Contacts of the helix formed by residues 270 - 284 (chain A) in PDB entry 3EDY
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 GLY 270 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A GLN* 3.2 30.1 - - - +
234A TYR 4.2 2.0 + - - -
269A ALA* 1.3 76.6 - - - +
271A ILE* 1.3 60.2 + - - -
273A ALA* 3.5 1.6 + - - +
274A SER* 2.7 28.9 + - - -
463A SER* 3.4 7.6 - - - -
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Residues in contact with ILE 271 (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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185A ARG* 3.3 42.2 - - - +
233A GLN* 3.6 1.4 + - - +
270A GLY* 1.3 71.2 - - - -
272A GLU* 1.3 75.8 + - - +
274A SER* 3.1 7.4 + - - -
275A LEU* 2.9 27.9 + - + +
461A VAL* 4.3 8.5 - - + +
463A SER* 4.5 1.8 - - - -
468A ILE* 3.8 29.8 - - + -
471A VAL* 3.7 34.3 - - + -
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Residues in contact with GLU 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A SER* 4.2 11.2 - - - -
181A SER* 5.0 2.8 + - - -
229A GLN* 3.7 22.6 - - + +
231A LEU* 3.4 22.0 - - + +
233A GLN* 2.7 30.4 + - - +
271A ILE* 1.3 91.0 + - + +
273A ALA* 1.3 60.5 + - - +
274A SER 3.2 0.8 + - - -
275A LEU* 3.5 9.8 + - + +
276A ASP* 3.4 26.5 + - - +
475A SER* 5.5 10.8 - - - +
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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
----------------------------------------------------------
229A GLN* 3.8 18.1 - - - +
233A GLN* 3.0 34.9 + - + +
234A TYR 4.0 17.9 - - - +
235A PHE* 4.3 15.3 - - + +
270A GLY 4.0 3.1 - - - +
272A GLU* 1.3 75.5 - - - +
274A SER* 1.3 59.0 + - - +
276A ASP* 3.3 14.6 - - - +
277A VAL* 3.8 9.5 - - - +
291A VAL* 5.6 1.9 - - - +
293A SER* 5.6 1.6 - - - +
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Residues in contact with SER 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A PHE* 6.1 0.2 - - - -
239A ASP* 4.6 4.2 + - - +
269A ALA* 4.7 1.6 - - - +
270A GLY 2.7 20.5 + - - -
271A ILE 3.1 7.5 + - - -
273A ALA* 1.3 78.6 - - - +
275A LEU* 1.3 65.5 + - - +
276A ASP 3.3 0.4 - - - -
277A VAL* 3.3 4.3 - - - +
278A GLN* 3.0 41.8 + - - +
461A VAL* 4.2 7.6 - - - -
462A VAL 3.2 26.8 + - - -
463A SER* 3.4 11.0 + - - -
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Residues in contact with LEU 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A ILE* 2.9 17.2 + - + +
272A GLU* 3.8 11.7 - - + +
274A SER* 1.3 79.9 - - - +
276A ASP* 1.3 66.4 + - + +
279A TYR* 3.4 44.1 + - + +
459A TYR* 4.2 10.5 - - + -
461A VAL* 3.8 22.0 - - + -
471A VAL* 4.1 15.9 - - + -
472A SER 5.8 2.7 - - - +
475A SER* 3.7 22.0 - - - +
476A ALA* 3.7 42.4 - - + +
479A PRO* 4.6 0.3 - - - +
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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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227A CYS* 3.5 31.3 - - + +
228A ALA* 3.8 3.2 - - - +
229A GLN* 3.7 28.9 + - + +
272A GLU 3.4 12.9 + - - +
273A ALA* 3.3 19.6 - - - +
275A LEU* 1.3 81.5 - - + +
277A VAL* 1.3 69.7 + - - +
280A LEU* 3.0 32.4 + - - +
291A VAL* 5.3 4.7 - - - +
292A TYR 5.4 0.2 - - - +
322A THR* 5.3 1.1 - - - +
324A SER* 6.2 3.1 - - - -
475A SER* 4.9 4.7 - - - +
479A PRO* 3.5 18.3 - - + +
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Residues in contact with VAL 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A CYS* 3.8 14.4 - - - -
235A PHE* 3.8 20.6 - - + -
240A LEU* 4.4 5.8 - - + -
257A VAL* 3.7 21.1 - - + -
273A ALA 3.8 12.3 - - - +
274A SER* 3.3 12.6 - - - +
276A ASP* 1.3 79.1 + - - +
278A GLN* 1.3 81.4 + - + +
279A TYR 2.9 6.1 + - - -
280A LEU* 4.5 1.6 - - - -
281A MET* 3.0 46.9 + - + +
289A THR* 4.6 3.6 - - + -
291A VAL* 3.9 10.5 - - + -
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Residues in contact with GLN 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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239A ASP* 3.9 17.6 + - - +
240A LEU* 4.1 18.3 - - + +
243A PHE* 3.0 52.6 - - + -
244A MET* 4.0 2.3 - - - +
274A SER* 3.0 24.8 + - - +
276A ASP 3.4 0.2 - - - -
277A VAL* 1.3 84.3 - - + +
279A TYR* 1.3 56.5 + - + +
281A MET* 4.1 1.6 - - - -
282A SER* 2.6 29.3 + - - -
461A VAL* 3.4 12.5 - - - +
462A VAL 2.7 40.5 + - - +
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Residues in contact with TYR 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A VAL 3.0 21.3 + - - -
201A THR* 3.6 10.6 - - - -
202A PRO* 3.7 28.4 - - + +
205A ILE* 4.5 5.2 - - + -
243A PHE* 3.7 10.0 - + - -
275A LEU* 3.4 34.5 + - + +
276A ASP 4.5 0.2 - - - +
277A VAL 3.0 0.2 - - - -
278A GLN* 1.3 85.9 - - + +
280A LEU* 1.3 61.4 + - - +
281A MET 3.2 0.4 - - - -
282A SER* 3.6 10.3 - - - -
283A ALA* 3.0 29.8 + - - +
459A TYR* 3.4 31.6 - + + -
460A TRP* 2.7 33.7 + - - +
461A VAL* 4.3 1.6 - - + -
476A ALA 5.3 0.2 - - - +
479A PRO* 4.1 8.5 - - + +
480A VAL* 4.4 15.7 - - + +
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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
----------------------------------------------------------
225A GLN* 3.3 24.7 + - + +
226A ALA 3.5 37.5 - - - +
227A CYS* 3.7 13.0 - - + +
276A ASP 3.0 19.9 + - - +
277A VAL 3.9 2.9 - - - +
279A TYR* 1.3 77.4 - - - +
281A MET* 1.3 56.8 + - + +
282A SER 3.2 0.2 - - - -
284A GLY* 2.9 24.8 + - - -
289A THR* 3.9 17.7 - - + -
320A VAL* 5.4 0.4 - - + -
322A THR* 4.0 11.9 - - + +
479A PRO* 3.5 26.7 - - + +
482A GLY 4.2 1.3 - - - -
483A GLY* 3.6 17.3 - - - +
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Residues in contact with MET 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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225A GLN* 4.2 0.4 - - - +
240A LEU* 3.6 15.0 - - + -
244A MET* 3.6 21.2 - - + +
251A PHE* 4.2 1.4 - - - -
253A HIS* 4.9 1.6 - - - +
254A GLN* 3.5 38.0 + - + +
256A SER 3.6 21.1 - - - +
257A VAL* 4.1 2.7 - - - -
277A VAL* 3.0 37.8 + - - +
280A LEU* 1.3 73.9 - - - +
282A SER* 1.3 59.9 + - - +
284A GLY 3.8 8.7 - - - -
285A ALA* 3.4 19.2 - - - +
286A ASN 4.5 2.6 + - - +
287A ILE 4.7 2.5 - - - +
289A THR* 3.4 38.8 - - + +
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Residues in contact with SER 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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202A PRO* 3.5 27.2 - - - +
205A ILE* 6.0 2.0 - - - -
206A ARG* 2.9 34.0 + - - +
243A PHE* 3.4 16.1 - - - -
244A MET* 3.8 4.7 - - - +
251A PHE* 4.1 8.4 - - - -
278A GLN 2.6 24.0 + - - -
279A TYR* 3.4 11.8 + - - -
280A LEU 3.2 0.4 - - - -
281A MET* 1.3 79.7 - - - +
283A ALA* 1.3 60.2 + - - +
284A GLY 3.5 0.2 - - - -
285A ALA* 3.9 2.9 - - - +
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Residues in contact with ALA 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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205A ILE* 4.7 8.9 - - + +
206A ARG* 4.3 2.3 + - - -
211A LEU* 3.9 23.9 - - - +
279A TYR 3.0 16.9 + - - +
282A SER* 1.3 79.4 - - - +
284A GLY* 1.3 56.3 + - - +
285A ALA 3.6 2.1 + - - -
480A VAL* 3.3 39.7 - - + +
483A GLY* 3.7 13.6 - - - +
484A ILE* 4.0 8.8 + - + +
487A LEU* 4.7 4.5 - - - +
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Residues in contact with GLY 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A GLN* 3.0 23.7 + - - -
280A LEU 2.9 16.2 + - - +
281A MET* 3.8 4.9 - - - -
283A ALA* 1.3 75.0 - - - +
285A ALA* 1.3 63.7 + - - -
286A ASN 3.9 0.2 + - - -
287A ILE* 3.8 19.0 + - - +
483A GLY* 3.3 21.2 - - - -
487A LEU* 5.1 1.6 - - - -
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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