Contacts of the helix formed by residues 236 - 256 (chain A) in PDB entry 4QA7
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 GLN 236 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A GLY 3.8 2.1 + - - +
235A ILE* 1.3 76.4 - - - +
237A ASP* 1.3 69.7 + - - +
238A GLU* 3.2 4.3 + - + +
239A LYS* 3.2 31.3 + - - +
240A TYR* 3.1 22.7 + - - +
278A ASN* 3.1 44.6 - - + +
279A MET* 3.4 6.3 - - - -
350A PRO* 4.4 14.9 - - + +
351A SER 4.2 5.3 + - - -
353A ARG 4.5 8.1 + - - -
355A ASP* 6.0 0.4 - - - +
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Residues in contact with ASP 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A GLN* 1.3 77.2 - - - +
238A GLU* 1.3 61.8 + - - +
240A TYR* 3.8 0.9 - - - +
241A TYR* 3.1 27.0 + - - +
278A ASN 5.3 0.4 - - - -
279A MET* 3.3 16.0 - - - +
280A THR* 2.2 63.5 + - - +
282A VAL* 4.4 4.2 - - + +
283A GLY* 3.4 20.1 + - - +
286A LYS* 4.9 4.1 - - - -
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Residues in contact with GLU 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A GLN* 3.2 2.3 + - + +
237A ASP* 1.3 81.2 - - - +
239A LYS* 1.3 70.8 + - + +
241A TYR* 3.6 3.8 + - - +
242A GLN* 3.3 43.8 + - - +
286A LYS* 5.1 9.5 + - - +
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Residues in contact with LYS 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A ILE* 3.9 9.4 - - + -
236A GLN* 3.2 57.3 - - + +
238A GLU* 1.3 80.3 - - + +
240A TYR* 1.3 64.9 + - - +
242A GLN* 3.2 17.0 + - - +
243A ILE* 3.0 31.6 + - + +
355A ASP* 3.3 38.6 + - - +
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Residues in contact with TYR 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A LEU* 3.5 41.4 + - + +
200A LEU* 3.7 21.0 + - + +
231A ILE* 4.1 18.8 - - + -
235A ILE* 3.8 26.6 - - + +
236A GLN 3.1 18.5 + - - +
237A ASP 3.8 0.4 - - - +
239A LYS* 1.3 79.0 - - - +
241A TYR* 1.3 57.8 + - - +
243A ILE* 3.4 5.2 + - + +
244A CYS* 2.9 30.1 + - + +
268A THR* 5.1 1.5 - - + +
277A PHE* 4.4 16.6 - + - -
279A MET* 3.6 32.3 - - + -
283A GLY 5.1 0.2 - - - -
284A ILE* 4.2 15.0 - - + -
287A CYS* 3.9 24.9 - - - -
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Residues in contact with TYR 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A ASP 3.1 18.1 + - - +
238A GLU 4.0 4.0 - - - +
240A TYR* 1.3 77.1 - - - +
242A GLN* 1.3 58.7 + - + +
244A CYS* 4.2 3.4 - - + -
245A GLU* 2.7 72.2 + - + +
283A GLY 4.7 4.0 - - - +
286A LYS* 3.2 71.9 + - + -
287A CYS* 3.8 15.5 - - - -
290A TYR* 3.6 28.2 - - + +
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Residues in contact with GLN 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A GLU* 3.3 40.2 + - - +
239A LYS* 3.2 16.2 + - - +
241A TYR* 1.3 84.1 - - + +
243A ILE* 1.3 61.2 + - + +
245A GLU* 4.2 8.1 - - - +
246A SER* 3.1 25.1 + - - -
366A LEU* 5.3 1.0 - - - +
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Residues in contact with ILE 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A LEU* 4.6 8.1 - - + -
229A VAL* 3.7 28.7 - - + -
231A ILE* 4.7 7.0 - - + -
235A ILE* 3.8 30.1 - - + -
239A LYS* 3.0 13.4 + - + +
240A TYR* 3.7 5.4 - - - +
242A GLN* 1.3 77.1 - - + +
244A CYS* 1.3 62.7 + - - +
246A SER* 3.5 4.9 + - - -
247A VAL* 3.2 25.9 + - + +
362A ILE* 3.7 42.6 - - + -
366A LEU* 4.0 17.7 - - + +
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Residues in contact with CYS 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A VAL* 5.4 0.4 - - - -
177A LEU* 4.3 20.2 - - - -
200A LEU* 3.9 18.4 - - + +
240A TYR* 2.9 18.0 + - + +
241A TYR* 3.8 3.6 - - + +
243A ILE* 1.3 75.8 - - - +
245A GLU* 1.3 59.4 + - - +
247A VAL* 3.4 3.6 + - - +
248A LEU* 2.9 59.3 + - - +
287A CYS* 3.7 32.5 - - - -
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Residues in contact with GLU 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A TYR* 2.7 57.4 + - + +
242A GLN* 4.2 7.2 - - - +
244A CYS* 1.3 72.3 - - - +
246A SER* 1.3 63.0 + - - +
248A LEU* 4.7 4.0 - - - -
249A LYS* 3.0 32.1 + - + +
290A TYR* 3.6 33.9 + - + +
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Residues in contact with SER 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A GLN 3.1 20.2 + - - -
243A ILE 3.6 4.7 - - - -
244A CYS 3.2 0.2 - - - -
245A GLU* 1.3 78.5 - - - +
247A VAL* 1.3 62.5 + - - +
249A LYS* 3.4 7.2 + - - +
250A GLU* 3.3 27.9 + - - +
366A LEU* 3.9 27.8 - - - +
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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
----------------------------------------------------------
198A VAL* 4.0 22.0 - - + -
200A LEU* 5.4 2.5 - - + -
227A VAL* 4.1 13.0 - - + -
229A VAL* 4.1 11.4 - - + -
243A ILE* 3.2 19.1 + - + +
244A CYS* 3.9 4.9 - - - +
246A SER* 1.3 75.7 - - - +
248A LEU* 1.3 53.0 + - + +
250A GLU* 3.2 7.5 + - - +
251A VAL* 2.8 54.3 + - + +
366A LEU* 3.9 18.2 - - + -
369A ILE* 4.0 24.2 - - + -
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Residues in contact with LEU 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A LEU* 4.8 4.5 - - + -
175A VAL* 3.9 28.9 - - + -
198A VAL* 4.6 15.9 - - + -
200A LEU* 6.1 0.4 - - + -
244A CYS* 2.9 42.6 + - - +
245A GLU* 5.4 0.2 - - - -
247A VAL* 1.3 77.3 - - + +
249A LYS* 1.3 57.0 + - - +
251A VAL* 4.0 7.1 - - + +
252A TYR* 2.9 31.9 + - - +
287A CYS 4.9 2.2 - - - +
290A TYR* 4.0 23.8 - - + -
291A ILE* 3.8 31.6 - - + -
294A TRP* 3.7 13.8 - - + -
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Residues in contact with LYS 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A GLU* 3.0 24.7 + - + +
246A SER* 3.7 7.2 - - - +
247A VAL 3.2 0.2 - - - -
248A LEU* 1.3 78.7 - - - +
250A GLU* 1.3 78.6 + - - +
252A TYR* 4.1 3.8 - - - +
253A GLN* 3.3 24.1 + - - +
290A TYR* 3.3 21.9 + - - +
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Residues in contact with GLU 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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246A SER* 3.3 15.9 + - - +
247A VAL* 3.2 5.3 + - - +
249A LYS* 1.3 95.5 + - + +
251A VAL* 1.3 65.1 + - - +
253A GLN* 3.5 4.3 + - - +
254A ALA* 3.0 26.5 + - - +
369A ILE* 5.9 0.7 - - + -
370A LYS* 4.8 21.4 - - + +
373A LEU* 3.6 24.1 - - + +
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Residues in contact with VAL 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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173A LEU* 3.7 39.5 - - + -
196A MET* 3.8 12.1 - - - -
198A VAL* 4.0 13.5 - - + -
227A VAL* 4.6 2.5 - - + -
247A VAL* 2.8 38.3 + - + +
248A LEU* 4.0 7.6 - - + +
250A GLU* 1.3 73.2 - - - +
252A TYR* 1.3 54.7 + - - +
254A ALA* 3.9 0.4 - - - +
255A PHE* 2.7 37.2 + - + +
373A LEU* 3.7 27.8 - - + -
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Residues in contact with TYR 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A LEU 2.9 19.5 + - - +
249A LYS* 4.1 4.7 - - - +
251A VAL* 1.3 79.2 - - - +
253A GLN* 1.3 64.1 + - + +
256A ASN* 2.9 47.0 + - - +
257A PRO* 3.7 28.5 - - + -
294A TRP* 3.6 60.1 + + + +
296A LEU* 4.3 12.3 - - + +
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Residues in contact with GLN 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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249A LYS 3.3 15.6 + - - +
250A GLU* 4.0 4.9 - - - +
252A TYR* 1.3 87.1 - - + +
254A ALA* 1.3 59.7 + - - +
256A ASN* 4.7 5.2 + - - +
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Residues in contact with ALA 254 (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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250A GLU 3.0 19.2 + - - +
251A VAL* 3.9 2.5 - - - +
253A GLN* 1.3 80.0 - - - +
255A PHE* 1.3 61.5 + - + +
256A ASN* 5.0 1.0 - - - +
373A LEU* 3.7 29.4 - - + +
376A VAL* 3.7 30.9 - - + +
377A VAL* 4.7 4.9 - - - -
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Residues in contact with PHE 255 (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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171A ARG* 2.6 64.5 + - + -
172A ILE 3.4 34.3 - - - -
173A LEU* 3.9 9.4 - - + -
193A SER 3.4 22.2 - - - -
194A LYS 3.8 4.9 - - - -
196A MET* 3.6 42.2 - - + -
225A TYR* 4.0 16.2 - + - -
251A VAL* 2.7 23.0 + - + +
254A ALA* 1.3 74.3 - - - +
256A ASN* 1.3 54.6 + - - +
257A PRO* 3.8 18.2 - - + -
376A VAL* 4.3 3.1 - - + -
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Residues in contact with ASN 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A ARG* 2.3 43.5 + - - +
252A TYR* 2.9 34.2 + - - +
253A GLN 4.9 5.8 - - - +
254A ALA 5.0 1.1 - - - +
255A PHE* 1.3 77.2 - - - +
257A PRO* 1.3 71.7 + - - +
258A LYS* 5.3 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
------------------------------------------------------------
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