Contacts of the helix formed by residues 276 - 289 (chain L) in PDB entry 1XFB
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 276 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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274L GLY 3.8 0.8 + - - -
275L GLN* 1.3 75.1 - - - +
277L GLU* 1.3 66.4 + - - +
278L GLU* 3.0 5.6 + - - +
279L GLU* 3.0 32.6 + - - +
280L ALA* 2.9 21.7 + - - +
305L ALA* 4.9 1.1 - - - -
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Residues in contact with GLU 277 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276L SER* 1.3 73.9 - - - +
278L GLU* 1.3 61.2 + - + +
280L ALA* 3.9 2.6 - - - +
281L SER* 2.9 14.4 + - - -
305L ALA* 3.5 23.9 - - - +
306L LEU 4.0 2.8 - - - +
308L ALA* 3.3 23.8 + - + +
309L SER* 2.8 50.0 + - - -
331L ARG* 2.8 51.5 + - - +
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Residues in contact with GLU 278 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276L SER* 3.1 5.0 + - - +
277L GLU* 1.3 78.1 - - + +
279L GLU* 1.3 56.6 + - - +
280L ALA 3.1 1.8 - - - -
281L SER* 2.9 3.9 + - - -
282L PHE* 2.7 73.9 + - + -
331L ARG* 2.5 35.0 + - - -
343L TYR* 3.1 14.4 + - - -
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Residues in contact with GLU 279 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274L GLY 4.7 1.4 - - - +
275L GLN* 3.5 25.9 - - + +
276L SER* 3.0 36.6 + - - +
278L GLU* 1.3 76.2 - - - +
280L ALA* 1.3 57.3 + - - +
282L PHE* 3.9 5.1 - - - +
283L ASN* 3.0 45.5 + - - +
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Residues in contact with ALA 280 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233L MET* 4.1 0.2 - - - +
272L SER* 4.4 2.5 - - - -
275L GLN* 3.6 20.3 + - + +
276L SER 2.9 15.5 + - - +
277L GLU 3.9 2.0 - - - +
279L GLU* 1.3 78.5 - - - +
281L SER* 1.3 56.4 + - - +
283L ASN* 3.9 0.7 - - - +
284L LEU* 2.8 26.3 + - - +
302L TYR* 3.1 41.5 + - + -
305L ALA* 3.8 14.6 - - + -
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Residues in contact with SER 281 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277L GLU 2.9 15.1 + - - -
278L GLU* 2.9 8.4 + - - -
280L ALA* 1.3 78.9 - - - +
282L PHE* 1.3 58.0 + - - +
284L LEU* 4.5 0.2 - - - -
285L ASN* 2.9 31.6 + - - +
331L ARG* 3.0 17.4 + - - -
334L VAL* 3.7 18.6 - - - +
335L ASN* 2.7 26.5 + - - -
338L ALA* 3.3 7.7 - - - +
343L TYR* 4.4 9.1 - - - -
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Residues in contact with PHE 282 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246L PRO* 4.5 16.4 - - + +
278L GLU* 2.7 54.6 + - + +
279L GLU* 3.9 5.4 - - - +
281L SER* 1.3 72.2 - - - +
283L ASN* 1.3 64.2 + - - +
285L ASN* 3.2 7.2 + - - +
286L ALA* 2.8 30.1 + - - +
343L TYR* 3.8 21.1 - + - -
344L GLU 6.0 3.6 - - - -
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Residues in contact with ASN 283 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233L MET* 3.7 20.0 - - - +
235L THR* 5.2 1.2 - - - +
246L PRO* 3.1 34.1 - - - +
249L ILE* 3.8 28.6 - - + +
250L ALA* 4.6 0.3 + - - +
275L GLN* 2.7 21.1 - - - +
279L GLU* 3.0 27.5 + - - +
280L ALA 3.9 0.7 - - - +
282L PHE* 1.3 77.9 - - - +
284L LEU* 1.3 63.9 + - - +
286L ALA* 3.2 6.0 + - - +
287L ILE* 2.9 29.7 + - - +
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Residues in contact with LEU 284 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233L MET* 4.1 5.5 - - + +
270L PHE* 4.2 14.6 - - + -
280L ALA 2.8 22.5 + - - +
281L SER* 3.8 3.6 - - - +
283L ASN* 1.3 72.2 - - - +
285L ASN* 1.3 65.2 + - - +
287L ILE* 3.1 9.1 + - + +
288L ASN* 3.0 22.2 + - - +
298L LEU 3.3 25.8 - - - +
299L THR 3.8 11.2 - - - +
300L PHE* 3.7 42.0 - - + -
302L TYR* 3.5 9.4 - - + +
335L ASN* 4.0 14.6 - - - +
338L ALA* 3.7 13.5 - - + +
339L ALA* 4.1 3.4 - - - +
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Residues in contact with ASN 285 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281L SER 2.9 18.6 + - - +
282L PHE* 3.4 7.0 - - - +
284L LEU* 1.3 76.6 - - - +
286L ALA* 1.3 65.2 + - - +
288L ASN* 2.9 14.2 + - - +
289L ARG* 3.0 44.9 + - - +
338L ALA* 3.2 14.8 - - + +
341L GLY* 3.0 13.9 + - - -
343L TYR* 2.9 51.5 + - + +
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Residues in contact with ALA 286 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246L PRO* 3.2 38.8 - - + +
247L GLU* 4.1 14.6 - - - +
250L ALA* 3.5 7.5 - - + +
282L PHE 2.8 16.6 + - - +
283L ASN 3.5 7.0 - - - +
285L ASN* 1.3 73.8 - - - +
287L ILE* 1.3 58.5 + - - +
289L ARG* 2.9 25.5 + - - +
290L CYS* 3.0 10.6 + - - -
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Residues in contact with ILE 287 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233L MET* 4.0 23.8 - - + -
249L ILE* 5.5 1.1 - - + -
250L ALA* 3.4 25.8 - - - +
253L THR* 3.8 13.5 - - + +
254L VAL* 3.8 10.1 - - + +
270L PHE* 3.8 36.1 - - + -
283L ASN* 2.9 18.8 + - + +
284L LEU* 3.1 9.8 + - + +
286L ALA* 1.3 75.9 - - - +
288L ASN* 1.3 57.9 + - - +
290L CYS* 3.0 24.9 + - - +
294L ARG* 3.6 7.3 - - - -
298L LEU* 3.4 29.8 - - + -
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Residues in contact with ASN 288 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242C ILE* 5.7 5.2 - - - +
243C LYS* 5.4 3.6 + - - -
284L LEU* 3.0 15.2 + - - +
285L ASN 2.9 4.0 + - - +
287L ILE* 1.3 73.5 - - - +
289L ARG* 1.3 59.0 + - - +
294L ARG* 2.8 33.3 + - - +
298L LEU* 2.8 39.1 + - - +
338L ALA 2.9 19.9 + - - +
339L ALA* 3.2 21.0 - - - +
340L GLN* 3.9 5.2 - - - +
341L GLY* 3.4 23.0 - - - +
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Residues in contact with ARG 289 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242C ILE* 4.7 28.3 - - + +
243C LYS 6.0 0.7 - - - +
244C TYR* 6.1 2.8 - - - -
248C GLU* 4.7 12.3 + - - -
247L GLU* 5.0 9.5 + - - -
285L ASN* 3.0 26.8 + - - +
286L ALA* 2.9 14.2 + - - +
288L ASN* 1.3 79.9 - - - +
290L CYS* 1.3 67.3 + - - +
291L PRO* 3.5 6.2 - - - +
341L GLY* 2.8 31.1 + - - +
344L GLU* 5.2 5.3 + - - -
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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