Contacts of the helix formed by residues 231 - 249 (chain A) in PDB entry 2QNJ
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 GLY 231 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A VAL* 3.7 12.9 - - - +
177A ARG* 3.9 5.8 - - - +
230A ASP* 1.3 83.5 + - - +
232A PRO* 1.3 74.6 - - - +
233A GLU* 3.1 15.5 + - - -
234A VAL* 3.3 14.2 + - - +
235A ASP 4.4 0.2 + - - -
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Residues in contact with PRO 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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170A HIS* 3.5 31.1 - - + +
175A VAL* 3.5 22.9 - - + -
231A GLY* 1.3 82.2 - - - +
233A GLU* 1.3 78.6 + - - +
234A VAL 3.1 0.4 - - - -
235A ASP* 3.0 7.3 + - - +
236A VAL* 3.0 26.9 + - + +
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Residues in contact with GLU 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A GLU* 4.5 3.7 - - - +
230A ASP 3.4 7.6 - - - +
231A GLY* 3.1 19.3 - - - -
232A PRO* 1.3 100.2 - - - +
234A VAL* 1.3 62.3 + - - +
236A VAL* 3.1 10.3 + - - +
237A TRP 3.1 18.0 + - - -
292A PRO* 3.6 28.7 - - + +
295A ARG* 3.1 31.7 + - + +
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Residues in contact with VAL 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A ARG* 4.1 19.3 - - + -
220A ALA* 4.1 4.6 - - + +
222A GLU* 3.5 18.2 - - + +
229A TYR* 3.1 55.0 - - + +
230A ASP 3.9 18.8 - - - +
231A GLY 3.7 14.1 - - - +
232A PRO 3.1 0.4 - - - -
233A GLU* 1.3 75.3 - - + +
235A ASP* 1.3 64.9 + - - +
237A TRP* 3.2 5.5 + - - +
238A SER* 3.1 24.5 + - - +
295A ARG* 4.0 4.7 - - - +
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Residues in contact with ASP 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A VAL* 4.3 5.4 - - + -
170A HIS* 3.0 29.3 + - + +
175A VAL* 3.3 8.1 - - - +
176A HIS* 2.8 24.7 + - - -
177A ARG* 2.8 26.3 + - - -
178A ASP 4.2 0.3 + - - -
179A LEU* 3.5 22.4 - - + +
197A PHE* 3.6 4.0 - - - -
232A PRO 3.0 9.2 + - - +
234A VAL* 1.3 78.3 - - - +
236A VAL* 1.3 57.5 + - - +
238A SER* 3.2 8.1 + - - -
239A LEU* 2.8 33.3 + - - +
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Residues in contact with VAL 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A HIS* 4.7 4.9 - - + -
232A PRO* 3.0 22.9 + - + +
233A GLU* 3.3 12.1 - - - +
234A VAL 3.1 0.4 - - - -
235A ASP* 1.3 78.2 - - - +
237A TRP* 1.3 62.0 + - - +
239A LEU* 3.1 8.1 - - - +
240A GLY 3.1 5.5 + - - -
287A PHE* 3.0 50.0 - - + -
295A ARG* 4.7 8.5 - - + +
296A GLY 3.5 25.1 - - - +
297A THR* 5.3 0.7 - - - -
298A LEU* 3.9 28.0 - - + +
301A ILE* 4.5 2.2 - - + -
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Residues in contact with TRP 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A PRO 5.0 0.8 + - - -
218A TYR 3.6 8.9 - - - -
219A ALA 3.0 24.5 + - - -
220A ALA* 3.4 17.3 - - + -
221A PRO* 3.4 30.1 - - + -
233A GLU 3.1 5.1 + - - -
234A VAL 3.4 7.9 - - - +
236A VAL* 1.3 73.3 - - - +
238A SER* 1.3 62.6 + - - +
240A GLY* 2.8 18.2 + - - -
241A VAL* 3.1 20.7 + - + +
253A PHE* 3.7 33.1 - + - -
265A VAL* 4.0 19.7 - - + +
268A GLY* 4.8 2.5 - - - -
287A PHE 3.8 14.1 - - - -
288A LEU* 3.5 46.3 - - + +
289A VAL 3.6 10.1 - - - -
290A LEU* 4.2 7.9 - - + -
295A ARG* 3.9 16.3 - - - +
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Residues in contact with SER 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A ASP 5.8 0.5 + - - -
179A LEU* 3.6 33.9 + - - +
218A TYR* 2.5 31.4 + - - +
229A TYR* 5.1 0.5 + - - -
234A VAL* 3.1 15.0 + - - +
235A ASP* 3.2 9.7 + - - -
237A TRP* 1.3 78.7 - - - +
239A LEU* 1.3 56.6 + - - +
241A VAL* 2.9 23.1 + - - +
242A ILE* 3.0 18.1 + - - +
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Residues in contact with LEU 239 (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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159A PHE* 3.6 24.2 - - + -
162A ILE* 3.8 26.5 - - + -
163A VAL* 4.7 6.7 - - + -
166A VAL* 4.1 22.4 - - + -
179A LEU* 5.3 4.9 - - + -
235A ASP 2.8 15.5 + - - +
236A VAL* 3.1 13.9 - - - +
238A SER* 1.3 77.4 - - - +
240A GLY* 1.3 59.4 + - - +
242A ILE* 3.4 14.8 + - + +
243A LEU 3.1 16.8 + - - -
287A PHE* 3.9 10.3 - - + -
298A LEU* 3.8 39.9 - - + -
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Residues in contact with GLY 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A VAL 3.1 6.7 + - - -
237A TRP 2.8 9.9 + - - -
239A LEU* 1.3 76.5 - - - +
241A VAL* 1.3 60.5 + - - +
243A LEU* 3.4 2.3 + - - -
244A TYR* 3.3 16.8 + - - +
284A LEU* 3.3 15.0 - - - +
287A PHE* 3.3 30.3 - - - -
288A LEU* 3.6 11.7 - - - +
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Residues in contact with VAL 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A PRO 3.8 20.0 - - - +
218A TYR* 3.8 25.4 - - + -
237A TRP* 3.6 33.7 - - + +
238A SER 2.9 10.2 + - - +
240A GLY* 1.3 74.8 - - - +
242A ILE* 1.3 62.0 + - - +
244A TYR* 3.2 12.3 + - - +
245A THR* 3.2 13.5 + - - +
251A LEU* 4.2 8.7 - - + -
252A PRO* 3.6 32.3 - - + -
253A PHE* 4.4 3.6 - - + -
288A LEU* 4.1 7.4 - - + -
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Residues in contact with ILE 242 (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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140A VAL* 6.0 0.4 - - + -
159A PHE* 4.8 2.9 - - + -
162A ILE* 3.9 19.1 - - + -
179A LEU* 4.4 18.4 - - + -
180A LYS 5.5 0.9 - - - +
184A LEU* 3.5 38.8 - - + -
218A TYR* 3.5 25.1 - - + +
238A SER 3.0 18.9 + - - +
239A LEU* 3.8 26.5 - - + +
240A GLY 3.2 0.2 - - - -
241A VAL* 1.3 74.9 - - - +
243A LEU* 1.3 67.1 + - - +
245A THR* 2.6 27.5 + - - +
246A LEU* 3.0 15.4 + - + +
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Residues in contact with LEU 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A PHE* 3.6 24.1 - - + -
239A LEU 3.1 14.0 + - - +
240A GLY* 3.5 10.3 - - - +
241A VAL 3.3 0.2 - - - -
242A ILE* 1.3 76.8 - - - +
244A TYR* 1.3 63.5 + - - +
246A LEU* 3.0 22.5 + - + +
247A VAL* 3.1 27.0 + - + +
280A CYS* 4.7 5.6 - - - +
283A LEU* 3.4 28.9 - - + -
284A LEU* 3.8 26.9 - - + +
287A PHE* 4.5 6.1 - - + -
306A TRP* 3.8 31.2 - - + -
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Residues in contact with TYR 244 (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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240A GLY 3.3 7.6 + - - +
241A VAL 3.2 11.1 + - - +
242A ILE 3.1 0.4 - - - -
243A LEU* 1.3 80.1 - - - +
245A THR* 1.3 52.6 + - - +
247A VAL* 3.5 5.6 - - - +
248A SER* 2.8 70.6 + - - -
250A SER* 3.4 13.9 - - - -
251A LEU 3.7 7.1 + - - -
252A PRO* 3.4 41.4 - - + +
270A TYR* 3.8 18.6 - + - -
271A ARG* 2.5 44.4 + - - +
273A PRO* 4.1 5.3 - - + +
276A MET* 4.5 10.5 - - + -
284A LEU* 4.0 22.2 - - + +
288A LEU* 5.3 0.9 - - + -
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Residues in contact with THR 245 (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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140A VAL* 5.6 0.7 - - - +
141A PHE* 4.0 15.5 - - + -
144A LEU* 3.5 22.1 - - - +
218A TYR* 4.2 7.9 + - - +
241A VAL 3.4 13.0 - - - +
242A ILE* 2.6 26.2 + - - +
244A TYR* 1.3 72.2 - - - +
246A LEU* 1.3 62.1 + - - +
249A GLY* 2.7 28.9 + - - +
250A SER 3.2 21.3 - - - +
251A LEU* 3.7 24.9 - - + -
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Residues in contact with LEU 246 (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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140A VAL* 3.9 27.4 - - + -
144A LEU* 3.8 6.7 - - + +
149A ARG 4.0 0.2 - - - -
150A MET* 3.1 49.3 + - - +
155A ALA* 3.8 25.6 - - + +
158A LYS* 4.5 10.1 - - + -
159A PHE* 3.7 33.0 - - + +
162A ILE* 4.4 13.2 - - + -
192A ILE* 5.8 0.2 - - + -
242A ILE* 3.0 16.8 + - + +
243A LEU* 3.0 10.7 + - + +
245A THR* 1.3 83.2 + - - +
247A VAL* 1.3 60.9 + - + +
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Residues in contact with VAL 247 (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 ARG* 3.4 20.0 + - - +
150A MET 4.1 6.9 - - - +
152A GLU* 4.2 13.6 - - + +
155A ALA* 3.6 22.2 - - + -
243A LEU* 3.1 21.0 + - + +
244A TYR* 3.5 8.3 - - - +
246A LEU* 1.3 77.4 - - - +
248A SER* 1.3 61.5 + - - +
275A TYR* 3.5 11.1 - - + -
276A MET* 3.7 26.0 - - + -
280A CYS* 3.9 25.4 - - - -
284A LEU* 5.1 1.1 - - + -
306A TRP* 4.1 12.6 - - + -
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Residues in contact with SER 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A ARG* 3.4 14.6 - - - +
244A TYR* 2.8 43.1 + - - -
247A VAL* 1.3 80.3 - - - +
249A GLY* 1.3 57.4 + - - +
250A SER* 2.9 27.8 + - - -
273A PRO* 4.7 9.0 - - - -
275A TYR* 3.4 22.3 + - - -
276A MET* 4.9 0.9 - - - -
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Residues in contact with GLY 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A PHE* 4.7 8.7 - - - -
144A LEU* 4.4 18.2 - - - +
145A VAL* 4.9 8.1 - - - +
148A GLY* 4.9 1.3 - - - -
149A ARG* 3.6 17.8 - - - +
245A THR* 2.7 24.6 + - - -
248A SER* 1.3 71.9 + - - +
250A SER* 1.3 59.7 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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