Contacts of the helix formed by residues 277 - 291 (chain B) in PDB entry 2E4Y
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 ARG 277 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B LYS* 5.2 7.2 - - - +
100B SER* 3.1 28.9 + - - -
102B ASP 6.1 0.2 - - - +
150B TYR* 3.4 42.8 - - + +
152B SER* 3.4 26.7 + - - -
218B SER* 2.7 16.3 + - - +
219B GLU 4.5 8.3 - - - -
222B TYR* 4.1 26.4 - - + -
276B MET* 1.3 72.9 - - - +
278B SER* 1.3 64.2 + - - +
279B ASP* 2.9 32.9 + - - +
280B ASP* 3.7 14.1 - - - -
281B SER* 2.6 30.8 + - - -
302B GLY* 4.6 0.7 - - - -
2001B 52A 4.9 0.7 - - - -
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Residues in contact with SER 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B GLU* 5.6 1.1 - - - -
61B ASN* 6.2 1.1 - - - -
64B ARG* 3.5 12.2 - - - +
150B TYR* 4.1 17.9 - - - -
277B ARG* 1.3 73.8 - - - +
279B ASP* 1.3 63.6 + - - +
281B SER* 3.4 4.8 + - - -
282B ARG* 3.4 16.3 + - - +
302B GLY* 3.0 17.1 + - - -
306B GLN* 2.8 36.2 + - - +
309B ILE* 4.4 9.0 - - - +
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Residues in contact with ASP 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B GLU* 4.1 23.4 + - + +
50B LYS* 5.3 13.5 + - + +
100B SER* 5.2 0.7 - - - -
150B TYR* 3.9 6.5 + - - -
277B ARG* 2.9 36.3 + - - +
278B SER* 1.3 75.7 - - - +
280B ASP* 1.3 97.0 + - - +
281B SER 3.0 4.5 - - - -
282B ARG* 2.8 25.4 + - - +
283B GLU* 3.2 16.1 + - + +
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Residues in contact with ASP 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B LYS* 5.2 5.2 + - - -
218B SER* 2.7 39.8 + - - +
219B GLU 4.3 3.3 + - - +
247B VAL* 3.7 15.4 - - + +
248B GLY 4.1 11.5 - - - +
256B TYR* 3.1 29.3 + - - +
276B MET* 3.5 4.9 - - - +
277B ARG* 3.4 12.0 + - - +
279B ASP* 1.3 102.7 + - - +
281B SER* 1.3 60.4 + - - +
283B GLU* 4.0 0.8 - - - +
284B LEU* 3.3 23.9 + - - +
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Residues in contact with SER 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B LEU* 5.4 1.6 - - - +
276B MET* 2.9 37.2 + - - +
277B ARG 2.6 24.2 + - - -
278B SER* 3.5 7.2 - - - -
280B ASP* 1.3 77.5 - - - +
282B ARG* 1.3 61.0 + - - +
284B LEU* 4.0 1.8 - - - +
285B ILE* 3.4 26.2 + - - +
303B TRP* 4.3 29.4 - - - +
309B ILE* 3.9 6.5 - - - +
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Residues in contact with ARG 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B ARG* 5.0 12.9 - - - +
278B SER 3.4 8.4 + - - +
279B ASP* 2.8 11.5 + - - +
281B SER* 1.3 76.4 - - - +
283B GLU* 1.3 59.0 + - + +
284B LEU 3.1 1.6 - - - -
285B ILE* 3.1 4.3 + - - +
286B ALA* 2.8 37.4 + - + +
308B SER 4.2 19.5 + - - -
309B ILE* 3.9 26.5 - - + +
311B LYS* 4.6 24.0 + - - +
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Residues in contact with GLU 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251B ASN 4.4 11.8 - - - +
252B ILE* 5.2 4.6 - - - -
253B ARG* 5.5 2.8 + - - +
256B TYR* 3.2 44.3 - - + +
279B ASP* 3.2 12.4 + - + +
282B ARG* 1.3 82.3 - - + +
284B LEU* 1.3 54.5 + - - +
286B ALA* 3.5 11.6 - - - +
287B ALA* 3.0 29.1 + - - +
290B ARG* 4.4 7.0 + - - -
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Residues in contact with LEU 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216B VAL* 4.6 5.4 - - + -
247B VAL* 5.0 1.1 - - + -
256B TYR* 3.3 17.8 - - + +
259B VAL* 4.1 24.5 - - + -
260B ILE* 3.7 17.5 - - + -
263B LEU* 4.8 3.4 - - + -
274B LEU* 4.5 5.6 - - + -
276B MET* 3.7 24.2 - - + -
280B ASP 3.3 15.9 + - - +
281B SER 4.0 1.8 - - - +
282B ARG 3.1 0.4 - - - -
283B GLU* 1.3 76.6 - - - +
285B ILE* 1.3 73.8 + - + +
287B ALA* 3.2 4.4 + - - +
288B ALA* 2.8 25.3 + - - +
297B TRP* 3.6 34.1 - - + -
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Residues in contact with ILE 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281B SER 3.4 15.5 + - - +
282B ARG* 3.1 8.6 + - - +
284B LEU* 1.3 80.2 - - + +
286B ALA* 1.3 65.9 + - - +
288B ALA* 3.4 3.8 + - + +
289B ASN* 3.0 22.7 + - - +
297B TRP* 3.2 44.4 - - + +
303B TRP* 3.6 27.4 - - + -
309B ILE* 4.7 11.9 - - + +
310B VAL* 5.2 0.4 - - - -
313B SER* 3.7 25.1 - - - -
316B VAL* 4.3 5.5 - - + +
317B ALA* 4.2 13.2 - - + -
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Residues in contact with ALA 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282B ARG* 2.8 24.2 + - + +
283B GLU* 3.5 17.7 - - - +
285B ILE* 1.3 73.1 - - - +
287B ALA* 1.3 63.8 + - - +
289B ASN* 3.1 13.4 + - - +
290B ARG* 3.2 26.4 + - - +
313B SER* 4.2 10.5 - - - -
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Residues in contact with ALA 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256B TYR* 3.4 41.7 - - + -
257B ASP* 3.7 11.3 - - - +
260B ILE* 3.9 4.0 - - + -
283B GLU 3.0 7.7 + - - +
284B LEU 3.2 7.8 + - - +
286B ALA* 1.3 71.2 - - - +
288B ALA* 1.3 55.6 + - - +
289B ASN 2.7 15.6 + - - -
290B ARG* 2.9 36.5 + - - +
291B VAL* 3.6 8.1 + - - +
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Residues in contact with ALA 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260B ILE* 3.1 35.1 - - + +
284B LEU 2.8 16.1 + - - +
285B ILE* 3.7 6.5 - - - +
287B ALA* 1.3 71.2 - - - +
289B ASN* 1.3 56.7 + - - +
291B VAL 4.3 0.9 - - - -
292B ASN 3.9 0.2 + - - -
293B ALA* 2.9 39.1 + - + +
295B PHE* 5.3 0.2 - - + -
297B TRP* 4.0 22.0 - - + -
316B VAL* 3.7 8.5 - - + -
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Residues in contact with ASN 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285B ILE 3.0 16.0 + - - +
286B ALA* 3.4 5.7 + - - +
287B ALA 2.7 5.5 + - - -
288B ALA* 1.3 73.5 - - - +
290B ARG* 1.3 71.1 + - - +
291B VAL 2.9 3.9 + - - -
292B ASN* 2.9 22.0 + - - -
312B GLY 3.6 17.3 + - - -
313B SER* 3.5 13.1 + - - +
315B HIS* 3.5 12.8 - - - -
316B VAL* 2.9 33.0 - - + +
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Residues in contact with ARG 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253B ARG* 3.4 53.4 - - - +
256B TYR* 4.9 1.0 - - - +
257B ASP* 2.8 43.4 + - - +
283B GLU* 4.4 9.3 + - - -
286B ALA* 3.3 17.5 + - - +
287B ALA* 2.9 35.0 + - - +
289B ASN* 1.3 83.7 - - - +
291B VAL* 1.3 63.8 + - + +
292B ASN* 3.8 2.8 + - - -
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Residues in contact with VAL 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257B ASP* 4.4 15.0 - - + +
260B ILE* 3.9 25.4 - - + -
264B LEU* 5.3 5.3 - - + +
287B ALA 3.7 13.2 - - - +
288B ALA 4.1 2.9 - - - +
289B ASN 2.9 0.2 - - - -
290B ARG* 1.3 82.8 - - + +
292B ASN* 1.3 54.5 + - - +
293B ALA* 2.4 23.0 + - + +
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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