Contacts of the helix formed by residues 273 - 288 (chain A) in PDB entry 4E52
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 273 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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271A PRO 3.5 1.0 - - - -
272A ARG* 1.3 80.4 + - - +
274A ALA* 1.3 64.9 + - - +
275A ALA* 3.4 8.8 + - - +
276A GLU* 3.1 27.4 + - - +
277A ASN* 2.9 23.7 + - - +
314A TYR* 3.6 16.8 - - - -
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Residues in contact with ALA 274 (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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273A SER* 1.3 73.9 - - - +
275A ALA* 1.3 57.2 + - - +
277A ASN* 3.3 2.1 + - - +
278A ALA* 2.9 30.0 + - - +
314A TYR* 3.6 23.9 - - + +
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Residues in contact with ALA 275 (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* 4.0 16.3 - - + +
273A SER* 3.2 8.4 + - - +
274A ALA* 1.3 79.8 - - - +
276A GLU* 1.3 62.6 + - - +
278A ALA* 3.3 7.5 + - - +
279A ALA* 3.1 21.8 + - - +
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Residues in contact with GLU 276 (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* 4.1 24.4 - - + +
243A LYS* 2.9 46.9 + - - +
245A PHE* 3.4 14.3 - - + -
271A PRO* 3.5 10.4 - - + +
272A ARG* 2.8 28.2 + - - +
273A SER* 3.1 20.2 + - - +
275A ALA* 1.3 77.3 - - + +
277A ASN* 1.3 64.3 + - - +
279A ALA* 3.2 1.2 + - - +
280A LEU* 3.0 20.1 + - - +
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Residues in contact with ASN 277 (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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271A PRO* 3.6 19.1 - - + +
273A SER 2.9 11.7 + - - +
274A ALA 3.6 3.1 - - - +
276A GLU* 1.3 76.6 - - - +
278A ALA* 1.3 58.1 + - - +
280A LEU* 3.4 3.5 + - - +
281A GLN* 2.8 31.4 + - - +
314A TYR* 3.5 24.6 + - + +
316A ASN* 3.4 11.3 - - - +
334A ILE* 3.6 8.7 - - - +
338A GLY* 2.9 30.9 + - - -
340A TRP* 2.8 26.0 + - - -
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Residues in contact with ALA 278 (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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274A ALA 2.9 17.5 + - - +
275A ALA* 3.6 8.1 - - - +
276A GLU 3.2 0.2 - - - -
277A ASN* 1.3 77.6 - - - +
279A ALA* 1.3 61.6 + - - +
281A GLN* 3.3 16.4 + - - +
282A GLN* 3.2 28.1 + - - +
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Residues in contact with ALA 279 (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 GLN* 3.5 23.9 - - + +
239A SER 4.9 2.7 - - - +
240A VAL* 3.9 26.5 - - + -
245A PHE* 4.3 5.8 - - + -
275A ALA 3.1 12.4 + - - +
276A GLU 3.5 7.9 - - - +
278A ALA* 1.3 75.7 - - - +
280A LEU* 1.3 64.3 + - - +
282A GLN* 3.1 32.8 + - - +
283A LEU 3.7 0.7 + - - -
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Residues in contact with LEU 280 (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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245A PHE* 4.0 17.4 - - + -
269A ALA* 3.7 15.9 - - + -
271A PRO* 4.0 13.5 - - + -
276A GLU 3.0 15.9 + - - +
277A ASN 3.7 3.1 - - - +
279A ALA* 1.3 76.6 - - - +
281A GLN* 1.3 63.2 + - - +
283A LEU* 3.0 16.6 + - + +
284A VAL* 3.2 15.7 + - + +
291A ALA* 5.2 0.9 - - + -
293A LEU* 3.5 32.5 - - + -
334A ILE* 3.9 21.5 - - + -
352A VAL* 3.5 38.4 - - + -
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Residues in contact with GLN 281 (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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277A ASN* 2.8 18.4 + - - +
278A ALA* 3.3 16.6 - - - +
279A ALA 3.2 0.2 - - - -
280A LEU* 1.3 77.9 - - - +
282A GLN* 1.3 56.6 + - + +
284A VAL* 3.3 7.7 + - - +
285A VAL* 2.9 40.3 + - + +
334A ILE* 4.5 4.0 - - + +
335A PHE 4.4 1.6 - - - +
336A THR 3.1 23.8 + - - +
337A ASN* 3.2 15.5 + - - +
338A GLY* 3.5 29.9 - - - +
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Residues in contact with GLN 282 (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 GLN* 3.4 34.2 + - - +
278A ALA* 3.2 12.5 + - - +
279A ALA* 3.1 21.9 + - - +
280A LEU 3.1 0.6 - - - -
281A GLN* 1.3 77.8 - - - +
283A LEU* 1.3 57.6 + - - +
285A VAL* 3.8 5.7 - - - +
286A ALA* 2.9 30.0 + - - +
263B GLN* 4.7 15.2 + - - +
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Residues in contact with LEU 283 (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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235A PRO 4.1 9.4 - - - +
236A ASN* 3.6 36.6 - - - +
237A GLY 3.8 4.0 - - - +
238A GLN* 3.7 24.2 - - + +
245A PHE* 3.7 36.3 - - + +
246A LYS 4.2 0.2 - - - +
247A THR* 4.3 13.9 - - + +
279A ALA 3.7 1.3 + - - +
280A LEU* 3.0 12.7 + - + +
282A GLN* 1.3 74.9 - - - +
284A VAL* 1.3 66.8 + - + +
286A ALA* 3.3 6.3 + - + +
287A LYS* 3.0 31.4 + - + +
350A LEU* 4.9 1.1 - - - -
352A VAL* 4.1 15.5 - - + -
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Residues in contact with VAL 284 (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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280A LEU* 3.2 20.1 + - + +
281A GLN* 3.3 10.5 + - - +
283A LEU* 1.3 76.9 - - + +
285A VAL* 1.3 52.5 + - - +
287A LYS 3.6 0.2 - - - -
288A ASN* 2.7 29.3 + - - -
289A GLU 3.2 28.5 + - - +
290A ALA* 4.0 0.2 - - - -
291A ALA* 4.0 15.0 - - + -
334A ILE* 3.8 30.1 - - + +
335A PHE 3.8 20.9 - - - +
336A THR* 3.8 14.3 - - + +
350A LEU* 4.6 4.5 - - + -
352A VAL* 5.3 0.2 - - + -
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Residues in contact with VAL 285 (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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281A GLN* 2.9 25.9 + - + +
282A GLN* 3.8 7.0 - - - +
284A VAL* 1.3 73.8 - - - +
286A ALA* 1.3 65.9 + - - +
288A ASN* 3.0 16.2 + - - +
336A THR* 3.1 38.8 - - - +
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Residues in contact with ALA 286 (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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235A PRO 5.3 9.0 - - - +
282A GLN 2.9 18.5 + - - +
283A LEU* 3.3 8.9 + - + +
285A VAL* 1.3 79.9 - - - +
287A LYS* 1.3 65.4 + - + +
288A ASN* 4.8 0.7 - - - +
250B PHE* 6.5 1.3 - - + -
252B LYS* 5.5 4.9 + - - -
260B LEU* 5.8 8.3 - - + -
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Residues in contact with LYS 287 (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 ASN* 4.4 17.1 + - - +
247A THR* 4.3 11.9 - - + -
249A GLY* 3.4 39.1 + - - -
283A LEU* 3.0 19.6 + - + +
284A VAL 4.1 0.7 - - - +
286A ALA* 1.3 80.6 - - + +
288A ASN* 1.3 71.3 + - - +
289A GLU* 3.2 13.2 + - + +
350A LEU* 3.9 28.7 - - + -
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Residues in contact with ASN 288 (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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284A VAL 2.7 12.7 + - - -
285A VAL 3.0 12.6 + - - +
286A ALA 4.8 1.3 - - - +
287A LYS* 1.3 80.4 - - - +
289A GLU* 1.3 65.4 + - - +
336A THR* 4.1 19.4 - - - +
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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