Contacts of the helix formed by residues 268 - 282 (chain Y) in PDB entry 2Q4G
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 THR 268 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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240Y ASP* 2.5 35.6 + - - +
266Y GLY 4.5 6.3 - - - +
267Y ILE* 1.3 80.6 - - - +
269Y ALA* 1.3 67.8 + - - +
270Y LYS* 3.1 16.7 + - - -
271Y GLY 3.1 0.7 + - - -
272Y CYS* 2.9 19.6 + - - +
294Y GLU* 3.6 22.9 - - + +
295Y LEU* 4.2 6.5 - - - -
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Residues in contact with ALA 269 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268Y THR* 1.3 77.1 - - - +
270Y LYS* 1.3 58.2 + - + +
272Y CYS* 3.4 9.4 - - - +
273Y GLY* 2.8 25.6 + - - -
294Y GLU 4.2 0.6 + - - -
295Y LEU 3.8 22.6 + - - +
298Y GLU* 3.7 31.2 - - + -
299Y GLY* 4.0 4.0 - - - +
302Y LEU* 3.5 7.5 - - - +
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Residues in contact with LYS 270 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240Y ASP* 3.3 24.5 - - + +
268Y THR* 3.0 10.1 + - - -
269Y ALA* 1.3 80.2 - - + +
271Y GLY* 1.3 62.9 + - - +
273Y GLY* 3.4 2.1 + - - -
274Y ASP* 3.3 21.5 + - - +
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Residues in contact with GLY 271 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240Y ASP* 2.9 34.5 + - - -
243Y MET* 3.3 20.4 - - - +
267Y ILE* 3.8 10.8 - - - -
268Y THR 3.1 0.4 + - - -
270Y LYS* 1.3 74.0 - - - +
272Y CYS* 1.3 65.5 + - - +
274Y ASP* 3.2 6.9 + - - +
275Y LEU* 3.0 18.7 + - - +
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Residues in contact with CYS 272 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267Y ILE* 3.7 3.7 - - - +
268Y THR 2.9 16.6 + - - +
269Y ALA* 3.4 11.7 - - - +
271Y GLY* 1.3 77.6 - - - +
273Y GLY* 1.3 62.4 + - - +
275Y LEU* 3.0 10.0 + - - +
276Y CYS* 2.9 32.5 + - - -
290Y LEU* 4.5 8.1 - - + -
295Y LEU* 4.0 16.4 - - + -
299Y GLY* 4.1 16.8 - - - -
302Y LEU* 4.6 2.7 - - + -
303Y LEU* 3.9 33.9 - - - -
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Residues in contact with GLY 273 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269Y ALA 2.8 17.2 + - - -
270Y LYS 3.4 2.9 + - - -
271Y GLY 3.3 0.2 - - - -
272Y CYS* 1.3 76.8 - - - +
274Y ASP* 1.3 61.7 - - - +
276Y CYS* 3.4 15.2 + - - +
277Y ARG* 3.5 15.9 + - - +
302Y LEU* 3.8 20.8 - - - +
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Residues in contact with ASP 274 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240Y ASP 4.6 1.4 - - - +
243Y MET* 4.8 1.1 - - + -
244Y ALA* 3.1 32.2 - - - +
247Y CYS* 3.9 19.9 - - - -
270Y LYS 3.3 12.4 + - - +
271Y GLY* 3.2 12.1 + - - +
272Y CYS 3.1 0.6 - - - -
273Y GLY* 1.3 76.1 - - - +
275Y LEU* 1.3 65.5 + - - +
277Y ARG* 2.9 54.6 + - - +
278Y VAL* 3.7 2.1 + - - +
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Residues in contact with LEU 275 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243Y MET* 3.5 28.2 - - + +
247Y CYS* 4.6 0.2 - - - -
250Y LEU* 4.2 0.7 - - + -
260Y LEU* 3.6 19.5 - - + -
262Y ILE* 4.3 4.3 - - + -
267Y ILE* 5.9 0.4 - - + -
271Y GLY 3.0 12.7 + - - +
272Y CYS* 3.5 9.4 - - - +
274Y ASP* 1.3 74.2 - - - +
276Y CYS* 1.3 61.8 + - - +
278Y VAL* 2.7 55.4 + - + +
279Y LEU* 2.9 16.8 + - + +
288Y LEU* 3.8 18.8 - - + -
290Y LEU* 3.4 38.6 - - + -
303Y LEU* 5.6 1.1 - - + -
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Residues in contact with CYS 276 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272Y CYS* 2.9 19.4 + - - -
273Y GLY* 3.7 11.2 - - - +
274Y ASP 3.2 0.4 - - - -
275Y LEU* 1.3 77.7 - - - +
277Y ARG* 1.3 61.1 + - - +
279Y LEU* 3.7 9.5 - - - +
280Y ARG* 3.0 28.0 + - - +
302Y LEU* 3.6 29.4 - - + +
303Y LEU* 4.1 21.3 - - - -
306Y THR* 3.2 28.1 + - - +
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Residues in contact with ARG 277 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244Y ALA* 5.2 1.8 + - - +
247Y CYS* 4.2 17.8 - - - +
251Y LEU* 4.3 14.2 - - + +
273Y GLY 3.5 8.5 + - - +
274Y ASP* 2.9 51.6 + - - +
275Y LEU 3.0 0.6 - - - -
276Y CYS* 1.3 78.1 - - - +
278Y VAL* 1.3 64.3 + - + +
280Y ARG* 3.1 56.2 + - - +
281Y ALA* 3.3 8.1 + - - +
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Residues in contact with VAL 278 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247Y CYS* 3.9 24.7 - - + -
250Y LEU* 3.9 32.3 - - + -
251Y LEU* 3.9 19.1 - - + -
274Y ASP 3.9 10.5 - - - +
275Y LEU* 2.7 36.1 + - + +
277Y ARG* 1.3 75.4 - - + +
279Y LEU* 1.3 73.7 + - + +
281Y ALA* 3.2 0.9 + - - -
282Y LYS* 2.8 38.0 + - + +
285Y LEU* 5.1 3.8 - - + -
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Residues in contact with LEU 279 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275Y LEU* 2.9 29.3 + - + +
276Y CYS* 3.7 11.2 - - - +
278Y VAL* 1.3 97.0 - - + +
280Y ARG* 1.3 62.8 + - - +
281Y ALA 3.1 0.9 + - - -
282Y LYS* 3.2 13.5 + - - +
285Y LEU* 3.5 27.6 - - + -
288Y LEU* 4.0 22.4 - - + -
303Y LEU* 4.3 13.9 - - + -
306Y THR* 3.7 19.7 - - + -
307Y LEU* 5.6 2.0 - - + -
312Y CYS* 3.3 32.6 - - - -
314Y LEU* 4.7 8.1 - - + -
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Residues in contact with ARG 280 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251Y LEU* 5.8 1.2 - - - +
276Y CYS 3.0 15.3 + - - +
277Y ARG* 3.1 56.6 + - - +
279Y LEU* 1.3 76.6 - - - +
281Y ALA* 1.3 66.0 + - - +
306Y THR* 4.1 9.8 - - + +
309Y GLU* 4.7 21.3 - - + +
310Y PRO 4.9 2.1 - - - -
311Y GLY* 3.9 18.8 + - - -
312Y CYS* 4.2 10.3 - - - +
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Residues in contact with ALA 281 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251Y LEU* 3.9 20.0 - - + -
277Y ARG 3.3 17.0 + - - +
278Y VAL 3.2 3.5 + - - +
279Y LEU 3.0 1.0 - - - -
280Y ARG* 1.3 85.5 - - - +
282Y LYS* 1.3 67.2 + - + +
283Y GLU* 3.8 3.5 + - - +
311Y GLY* 5.7 0.8 - - - -
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Residues in contact with LYS 282 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250Y LEU* 3.4 23.3 + - + +
251Y LEU* 4.7 7.0 + - + -
252Y HIS 3.7 16.6 + - - -
253Y PRO* 4.0 10.1 + - - +
255Y SER 2.9 29.1 + - - -
256Y ARG* 5.2 2.3 - - - +
257Y LEU 5.8 0.7 - - - +
278Y VAL* 2.8 26.2 + - + +
279Y LEU 3.2 11.4 + - - +
281Y ALA* 1.3 85.8 - - + +
283Y GLU* 1.3 57.7 + - - +
284Y SER* 2.8 25.5 + - - +
285Y LEU* 3.2 20.5 + - + +
312Y CYS* 4.3 2.6 - - - -
313Y GLN 4.5 0.5 + - - -
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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