Contacts of the helix formed by residues 272 - 288 (chain B) in PDB entry 5EO3
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 ALA 272 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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272A ALA* 4.7 22.2 + - + +
275A VAL* 4.3 5.5 - - + +
271B ALA* 1.3 71.5 - - - +
273B GLY* 1.3 53.1 + - - +
275B VAL* 2.7 20.0 + - + +
276B LYS* 2.6 53.3 + - - +
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Residues in contact with GLY 273 (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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271B ALA* 3.2 8.0 - - - +
272B ALA* 1.3 77.5 - - - +
274B GLU* 1.3 61.5 + - - +
276B LYS* 3.5 10.6 + - - +
277B ALA* 3.2 21.1 + - - +
344B ARG* 5.0 11.2 + - - -
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Residues in contact with GLU 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B ALA* 3.7 25.7 + - + +
273B GLY* 1.3 78.3 - - - +
275B VAL* 1.3 62.7 + - + +
277B ALA* 3.3 10.7 + - - +
278B LEU* 3.3 20.6 + - - +
344B ARG* 5.7 1.8 - - - +
345B ILE 4.9 1.7 - - - +
346B PHE* 3.3 37.5 - - + -
347B SER 4.8 1.4 + - - -
350B HIS* 3.3 32.7 - - - +
352B SER* 2.7 30.8 + - - -
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Residues in contact with VAL 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A VAL* 4.1 24.5 - - + -
350A HIS* 6.0 4.9 - - + -
351A VAL* 4.1 10.5 - - + -
352A SER* 4.9 7.0 - - - +
271B ALA 3.7 2.2 - - - +
272B ALA* 2.7 43.6 + - + +
274B GLU* 1.3 75.2 - - - +
276B LYS* 1.3 61.2 + - + +
278B LEU* 3.1 7.0 + - - +
279B ASP* 2.8 39.2 + - - +
351B VAL* 3.0 36.8 - - + -
352B SER* 4.5 5.2 - - - +
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Residues in contact with LYS 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B ALA* 2.6 35.9 + - - +
273B GLY* 3.6 11.2 - - - +
275B VAL* 1.3 75.5 - - - +
277B ALA* 1.3 56.2 + - - +
279B ASP* 3.3 12.6 + - + +
280B ASP* 2.9 44.1 + - - +
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Residues in contact with ALA 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B GLY 3.2 11.2 + - - +
274B GLU 3.6 9.4 - - - +
275B VAL 3.1 0.6 - - - -
276B LYS* 1.3 79.6 - - - +
278B LEU* 1.3 56.2 + - - +
280B ASP* 3.2 11.2 + - - +
281B PHE* 2.9 23.2 + - - +
310B THR* 5.3 1.8 - - + -
312B LEU* 4.3 14.9 - - + +
344B ARG* 4.1 26.9 - - - +
346B PHE* 4.5 2.7 - - + -
365B ILE* 3.7 10.0 - - + +
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Residues in contact with LEU 278 (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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351A VAL* 4.1 15.7 - - + -
274B GLU 3.3 16.3 + - - +
275B VAL* 3.1 8.2 + - - +
277B ALA* 1.3 76.4 - - - +
279B ASP* 1.3 67.5 + - - +
281B PHE* 3.1 6.8 + - + +
282B TYR* 3.0 37.5 + - + -
312B LEU* 4.6 9.6 - - + -
346B PHE* 3.6 27.6 - - + -
352B SER* 3.8 22.0 - - - +
355B GLN* 4.1 23.1 - - + -
356B LEU* 4.0 23.1 - - + -
359B LEU* 4.6 4.5 - - + -
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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
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349A LEU 5.1 1.1 - - - -
350A HIS* 3.5 33.4 + - - +
351A VAL* 3.0 37.0 + - - +
275B VAL* 2.8 26.6 + - - +
276B LYS* 3.4 12.6 - - + +
278B LEU* 1.3 75.5 - - - +
280B ASP* 1.3 56.6 + - - +
282B TYR* 3.1 6.2 + - - +
283B LYS* 2.8 34.5 + - - +
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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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276B LYS* 2.9 26.2 + - - +
277B ALA* 3.4 12.1 - - - +
278B LEU 3.2 0.2 - - - -
279B ASP* 1.3 74.7 - - - +
281B PHE* 1.3 65.1 + - - +
283B LYS* 3.4 19.4 + - - +
284B MET* 3.0 27.4 + - + +
365B ILE* 4.0 14.9 - - + +
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Residues in contact with PHE 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B ALA 2.9 13.1 + - - +
278B LEU* 3.1 14.3 + - + +
280B ASP* 1.3 78.3 - - - +
282B TYR* 1.3 76.3 + + - +
284B MET* 3.2 5.9 + - - +
285B LEU* 3.2 39.3 + - + +
292B ALA* 3.7 19.5 - - + +
293B PHE 3.4 21.1 - - - -
294B TYR* 4.4 9.6 - + - -
312B LEU* 4.2 8.5 - - + -
359B LEU* 3.9 24.5 - - + -
363B ALA* 3.9 13.9 - - + -
364B ALA 3.4 28.3 - - - -
365B ILE* 3.8 17.2 - - + +
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Residues in contact with TYR 282 (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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351A VAL* 4.1 12.8 - - + -
278B LEU* 3.0 30.3 + - + -
279B ASP* 3.8 6.7 - - - +
281B PHE* 1.3 84.1 - + - +
283B LYS* 1.3 66.5 + - - +
285B LEU* 3.3 36.5 + - + +
286B GLN* 3.5 10.0 + - - +
355B GLN* 2.9 42.6 + - + -
358B GLN* 4.9 1.7 - - - +
359B LEU* 3.6 28.2 - - + +
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Residues in contact with LYS 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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279B ASP 2.8 17.0 + - - +
280B ASP* 3.5 20.6 + - - +
281B PHE 3.2 0.2 - - - -
282B TYR* 1.3 76.4 - - - +
284B MET* 1.3 57.6 + - - +
286B GLN* 3.0 11.0 + - + +
287B HIS* 2.8 33.4 + - + +
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Residues in contact with MET 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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280B ASP* 3.0 17.8 + - + +
281B PHE* 3.5 7.6 - - - +
283B LYS* 1.3 72.0 - - - +
285B LEU* 1.3 61.6 + - - +
286B GLN 3.0 2.5 - - - -
287B HIS* 4.2 10.1 - - + +
288B GLU* 2.7 51.8 + - - +
291B ARG* 3.4 71.6 - - - +
292B ALA* 4.1 4.9 - - + -
309B ASP* 5.5 0.7 - - - +
365B ILE* 3.8 20.6 - - + -
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Residues in contact with LEU 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 PHE* 3.2 36.4 + - + +
282B TYR* 3.3 32.5 + - + +
284B MET* 1.3 78.2 - - - +
286B GLN* 1.3 65.1 + - - +
289B PRO* 3.5 31.7 - - + +
292B ALA* 3.7 27.8 - - + +
294B TYR* 5.9 7.9 - - + -
359B LEU* 5.9 1.6 - - + -
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Residues in contact with GLN 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 TYR 3.5 8.3 + - - +
283B LYS* 3.0 12.0 + - + +
285B LEU* 1.3 89.0 - - - +
287B HIS* 1.3 64.5 + - - +
288B GLU 3.8 0.2 + - - -
289B PRO* 4.1 5.0 - - - +
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Residues in contact with HIS 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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283B LYS* 2.8 23.7 + - + +
284B MET* 4.2 15.7 - - + +
286B GLN* 1.3 79.5 - - - +
288B GLU* 1.3 73.1 + - + +
289B PRO* 3.9 1.6 - - - +
291B ARG* 4.4 9.0 + - - -
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Residues in contact with GLU 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B MET* 2.7 31.3 + - - +
287B HIS* 1.3 89.7 + - + +
289B PRO* 1.3 69.7 - - + +
290B ASP* 2.3 37.8 - - - +
291B ARG* 2.9 41.6 + - - +
369B PRO* 4.1 11.3 - - - +
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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