Contacts of the helix formed by residues 236 - 253 (chain A) in PDB entry 1Q4L
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 SER 236 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A HIS* 3.3 46.2 + - - +
176A GLY* 4.8 5.5 + - - -
177A ILE 4.0 4.7 + - - -
178A CYS* 3.6 27.2 - - - +
207A LEU* 3.9 6.9 - - - +
235A THR* 1.3 71.5 - - - +
237A SER* 1.3 56.8 + - - +
238A ILE 2.9 11.7 + - - -
239A ASP* 3.1 12.4 + - - +
240A VAL 4.0 0.2 + - - -
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Residues in contact with SER 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A GLU* 4.2 1.7 + - - -
235A THR* 3.0 18.7 + - - -
236A SER* 1.3 77.1 - - - +
238A ILE* 1.3 62.5 + - - +
239A ASP 3.2 0.7 - - - -
240A VAL* 3.3 17.0 + - - +
241A TRP 3.2 13.2 + - - -
325A PRO* 3.6 37.4 + - - +
328A ARG* 3.2 22.5 + - - -
329A LEU 5.8 1.1 - - - -
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Residues in contact with ILE 238 (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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178A CYS* 3.6 28.0 - - - -
180A ARG* 4.1 17.0 - - + -
217A ILE* 4.1 14.4 - - + -
218A CYS* 5.6 3.1 - - + -
224A ALA* 4.2 14.2 + - + +
226A GLU* 3.8 17.9 - - - +
227A LEU* 4.2 15.3 - - + -
234A TYR* 4.0 35.4 - - + -
235A THR 3.5 11.9 - - - +
236A SER 2.9 1.6 + - - -
237A SER* 1.3 77.7 - - - +
239A ASP* 1.3 66.2 + - - +
241A TRP* 3.2 4.0 + - - +
242A SER* 3.1 26.0 + - - +
328A ARG* 4.2 5.6 - - - +
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Residues in contact with ASP 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A LEU* 4.0 15.5 - - + +
173A HIS* 2.9 26.6 + - + +
178A CYS* 3.3 12.1 - - - -
179A HIS* 2.8 30.7 + - - +
180A ARG* 3.0 25.5 + - - -
181A ASP 4.4 0.2 + - - -
182A ILE* 3.8 12.4 + - + +
236A SER 3.1 7.8 + - - +
238A ILE* 1.3 82.2 - - - +
240A VAL* 1.3 59.6 + - - +
242A SER* 3.3 8.0 + - - -
243A ALA* 2.9 28.4 + - - +
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Residues in contact with VAL 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A PHE* 5.0 2.9 - - + -
169A LEU* 4.8 3.6 - - + -
173A HIS* 4.7 2.7 - - + -
236A SER 4.6 2.5 - - - +
237A SER* 3.3 21.7 + - - +
238A ILE 3.2 0.4 - - - -
239A ASP* 1.3 74.9 - - - +
241A TRP* 1.3 61.2 + - - +
243A ALA* 3.1 7.3 + - - +
244A GLY* 2.8 26.5 + - - -
320A LEU* 3.5 31.8 - - + +
328A ARG* 4.3 12.6 - - + -
329A LEU 3.6 22.7 - - - +
330A THR* 4.9 0.4 - - - -
331A PRO* 4.1 30.1 - - + -
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Residues in contact with TRP 241 (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 TYR 5.1 0.4 + - - -
222A TYR 3.4 15.0 - - - -
223A ARG 3.2 12.7 + - - -
224A ALA* 3.4 25.6 - - + -
225A PRO* 3.5 36.1 - - + -
237A SER 3.2 4.0 + - - -
238A ILE 3.2 7.6 + - - +
240A VAL* 1.3 77.5 - - - +
242A SER* 1.3 64.3 + - - +
244A GLY 3.0 1.9 + - - -
245A CYS* 2.9 30.7 + - - -
257A PHE* 3.6 31.3 - + - -
269A ILE* 3.9 12.5 - - + +
273A LEU* 4.0 16.6 - - + -
320A LEU 4.4 4.3 - - - -
321A LEU* 3.4 48.8 - - + +
322A GLU 3.5 18.2 - - - -
328A ARG* 3.9 12.8 - - - +
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Residues in contact with SER 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A ILE* 3.4 37.1 + - - +
218A CYS* 3.8 14.4 - - - -
222A TYR* 2.9 28.4 + - - -
238A ILE 3.1 14.6 + - - -
239A ASP* 3.5 7.2 + - - -
241A TRP* 1.3 77.7 - - - +
243A ALA* 1.3 62.7 + - - +
245A CYS* 3.0 14.0 + - - +
246A VAL* 3.0 16.1 + - - +
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Residues in contact with ALA 243 (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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162A MET* 3.4 10.0 - - + +
165A LEU* 4.0 18.8 - - + -
166A PHE* 3.7 27.1 - - + -
169A LEU* 4.3 7.4 - - + -
182A ILE* 4.0 8.0 - - + +
239A ASP 2.9 17.5 + - - +
240A VAL 3.1 4.9 + - - +
242A SER* 1.3 75.4 - - - +
244A GLY* 1.3 63.3 + - - +
246A VAL* 3.0 6.6 + - - +
247A LEU 3.0 19.8 + - - -
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Residues in contact with GLY 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 VAL 2.8 14.5 + - - -
241A TRP 3.0 5.3 + - - -
243A ALA* 1.3 78.0 - - - +
245A CYS* 1.3 55.9 + - - +
247A LEU* 3.4 3.0 + - - +
248A ALA* 3.1 28.9 + - - +
317A CYS* 4.7 2.0 - - - -
320A LEU* 3.9 24.2 - - - +
321A LEU* 3.9 19.5 - - - +
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Residues in contact with CYS 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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221A TYR 3.5 17.9 - - - +
222A TYR* 3.6 21.5 - - + -
241A TRP* 2.9 42.1 + - - -
242A SER 3.0 8.3 + - - +
244A GLY* 1.3 74.2 - - - +
246A VAL* 1.3 58.1 + - - +
248A ALA* 4.0 0.9 - - - +
249A GLU* 3.0 30.8 + - - +
256A ILE* 4.4 13.8 + - + +
257A PHE* 4.1 16.6 - - - -
321A LEU* 4.1 4.5 - - - -
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Residues in contact with VAL 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A VAL* 5.1 2.0 - - + -
162A MET* 4.0 16.4 - - + -
165A LEU* 4.8 0.9 - - + -
182A ILE* 4.5 10.3 - - + -
183A LYS* 4.3 9.9 - - - -
184A PRO* 4.1 34.3 - - + -
187A LEU* 4.1 20.0 - - + -
222A TYR* 4.4 4.3 - - + -
242A SER 3.0 17.0 + - - +
243A ALA* 3.0 8.9 + - - +
245A CYS* 1.3 75.2 - - - +
247A LEU* 1.3 65.9 + - - +
249A GLU* 3.3 6.9 + - - +
250A LEU* 3.0 34.5 + - + +
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Residues in contact with LEU 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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158A VAL* 3.7 19.3 - - + -
162A MET* 3.4 41.9 - - + +
243A ALA 3.0 6.9 + - - +
244A GLY* 3.7 7.0 - - - +
245A CYS 3.4 0.2 - - - -
246A VAL* 1.3 77.0 - - - +
248A ALA* 1.3 63.1 - - - +
250A LEU* 3.0 14.5 + - - +
251A LEU* 3.0 22.6 + - + +
313A ALA 4.2 7.0 - - - +
316A LEU* 3.7 27.4 - - + -
317A CYS* 3.5 24.7 - - - +
320A LEU* 4.1 10.3 - - + -
339A PHE* 4.1 14.4 - - + -
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Residues in contact with ALA 248 (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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244A GLY 3.1 15.3 + - - +
245A CYS 4.0 0.4 - - - +
247A LEU* 1.3 78.9 - - - +
249A GLU* 1.3 57.9 + - - +
251A LEU* 3.3 2.0 + - - -
252A LEU* 2.8 36.7 + - - +
256A ILE* 3.8 39.5 - - + -
305A PHE* 3.8 17.4 - - + -
317A CYS* 4.2 9.4 - - - -
321A LEU* 4.6 2.5 - - + -
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Residues in contact with GLU 249 (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 TYR* 5.9 2.3 - - - -
143A ALA* 5.7 5.4 - - + +
184A PRO* 4.0 14.4 - - + +
222A TYR* 2.6 38.8 + - - -
245A CYS 3.0 16.8 + - - +
246A VAL* 3.5 5.8 - - - +
247A LEU 3.1 0.2 - - - -
248A ALA* 1.3 77.7 - - - +
250A LEU* 1.3 61.5 + - + +
253A GLY* 2.8 29.7 + - - -
254A GLN* 3.5 28.0 - - - +
255A PRO* 3.6 26.4 - - + +
256A ILE* 5.0 0.8 - - - +
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Residues in contact with LEU 250 (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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139A VAL* 4.2 19.1 - - + -
143A ALA* 3.7 29.8 - - + -
152A THR* 4.4 12.5 - - - -
153A LEU* 4.2 31.9 + - + +
158A VAL* 4.3 28.3 - - + +
161A TYR* 4.9 8.3 - - + -
162A MET* 4.4 14.1 - - + -
184A PRO* 6.3 2.0 - - + -
246A VAL* 3.0 31.7 + - + +
247A LEU 3.0 6.7 + - - +
249A GLU* 1.3 81.3 - - + +
251A LEU* 1.3 63.4 + - - +
253A GLY* 4.1 3.5 + - - -
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Residues in contact with LEU 251 (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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152A THR* 3.8 15.1 - - - +
155A VAL* 4.8 15.0 - - + -
158A VAL* 4.1 24.5 - - + -
247A LEU* 3.0 31.4 + - + +
248A ALA 3.8 4.5 - - - +
250A LEU* 1.3 79.0 - - - +
252A LEU* 1.3 60.7 + - - +
305A PHE* 4.0 26.0 - - + -
306A ARG* 4.3 14.0 + - - +
309A THR* 4.5 15.3 + - + +
310A PRO* 5.5 0.4 - - + -
313A ALA* 3.7 32.3 - - + +
317A CYS* 4.3 9.2 - - - -
339A PHE* 5.1 2.5 - - + -
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Residues in contact with LEU 252 (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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152A THR* 4.5 5.2 - - - +
248A ALA 2.8 16.1 + - - +
251A LEU* 1.3 76.3 - - - +
253A GLY* 1.3 60.3 + - - +
254A GLN* 3.7 23.3 + - + +
255A PRO 4.6 1.6 - - - +
256A ILE* 3.9 40.4 - - + -
304A VAL* 3.2 32.1 - - + +
305A PHE* 3.4 28.7 - - + -
306A ARG* 5.1 6.1 - - + +
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Residues in contact with GLY 253 (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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147A SER* 3.2 29.8 + - - -
151A GLN 5.6 3.6 - - - -
152A THR* 4.7 11.0 - - - -
249A GLU* 2.8 16.5 + - - -
250A LEU 4.1 2.6 + - - -
251A LEU 3.6 1.6 - - - -
252A LEU* 1.3 74.8 - - - +
254A GLN* 1.3 63.9 + - - +
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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
------------------------------------------------------------
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