 15.3 + - - -
236A THR* 3.2 12.0 + - - -
345A ARG* 3.7 26.9 + - - +
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Residues in contact with ILE 233 (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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229A SER* 3.0 14.8 + - - +
230A GLU 3.8 7.0 - - - +
232A GLU* 1.3 74.9 - - + +
234A PHE* 1.3 62.2 + - - +
236A THR* 2.8 23.9 + - - -
239A MET* 3.7 22.2 - - + +
317A ILE* 4.3 11.7 - - + -
340A PHE* 3.6 37.0 - - + +
343A ALA* 3.8 32.1 - - + +
344A VAL* 4.7 0.2 - - - -
345A ARG* 3.6 35.2 - - + +
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Residues in contact with PHE 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 GLU* 3.1 54.8 + - + -
231A ARG 3.8 5.6 - - - +
232A GLU 3.3 0.4 - - - -
233A ILE* 1.3 74.5 - - - +
235A SER* 1.3 59.0 + - - +
236A THR 3.6 1.4 + - - +
239A MET* 3.8 23.1 - - + +
245A LEU* 3.3 47.8 - - + -
247A PHE* 3.5 50.5 - + + +
263A LEU* 3.8 12.8 - - + -
265A THR* 4.1 4.3 - - + -
339A ASP 5.3 0.4 - - - -
340A PHE* 3.5 31.6 - + - -
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Residues in contact with SER 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 ARG* 2.5 26.8 + - - +
232A GLU* 3.7 8.3 - - - -
233A ILE 3.1 0.6 + - - -
234A PHE* 1.3 74.4 - - - +
236A THR* 1.3 61.9 + - - +
237A PRO* 3.6 4.0 - - - +
247A PHE* 4.5 13.4 - - - -
345A ARG* 5.2 0.4 - - - -
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Residues in contact with THR 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 GLU 3.2 2.9 + - - -
233A ILE* 2.8 19.2 + - - -
234A PHE 4.0 1.0 - - - +
235A SER* 1.3 78.6 - - - +
237A PRO* 1.4 90.8 - - + +
238A GLY 3.5 0.9 + - - -
239A MET* 3.1 21.6 + - + +
311A GLU* 4.3 1.4 - - - +
314A LYS* 4.3 4.9 - - + -
315A PRO* 3.7 26.9 - - + -
317A ILE* 4.5 5.4 - - + +
345A ARG* 3.0 35.7 + - - +
347A GLU* 5.7 0.2 - - - +
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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