Contacts of the helix formed by residues 270 - 285 (chain Y) in PDB entry 5A31
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 ASN 270 (chain Y).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59X LEU* 3.4 20.6 - - + +
62X THR* 3.5 16.6 + - + -
239Y TRP* 5.6 0.4 - - - +
267Y LEU* 3.0 47.5 + - - +
268Y ARG 3.9 2.6 + - - -
269Y ASP* 1.3 80.4 - - - +
271Y VAL* 1.3 65.8 + - - +
272Y ASP 4.2 1.1 - - - +
273Y LEU* 3.3 37.8 - - + +
274Y LEU* 3.0 34.6 + - - +
300Y LEU* 4.4 2.0 - - - +
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Residues in contact with VAL 271 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58X SER* 4.6 12.3 + - - +
62X THR* 4.5 16.0 - - + +
270Y ASN* 1.3 73.2 - - - +
272Y ASP* 1.3 64.7 + - + +
274Y LEU* 4.1 3.4 - - - +
275Y GLY* 3.2 17.7 + - - -
297Y ALA* 4.7 1.3 - - - +
300Y LEU* 5.1 10.8 - - + -
301Y ASP* 3.2 35.9 - - + +
304Y LEU* 3.0 47.4 - - + +
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Residues in contact with ASP 272 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55X LEU* 4.4 25.9 - - + +
58X SER* 5.3 6.9 + - - +
59X LEU* 5.0 13.9 - - + +
239Y TRP* 5.7 1.7 - - - -
243Y TYR* 3.4 11.0 + - - -
270Y ASN* 4.2 0.6 - - - +
271Y VAL* 1.3 80.3 - - + +
273Y LEU* 1.3 55.1 + - - +
275Y GLY* 3.1 3.3 + - - -
276Y SER* 2.6 45.2 + - - -
306Y LYS* 5.5 8.0 + - - +
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Residues in contact with LEU 273 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59X LEU* 5.7 0.4 - - + -
239Y TRP* 4.4 9.0 - - + +
243Y TYR* 3.6 23.8 - - + +
258Y ILE* 3.6 35.3 - - + +
261Y LEU* 3.9 35.4 - - + -
262Y GLU* 5.1 1.6 - - + +
267Y LEU* 4.2 9.6 - - + +
270Y ASN* 3.3 40.8 + - + +
271Y VAL 3.4 0.4 - - - -
272Y ASP* 1.3 79.4 + - - +
274Y LEU* 1.3 55.7 + - - +
276Y SER* 3.3 3.9 + - - +
277Y LEU* 3.0 30.1 + - - +
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Residues in contact with LEU 274 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262Y GLU* 4.0 21.8 - - + +
268Y ARG 5.5 2.7 - - - +
269Y ASP* 5.0 1.8 - - - -
270Y ASN 3.0 26.2 + - - +
271Y VAL* 4.1 0.9 - - - +
273Y LEU* 1.3 73.1 - - - +
275Y GLY* 1.3 60.4 + - - +
277Y LEU* 3.3 12.2 + - + +
278Y ALA* 2.9 30.0 + - - +
293Y LYS* 4.2 26.0 - - + +
296Y GLN* 3.9 32.8 - - + +
297Y ALA* 3.8 23.5 - - + +
300Y LEU* 3.9 22.9 - - + -
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Residues in contact with GLY 275 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271Y VAL 3.2 9.8 + - - -
272Y ASP* 3.1 7.9 + - - -
274Y LEU* 1.3 79.0 - - - +
276Y SER* 1.3 60.5 + - - +
278Y ALA* 3.3 7.7 + - - +
279Y ASP* 3.1 27.1 + - - +
294Y PHE* 6.1 1.8 - - - -
297Y ALA* 4.5 6.5 - - - +
304Y LEU* 6.5 0.2 - - - -
307Y GLY* 5.9 6.3 - - - -
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Residues in contact with SER 276 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243Y TYR* 2.7 36.2 + - - -
246Y VAL* 5.9 1.8 - - - -
258Y ILE* 5.0 6.5 - - - -
272Y ASP* 2.6 28.0 + - - -
273Y LEU* 3.3 12.6 + - - -
275Y GLY* 1.3 72.2 - - - +
277Y LEU* 1.3 62.9 + - - +
279Y ASP* 3.1 21.4 + - - +
280Y LEU* 3.1 23.6 + - - +
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Residues in contact with LEU 277 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255Y ILE* 3.6 17.7 - - + -
258Y ILE* 3.9 28.5 - - + +
259Y CYS* 4.4 6.3 - - - +
262Y GLU* 4.3 20.6 - - + +
273Y LEU 3.0 16.9 + - - +
274Y LEU* 3.6 12.3 - - + +
276Y SER* 1.3 77.5 - - - +
278Y ALA* 1.3 60.7 + - - +
280Y LEU* 3.2 8.5 + - + +
281Y TYR* 3.1 57.8 + - + -
293Y LYS* 3.3 33.0 - - + -
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Residues in contact with ALA 278 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274Y LEU 2.9 14.6 + - - +
275Y GLY* 3.5 11.0 - - - +
277Y LEU* 1.3 76.4 - - - +
279Y ASP* 1.3 57.2 + - - +
281Y TYR* 3.3 7.6 + - - +
282Y PHE* 2.9 30.4 + - - +
290Y SER* 3.9 13.5 + - - +
293Y LYS* 5.2 3.0 - - - +
294Y PHE* 4.0 38.8 - - + +
310Y VAL* 6.3 0.7 - - - -
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Residues in contact with ASP 279 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275Y GLY 3.1 17.8 + - - +
276Y SER* 3.1 16.0 + - - +
278Y ALA* 1.3 76.0 - - - +
280Y LEU* 1.3 59.1 + - + +
282Y PHE* 3.3 6.0 + - - +
283Y ARG* 3.0 61.3 + - - +
307Y GLY* 6.0 2.1 - - - -
310Y VAL* 4.5 19.9 - - - +
406Y ARG* 5.7 2.1 + - - +
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Residues in contact with LEU 280 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246Y VAL* 4.1 31.4 - - + +
251Y ASN* 2.9 22.5 - - + +
254Y ALA* 3.7 28.5 - - + -
255Y ILE* 4.0 22.2 - - + +
258Y ILE* 4.3 14.8 - - + -
276Y SER* 3.1 18.8 + - - +
277Y LEU* 3.2 10.9 + - + +
279Y ASP* 1.3 75.7 - - + +
281Y TYR* 1.3 63.2 + - + +
283Y ARG* 4.1 15.3 - - - +
284Y ALA* 2.9 28.6 + - - +
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Residues in contact with TYR 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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98F ASN* 5.0 10.1 + - - -
255Y ILE* 3.0 38.6 - - + +
259Y CYS* 5.0 1.6 - - - -
277Y LEU* 3.1 40.1 + - + +
278Y ALA 3.7 3.1 - - - +
280Y LEU* 1.3 75.0 - - + +
282Y PHE* 1.3 63.7 + - - +
284Y ALA* 3.4 5.1 + - - -
285Y GLY 3.1 3.8 + - - -
286Y ASP* 3.0 47.0 + - + +
289Y ASN* 3.1 40.8 - - + -
290Y SER* 3.0 28.3 + - - +
293Y LYS* 3.0 22.3 + - + -
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Residues in contact with PHE 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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278Y ALA 2.9 17.4 + - - +
279Y ASP* 3.7 5.4 - - - +
281Y TYR* 1.3 74.4 - - - +
283Y ARG* 1.3 65.5 + - + +
285Y GLY* 3.3 12.6 + - - -
287Y ASN* 6.0 1.1 - - - +
290Y SER* 3.0 8.8 + - - +
310Y VAL* 3.7 34.5 - - + -
313Y TYR* 4.7 13.7 - + - -
314Y LEU* 3.9 29.2 - - + -
374Y GLN* 4.8 12.1 - - - -
406Y ARG* 3.9 31.9 - - + -
407Y LEU* 6.1 0.3 - - - +
408Y ASP* 4.2 26.2 - - + -
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Residues in contact with ARG 283 (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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246Y VAL* 3.9 33.1 + - - +
247Y HIS* 5.8 2.0 + - - -
251Y ASN* 3.3 21.2 + - - +
279Y ASP* 3.0 47.4 + - - +
280Y LEU* 4.1 8.9 - - - +
282Y PHE* 1.3 75.8 - - + +
284Y ALA* 1.3 64.6 + - - +
285Y GLY* 3.1 3.2 + - - -
405Y CYS 5.7 0.9 - - - +
406Y ARG* 3.3 51.0 - - - +
407Y LEU* 4.6 16.8 - - - +
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Residues in contact with ALA 284 (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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97F PHE* 5.2 2.3 - - - -
251Y ASN* 3.3 22.4 + - + +
280Y LEU 2.9 19.0 + - - +
281Y TYR* 3.7 7.2 - - - +
283Y ARG* 1.3 76.0 - - - +
285Y GLY* 1.3 58.7 + - - +
286Y ASP* 3.3 22.8 + - - +
407Y LEU* 5.3 3.5 - - - +
442Y GLN* 5.8 0.2 - - - +
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Residues in contact with GLY 285 (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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97F PHE* 3.5 21.2 - - - -
281Y TYR 3.1 3.4 + - - -
282Y PHE 3.3 9.3 + - - -
283Y ARG 3.1 6.4 + - - -
284Y ALA* 1.3 78.1 - - - +
286Y ASP* 1.3 57.0 + - - +
287Y ASN* 3.0 17.9 + - - +
407Y LEU* 5.1 10.8 - - - -
443Y THR* 6.4 0.7 - - - -
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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
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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