Contacts of the helix formed by residues 235 - 246 (chain A) in PDB entry 3QNQ
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 VAL 235 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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231A LEU* 3.0 23.5 + - + +
232A TRP* 2.7 27.9 + - + +
233A GLY 3.3 0.2 - - - -
234A ALA* 1.3 84.0 - - - +
236A ILE* 1.3 61.0 + - - +
237A ALA 3.1 0.7 - - - -
238A VAL* 3.4 4.4 - - + +
239A ILE* 2.9 38.7 + - + +
357A VAL* 4.0 26.7 - - + -
360A THR* 3.6 21.8 - - + -
361A ILE* 4.6 9.0 - - + -
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Residues in contact with ILE 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 TRP* 2.6 46.7 + - + +
233A GLY* 5.2 1.8 - - - -
235A VAL* 1.3 73.0 - - + +
237A ALA* 1.3 57.5 + - - +
239A ILE* 3.8 6.8 - - + +
240A LEU* 2.8 46.3 + - + +
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Residues in contact with ALA 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 GLY 3.1 24.5 + - - +
234A ALA* 4.6 1.8 - - - -
235A VAL 3.1 1.2 - - - +
236A ILE* 1.3 82.0 - - - +
238A VAL* 1.3 57.5 + - - +
240A LEU* 3.6 7.8 - - - +
241A VAL* 3.1 30.2 + - - +
255A VAL* 3.8 9.7 - - + +
259A MET* 4.7 7.2 - - + -
263A TRP* 3.7 27.8 - - + -
289A PHE* 5.5 0.2 - - + -
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Residues in contact with VAL 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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234A ALA 3.3 24.3 + - - +
235A VAL* 3.4 15.4 - - + +
237A ALA* 1.3 75.9 - - - +
239A ILE* 1.3 66.6 + - - +
241A VAL* 3.4 4.1 + - - -
242A HIS* 2.6 53.2 + - + -
289A PHE* 5.0 5.8 - - + -
293A ILE* 4.3 1.8 - - + -
294A TYR* 3.8 20.9 - - + +
356A PRO* 4.2 11.2 - - + +
357A VAL* 4.5 13.7 - - + -
360A THR* 3.9 19.3 - - - +
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Residues in contact with ILE 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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232A TRP* 6.4 0.7 - - + -
235A VAL* 2.9 32.9 + - + +
236A ILE* 3.8 6.3 - - - +
238A VAL* 1.3 76.4 - - - +
240A LEU* 1.3 73.1 + - + +
242A HIS* 3.0 14.5 + - - +
243A VAL* 3.0 31.8 + - + +
353A ILE* 5.2 11.2 - - + +
357A VAL* 4.4 24.9 - - + -
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Residues in contact with LEU 240 (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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236A ILE* 2.8 31.4 + - + +
237A ALA* 3.6 8.5 - - - +
239A ILE* 1.3 82.1 - - + +
241A VAL* 1.3 56.1 + - - +
243A VAL* 3.8 12.9 - - + +
244A LEU* 3.0 41.2 + - + +
255A VAL* 3.8 17.0 - - + -
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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
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237A ALA 3.1 14.5 + - - +
238A VAL* 3.6 5.4 - - - +
239A ILE 3.1 1.2 - - - -
240A LEU* 1.3 77.0 - - - +
242A HIS* 1.3 83.0 + - + +
245A TRP* 3.0 28.8 + - + -
251A GLY* 3.3 29.7 - - - +
252A ALA* 3.8 15.0 - - - +
255A VAL* 3.4 25.1 - - + -
263A TRP* 5.6 0.7 - - + -
294A TYR* 4.1 12.8 - - - +
2E NAG 4.4 12.8 - - + -
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Residues in contact with HIS 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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238A VAL* 2.6 43.9 + - + +
239A ILE* 3.0 4.4 + - - +
241A VAL* 1.3 95.5 - - + +
243A VAL* 1.3 58.8 + - - +
244A LEU 2.9 5.4 - - - -
245A TRP* 3.1 5.6 + + - +
246A ALA* 2.9 25.3 + - - +
294A TYR* 3.8 10.6 - + - -
298A SER 2.5 31.2 + - - -
352A PHE* 3.6 28.4 - + + -
353A ILE* 4.2 20.4 - - + +
356A PRO* 3.2 27.9 - - + +
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Residues in contact with VAL 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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6A GLU* 4.7 2.3 - - - +
9A VAL* 4.7 17.6 - - + +
239A ILE* 3.0 32.4 + - + +
240A LEU* 3.8 20.4 - - + +
242A HIS* 1.3 74.6 - - - +
244A LEU* 1.3 62.9 + - + +
246A ALA* 3.4 15.0 - - + +
247A CYS* 3.2 23.2 - - - -
353A ILE* 3.5 24.0 - - + -
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Residues in contact with LEU 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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13A ALA* 4.0 21.8 - - + -
16A VAL* 5.5 2.2 - - + -
17A ALA* 6.3 0.2 - - + -
240A LEU* 3.0 30.9 + - + +
241A VAL 3.7 6.3 - - - +
242A HIS 2.9 0.8 - - - -
243A VAL* 1.3 82.0 - - + +
245A TRP* 1.3 62.5 + - - +
246A ALA 3.1 1.3 - - - -
247A CYS* 3.4 10.2 + - - +
249A ILE* 3.1 71.1 + - + +
251A GLY* 3.9 13.7 - - - -
254A ILE* 4.4 23.1 - - + -
255A VAL* 5.1 5.8 - - + -
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Residues in contact with TRP 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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241A VAL* 3.0 29.6 + - + -
242A HIS* 3.1 9.2 + + - +
244A LEU* 1.3 72.5 - - - +
246A ALA* 1.3 56.3 + - - +
247A CYS 2.8 5.8 - - - -
248A GLY* 2.7 22.8 + - - +
249A ILE 3.3 12.8 - - - -
250A HIS* 3.4 29.8 - + - -
251A GLY* 3.0 20.3 - - - +
252A ALA 3.6 2.8 - - - +
298A SER* 3.7 20.9 - - - -
333A ASN* 4.7 0.2 - - - -
334A GLU* 3.4 31.9 - - - -
337A THR* 3.9 22.4 - - + -
338A PHE* 4.5 18.2 - + - -
343A VAL* 3.4 16.8 - - + +
352A PHE* 3.8 17.7 - + + -
2E NAG 3.0 33.3 + - - -
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Residues in contact with ALA 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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6A GLU* 4.1 11.5 - - - +
242A HIS 2.9 12.9 + - - +
243A VAL* 3.4 19.5 - - + +
244A LEU 3.1 0.8 - - - -
245A TRP* 1.3 75.8 - - - +
247A CYS* 1.3 59.8 + - - +
343A VAL 2.9 20.7 - - - +
344A MET* 3.2 18.5 - - - +
349A LEU* 3.4 33.2 - - + +
352A PHE* 4.8 0.2 - - - -
353A ILE* 4.9 3.8 - - + -
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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