Contacts of the helix formed by residues 270 - 287 (chain A) in PDB entry 5EJC
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 270 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A THR* 4.5 8.1 - - - +
246A PHE* 3.9 33.3 - - - -
267A PRO* 4.0 2.0 + - - +
268A GLN 3.4 0.4 - - - -
269A ASP* 1.3 86.8 + - - +
271A SER* 1.3 63.9 + - - +
272A ASP 3.2 2.7 - - - -
273A ALA* 3.1 20.2 + - - +
274A ILE* 3.2 15.7 + - - +
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Residues in contact with SER 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A LEU* 3.9 17.5 - - - -
216A PRO* 3.1 32.9 - - - +
219A SER* 3.6 7.1 + - - -
267A PRO 4.5 3.4 + - - -
268A GLN* 2.6 26.3 + - - -
269A ASP 3.3 0.4 - - - -
270A SER* 1.3 76.8 - - - +
272A ASP* 1.3 63.0 + - - +
274A ILE* 3.7 13.7 - - - +
275A VAL* 3.2 29.1 + - - +
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Residues in contact with ASP 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A SER* 5.1 4.5 + - - -
219A SER* 3.1 20.7 + - - -
222A ARG* 3.1 34.3 + - - +
269A ASP 4.3 8.1 + - - +
270A SER 3.1 1.0 + - - -
271A SER* 1.3 80.9 + - - +
273A ALA* 1.3 61.7 + - - +
276A SER* 3.4 8.1 + - - -
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Residues in contact with ALA 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A THR* 6.2 0.7 - - + +
270A SER* 3.1 11.9 + - - +
272A ASP* 1.3 78.1 - - - +
274A ILE* 1.3 65.8 + - + +
276A SER* 3.0 9.0 + - - -
277A LYS* 2.9 39.1 + - + +
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Residues in contact with ILE 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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215A LEU* 5.3 4.9 - - + -
238A VAL* 4.3 11.2 - - + +
241A GLU* 3.4 21.5 - - + +
242A ILE* 4.1 26.9 - - + +
245A THR* 3.5 26.7 - - + +
246A PHE* 3.9 28.7 - - + -
266A ILE* 5.0 5.4 - - + -
267A PRO 5.4 0.7 - - - +
270A SER 3.2 17.5 + - - +
271A SER* 3.7 18.4 - - - +
273A ALA* 1.3 78.2 - - + +
275A VAL* 1.3 59.9 + - + +
277A LYS* 4.7 0.7 - - - -
278A ALA* 2.8 32.1 + - - +
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Residues in contact with VAL 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A LEU* 4.3 14.1 - - + -
219A SER* 3.9 18.8 - - - +
222A ARG* 3.7 32.5 - - + +
223A VAL* 3.7 33.0 - - + -
238A VAL* 5.5 1.6 - - + -
271A SER 3.2 14.1 + - - +
274A ILE* 1.3 78.0 - - + +
276A SER* 1.3 64.4 + - - +
278A ALA* 3.2 6.8 + - + +
279A ILE* 3.0 42.0 + - + +
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Residues in contact with SER 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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222A ARG* 3.1 28.1 + - - +
272A ASP 3.4 5.1 + - - -
273A ALA* 3.0 11.5 + - - -
275A VAL* 1.3 79.7 - - - +
277A LYS* 1.3 63.0 + - - +
279A ILE* 3.4 6.1 + - - +
280A ASP* 3.3 27.7 + - - +
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Residues in contact with LYS 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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241A GLU* 3.4 34.4 + - + +
245A THR* 5.0 3.8 + - - +
273A ALA* 2.9 29.8 + - + +
276A SER* 1.3 77.4 - - - +
278A ALA* 1.3 57.9 + - - +
280A ASP* 3.3 10.5 + - - +
281A LEU* 2.9 28.9 + - - +
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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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234A ILE* 4.4 2.2 - - + -
237A PHE* 3.4 29.2 - - - +
238A VAL* 3.6 26.9 - - + +
241A GLU* 3.9 5.3 - - + +
274A ILE 2.8 19.5 + - - +
275A VAL* 3.2 6.0 + - - +
277A LYS* 1.3 76.0 - - - +
279A ILE* 1.3 58.1 + - - +
281A LEU* 3.3 5.8 + - - +
282A TRP* 2.9 28.6 + - - +
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Residues in contact with ILE 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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48A ARG 5.3 1.6 - - - +
50A PRO* 6.4 1.8 - - + -
222A ARG* 4.3 21.3 - - + +
223A VAL* 5.9 1.3 - - + -
226A LYS* 4.2 25.4 - - + +
234A ILE* 4.2 20.6 - - + -
238A VAL* 6.3 0.4 - - + -
275A VAL* 3.0 36.5 + - + +
276A SER* 3.7 5.4 - - - +
278A ALA* 1.3 73.6 - - + +
280A ASP* 1.3 63.9 + - - +
282A TRP* 3.2 8.8 + - + +
283A HIS* 2.9 53.0 + - + +
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Residues in contact with ASP 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 SER 3.3 14.9 + - - +
277A LYS* 3.5 10.8 - - - +
279A ILE* 1.3 80.1 - - - +
281A LEU* 1.3 57.7 - - - +
283A HIS* 3.3 9.4 + - - +
284A LYS* 2.9 30.4 + - - +
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Residues in contact with LEU 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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184A GLU* 3.6 32.5 - - + +
237A PHE* 4.0 24.2 - - + +
240A VAL* 3.9 27.6 - - + -
241A GLU* 3.7 22.0 - - + +
244A LEU* 4.1 6.1 - - + -
277A LYS 2.9 12.1 + - - +
278A ALA 3.4 9.4 - - - +
280A ASP* 1.3 77.8 - - - +
282A TRP* 1.3 60.7 + - - +
284A LYS* 3.4 16.8 + - - +
285A HIS* 3.2 33.9 + - + +
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Residues in contact with TRP 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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47A GLN* 3.2 38.1 - - + -
226A LYS* 3.6 25.1 - - + -
231A SER* 3.4 28.4 + - - -
233A LYS* 4.4 3.2 - - - +
234A ILE* 3.6 32.6 - - + +
237A PHE* 3.7 34.5 - + + -
278A ALA 2.9 16.8 + - - +
279A ILE* 3.2 10.5 + - + +
281A LEU* 1.3 74.7 - - - +
283A HIS* 1.3 87.0 + + - +
285A HIS 3.4 0.5 + - - -
286A CYS* 3.0 46.6 + - - +
288A THR* 4.0 15.7 - - - -
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Residues in contact with HIS 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A GLN 3.4 24.6 + - - -
48A ARG* 3.8 45.0 + - - +
279A ILE* 2.9 41.5 + - + +
280A ASP* 3.6 10.2 + - - +
282A TRP* 1.3 83.9 - + - +
284A LYS* 1.3 58.0 + - - +
287A GLY* 2.8 31.1 + - - +
288A THR* 3.4 28.8 + - - -
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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
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184A GLU* 3.1 33.6 + - - -
280A ASP 2.9 17.3 + - - +
281A LEU* 3.5 13.8 - - + +
282A TRP 3.2 0.2 - - - -
283A HIS* 1.3 80.1 - - - +
285A HIS* 1.3 76.5 + - + +
286A CYS 3.7 0.2 + - - -
287A GLY* 4.2 3.5 + - - -
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Residues in contact with HIS 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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180A TYR* 3.7 33.5 + + + -
183A LEU* 4.2 25.9 - - + +
184A GLU* 2.8 32.6 + - + +
237A PHE* 3.6 24.7 - + + -
281A LEU* 3.2 24.5 + - + -
284A LYS* 1.3 94.5 - - - +
286A CYS* 1.3 60.6 + - - +
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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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180A TYR* 4.4 2.0 - - - -
233A LYS* 3.2 39.0 - - - +
237A PHE* 4.0 10.5 - - - -
282A TRP* 3.0 40.4 + - + +
285A HIS* 1.3 81.8 - - - +
287A GLY* 1.3 67.1 + - - +
288A THR* 3.3 6.3 + - - +
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Residues in contact with GLY 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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48A ARG* 4.7 1.3 - - - -
283A HIS 2.8 20.2 + - - -
284A LYS 4.2 2.6 + - - -
285A HIS 3.7 1.2 - - - -
286A CYS* 1.3 76.8 - - - +
288A THR* 1.3 66.1 + - - +
289A PRO* 3.7 3.6 - - - +
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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