Contacts of the helix formed by residues 273 - 288 (chain B) in PDB entry 4E52
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 273 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271B PRO 3.5 1.0 - - - -
272B ARG* 1.3 81.4 + - - +
274B ALA* 1.3 64.5 + - - +
275B ALA* 3.4 9.5 + - - +
276B GLU* 3.1 26.9 + - - +
277B ASN* 2.9 23.6 + - - +
314B TYR* 3.7 15.1 - - - -
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Residues in contact with ALA 274 (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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273B SER* 1.3 73.6 - - - +
275B ALA* 1.3 56.5 + - - +
277B ASN* 3.3 2.4 + - - +
278B ALA* 2.9 30.3 + - - +
314B TYR* 3.4 27.6 - - + +
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Residues in contact with ALA 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B VAL* 3.8 13.1 - - + +
273B SER* 3.1 8.6 + - - +
274B ALA* 1.3 76.9 - - - +
276B GLU* 1.3 66.6 + - + +
278B ALA* 3.3 7.0 + - - +
279B ALA* 3.1 22.3 + - - +
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Residues in contact with GLU 276 (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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240B VAL* 4.0 22.9 - - + +
243B LYS* 2.8 47.1 + - - +
245B PHE* 3.3 14.0 - - + -
271B PRO* 3.5 11.2 - - + +
272B ARG* 2.7 33.8 + - - +
273B SER* 3.1 20.2 + - - +
275B ALA* 1.3 77.0 - - + +
277B ASN* 1.3 63.5 + - - +
279B ALA* 3.2 1.0 + - - +
280B LEU* 3.0 19.6 + - - +
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Residues in contact with ASN 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B PRO* 3.5 19.1 - - + +
273B SER 2.9 17.2 + - - +
274B ALA 3.6 2.7 - - - +
275B ALA 3.2 0.2 - - - -
276B GLU* 1.3 78.4 - - - +
278B ALA* 1.3 57.4 + - - +
280B LEU* 3.3 4.0 + - - +
281B GLN* 2.9 28.9 + - - +
314B TYR* 3.5 20.2 + - + +
316B ASN* 3.4 13.3 - - - +
334B ILE* 3.6 8.3 - - - +
338B GLY* 3.0 28.9 + - - -
340B TRP* 2.8 26.2 + - - -
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Residues in contact with ALA 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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274B ALA 2.9 18.0 + - - +
275B ALA* 3.7 7.0 - - - +
277B ASN* 1.3 74.0 - - - +
279B ALA* 1.3 66.4 + - - +
281B GLN* 3.3 16.5 + - - +
282B GLN* 3.1 25.8 + - - +
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Residues in contact with ALA 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B GLN* 3.4 34.3 - - + +
239B SER 4.8 0.2 - - - +
240B VAL* 3.7 26.5 - - + -
245B PHE* 4.3 2.2 - - + -
275B ALA 3.1 12.8 + - - +
276B GLU 3.2 8.3 + - - +
278B ALA* 1.3 74.8 - - - +
280B LEU* 1.3 67.4 + - - +
282B GLN* 3.1 27.2 + - - +
283B LEU 3.6 2.3 + - - -
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Residues in contact with LEU 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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245B PHE* 4.0 19.0 - - + -
269B ALA* 3.8 14.8 - - + -
271B PRO* 4.0 12.8 - - + -
276B GLU 3.0 13.4 + - - +
277B ASN* 3.5 8.3 - - - +
278B ALA 3.3 0.2 - - - -
279B ALA* 1.3 75.7 - - - +
281B GLN* 1.3 64.2 + - - +
283B LEU* 3.1 16.2 + - + +
284B VAL* 3.2 21.1 + - + +
291B ALA* 5.5 0.7 - - + -
293B LEU* 3.5 31.9 - - + -
334B ILE* 3.9 19.5 - - + -
352B VAL* 3.7 33.2 - - + -
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Residues in contact with GLN 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B ASN* 2.9 14.6 + - - +
278B ALA* 3.4 18.6 - - - +
279B ALA 3.2 0.4 - - - -
280B LEU* 1.3 78.4 - - - +
282B GLN* 1.3 55.3 + - - +
284B VAL* 3.2 8.6 + - - +
285B VAL* 2.8 34.8 + - + +
334B ILE* 4.4 3.6 - - + +
335B PHE 4.5 0.9 - - - +
336B THR 3.0 28.2 + - - +
337B ASN* 3.2 15.6 + - - +
338B GLY* 3.5 25.2 - - - +
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Residues in contact with GLN 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B GLN* 3.9 33.6 - - - +
278B ALA 3.1 12.6 + - - +
279B ALA* 3.1 18.5 + - - +
281B GLN* 1.3 76.7 - - - +
283B LEU* 1.3 57.8 + - - +
285B VAL* 3.7 6.3 - - - +
286B ALA* 2.9 29.1 + - - +
263C GLN* 4.8 19.6 + - - +
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Residues in contact with LEU 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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235B PRO 4.1 7.0 - - - +
236B ASN* 3.5 39.7 - - - +
237B GLY 4.0 7.6 - - - +
238B GLN* 4.1 14.4 - - + +
245B PHE* 3.9 35.4 - - + +
247B THR* 4.2 14.1 - - + +
279B ALA 3.6 1.3 + - - +
280B LEU* 3.1 12.4 + - + +
282B GLN* 1.3 75.7 - - - +
284B VAL* 1.3 62.4 + - + +
286B ALA* 3.2 5.4 + - + +
287B LYS* 2.9 39.7 + - - +
350B LEU* 5.2 0.9 - - - -
352B VAL* 4.1 16.4 - - + -
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Residues in contact with VAL 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B LEU* 3.2 21.0 + - + +
281B GLN* 3.6 9.4 - - - +
283B LEU* 1.3 77.0 - - + +
285B VAL* 1.3 52.9 + - - +
287B LYS 3.4 0.2 + - - -
288B ASN* 2.7 32.7 + - - -
289B GLU 3.2 28.7 + - - +
291B ALA* 4.1 14.6 - - + -
334B ILE* 3.9 31.6 - - + +
335B PHE 3.9 18.8 - - - +
336B THR* 3.9 11.8 - - + +
350B LEU* 4.6 5.8 - - + -
352B VAL* 5.2 0.4 - - + -
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Residues in contact with VAL 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B GLN* 2.8 27.4 + - + +
282B GLN* 3.7 6.7 - - - +
284B VAL* 1.3 73.6 - - - +
286B ALA* 1.3 65.2 + - - +
288B ASN* 3.1 15.6 + - - +
336B THR* 3.1 38.8 - - - +
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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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235B PRO 5.5 2.9 - - - +
282B GLN 2.9 18.3 + - - +
283B LEU* 3.5 10.1 - - + +
285B VAL* 1.3 79.7 - - - +
287B LYS* 1.3 75.0 + - - +
288B ASN* 3.7 1.4 + - - +
252C LYS* 5.0 10.6 + - - -
260C LEU* 5.1 15.3 - - + -
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Residues in contact with LYS 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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235B PRO* 3.7 17.4 + - - +
236B ASN* 2.7 29.5 + - - -
247B THR* 4.1 16.2 - - + -
249B GLY* 5.6 4.5 - - - -
283B LEU* 2.9 21.2 + - - +
284B VAL 4.1 0.7 - - - +
286B ALA* 1.3 87.3 + - - +
288B ASN* 1.3 71.5 + - - +
289B GLU* 3.3 10.0 + - + +
350B LEU* 4.0 32.1 - - + -
250C PHE* 4.0 25.7 - - - -
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Residues in contact with ASN 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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284B VAL 2.7 12.1 + - - -
285B VAL 3.1 13.0 + - - +
286B ALA 4.9 0.9 - - - +
287B LYS* 1.3 80.4 - - - +
289B GLU* 1.3 63.0 + - - +
336B THR* 4.2 17.7 - - - +
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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