Contacts of the helix formed by residues 275 - 290 (chain A) in PDB entry 3REO
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 275 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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274A TRP* 1.3 77.4 - - - +
276A ASP* 1.3 54.0 + - - +
277A GLU* 3.4 16.6 + - - +
278A HIS* 3.2 29.2 + - - +
279A CYS* 2.9 30.8 + - - -
328A PRO 3.5 10.7 + - - -
329A GLY* 3.4 18.5 + - - -
331A LYS* 5.2 2.2 - - - +
333A ARG* 3.5 2.0 - - - +
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Residues in contact with ASP 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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275A SER* 1.3 73.1 - - - +
277A GLU* 1.3 69.6 + - - +
279A CYS* 3.3 4.6 + - - +
280A LEU* 2.9 36.4 + - + +
331A LYS* 3.3 23.5 + - - +
333A ARG* 2.7 39.9 + - - +
337A GLU* 5.6 0.3 - - - +
341A LEU* 4.3 13.3 - - + +
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Residues in contact with GLU 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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275A SER* 3.4 19.6 + - - +
276A ASP* 1.3 83.0 + - - +
278A HIS* 1.3 70.5 + - + +
280A LEU* 3.4 10.3 + - + +
281A LYS* 3.2 22.0 + - - +
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Residues in contact with HIS 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A PHE* 3.3 26.2 - + + -
274A TRP* 3.3 41.3 - + + -
275A SER* 3.2 22.1 + - - +
277A GLU* 1.3 82.0 - - + +
279A CYS* 1.3 59.9 + - - +
281A LYS* 3.3 9.1 + - - +
282A LEU* 2.9 24.8 + - - +
328A PRO* 4.0 12.6 + - + +
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Residues in contact with CYS 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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271A CYS* 3.3 44.9 - - - -
274A TRP* 3.7 7.2 - - - -
275A SER 2.9 20.2 + - - +
276A ASP* 3.6 5.4 - - - +
278A HIS* 1.3 76.7 - - - +
280A LEU* 1.3 59.1 + - - +
282A LEU* 3.3 9.1 + - - +
283A LEU* 2.8 39.3 + - + +
333A ARG* 3.7 13.2 - - - -
341A LEU* 4.1 19.7 - - + -
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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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276A ASP* 2.9 20.3 + - + +
277A GLU* 3.7 8.7 - - + +
278A HIS 3.2 0.2 - - - -
279A CYS* 1.3 77.0 - - - +
281A LYS* 1.3 57.8 + - - +
283A LEU* 3.5 2.8 + - + +
284A LYS* 2.9 49.8 + - - +
341A LEU* 3.8 42.0 - - + +
344A ALA* 3.8 33.9 - - + +
345A SER* 4.3 3.1 - - - -
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Residues in contact with LYS 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A PHE* 4.0 42.1 + - + +
277A GLU 3.2 11.3 + - - +
278A HIS* 3.6 13.5 - - - +
280A LEU* 1.3 79.1 - - - +
282A LEU* 1.3 62.9 + - - +
284A LYS* 3.4 9.5 + - - +
285A ASN* 3.0 31.0 + - - +
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Residues in contact with LEU 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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210A VAL* 4.1 16.6 - - + -
255A MET* 4.1 20.0 - - + +
256A PHE* 4.3 11.8 - - + -
259A VAL* 4.2 9.2 - - + -
267A ILE* 4.2 23.3 - - + -
270A ILE* 3.6 31.4 - - + -
271A CYS* 5.2 6.3 - - - -
274A TRP* 5.8 1.8 - - + -
278A HIS 2.9 13.5 + - - +
279A CYS* 3.5 12.6 - - - +
281A LYS* 1.3 77.4 - - - +
283A LEU* 1.3 59.2 + - + +
285A ASN* 3.2 7.6 + - - +
286A CYS* 2.9 39.7 + - - -
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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
----------------------------------------------------------
267A ILE* 4.1 25.4 - - + -
271A CYS* 5.0 6.7 - - - -
279A CYS* 2.8 28.4 + - + +
280A LEU* 4.9 0.7 - - - -
282A LEU* 1.3 77.6 - - + +
284A LYS* 1.3 58.0 + - - +
286A CYS* 3.2 7.6 + - + +
287A TYR* 2.8 27.4 + - - +
296A VAL* 4.3 8.5 - - + -
341A LEU* 3.8 39.5 - - + +
345A SER* 3.4 19.1 - - - +
347A PHE* 3.8 9.0 - - + -
364A PHE* 3.9 32.1 - - + -
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Residues in contact with LYS 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A LEU* 2.9 39.7 + - - +
281A LYS* 3.8 7.4 - - - +
283A LEU* 1.3 73.4 - - - +
285A ASN* 1.3 70.1 + - - +
287A TYR* 3.4 8.2 + - + +
288A ALA* 3.1 22.9 + - - +
344A ALA 3.9 20.2 + - - -
345A SER* 4.1 17.3 - - - +
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Residues in contact with ASN 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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255A MET 2.9 28.0 + - - +
256A PHE* 3.1 24.7 + - - +
257A ASP 3.9 1.8 - - - +
258A GLY* 3.6 9.7 - - - +
259A VAL* 4.3 17.4 + - + +
281A LYS* 3.0 24.5 + - - +
282A LEU* 3.2 7.1 + - - +
284A LYS* 1.3 78.0 - - - +
286A CYS* 1.3 57.1 + - - +
288A ALA* 3.3 8.0 + - - +
289A ALA* 2.8 30.2 + - - +
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Residues in contact with CYS 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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210A VAL* 5.0 0.9 - - - -
259A VAL* 4.5 6.7 - - - -
265A ILE* 3.8 34.8 - - + -
267A ILE* 5.1 2.0 - - - -
282A LEU* 2.9 36.1 + - - +
283A LEU* 3.3 15.5 - - + +
284A LYS 3.1 0.2 - - - -
285A ASN* 1.3 75.5 - - - +
287A TYR* 1.3 65.1 + - - +
289A ALA* 3.0 12.6 + - - +
290A LEU* 3.2 21.0 + - - +
296A VAL* 3.8 23.8 - - + -
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Residues in contact with TYR 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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283A LEU 2.8 18.8 + - - +
284A LYS* 3.6 7.4 - - - +
286A CYS* 1.3 71.5 - - - +
288A ALA* 1.3 64.7 + - + +
290A LEU* 3.3 9.7 + - - +
345A SER 3.8 18.2 - - - +
346A GLY* 3.3 30.3 + - - -
347A PHE* 4.0 16.3 - + + -
348A ARG* 5.9 2.3 - - - -
366A LYS* 2.8 68.9 + - + +
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Residues in contact with ALA 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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261A LYS* 4.3 11.4 - - - +
284A LYS 3.1 14.4 + - - +
285A ASN* 3.5 11.7 - - - +
287A TYR* 1.3 80.0 - - - +
289A ALA* 1.3 61.5 + - - +
290A LEU 3.4 4.7 + - - +
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Residues in contact with ALA 289 (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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259A VAL* 3.5 23.3 - - + +
260A PRO 3.5 23.1 - - - +
261A LYS* 3.4 34.9 - - - +
262A GLY 3.5 7.3 + - - +
265A ILE* 3.8 3.6 - - + -
285A ASN 2.8 17.3 + - - +
286A CYS 3.0 6.6 + - - +
288A ALA* 1.3 76.1 - - - +
290A LEU* 1.3 58.8 + - - +
291A PRO* 4.5 0.3 - - - +
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Residues in contact with LEU 290 (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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262A GLY 3.6 15.0 - - - +
263A ASP 3.7 6.5 - - - +
264A ALA* 3.7 15.0 - - - -
265A ILE* 3.8 14.6 - - + -
286A CYS 3.2 18.2 - - - +
287A TYR 3.7 5.6 - - - +
288A ALA 3.2 5.4 - - - +
289A ALA* 1.3 80.4 - - - +
291A PRO* 1.3 76.0 - - + +
294A GLY* 4.3 0.9 - - - -
295A LYS 3.6 26.7 - - - +
296A VAL* 3.6 27.6 - - + -
347A PHE* 4.1 4.9 - - + -
366A LYS* 3.1 29.3 + - + -
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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