Contacts of the helix formed by residues 276 - 289 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274F GLY 3.8 0.8 + - - -
275F GLN* 1.3 75.5 - - - +
277F GLU* 1.3 66.5 + - - +
278F GLU* 3.0 5.2 + - - +
279F GLU* 3.0 32.7 + - - +
280F ALA* 2.9 21.4 + - - +
305F ALA* 4.9 1.1 - - - -
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Residues in contact with GLU 277 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276F SER* 1.3 74.0 - - - +
278F GLU* 1.3 60.5 + - + +
280F ALA* 3.9 2.8 - - - +
281F SER* 2.9 14.4 + - - -
305F ALA* 3.5 24.4 - - - +
306F LEU 4.0 2.8 - - - +
308F ALA* 3.3 24.9 + - + +
309F SER* 2.8 49.2 + - - -
331F ARG* 2.8 51.2 + - - +
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Residues in contact with GLU 278 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276F SER* 3.1 5.2 + - - +
277F GLU* 1.3 78.8 - - + +
279F GLU* 1.3 57.1 + - - +
280F ALA 3.1 1.8 - - - -
281F SER* 2.9 3.6 + - - -
282F PHE* 2.7 74.1 + - + -
331F ARG* 2.5 35.3 + - - -
343F TYR* 3.1 14.1 + - - -
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Residues in contact with GLU 279 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274F GLY 4.7 1.2 - - - +
275F GLN* 3.5 26.7 - - + +
276F SER* 3.0 36.4 + - - +
278F GLU* 1.3 76.0 - - - +
280F ALA* 1.3 57.7 + - - +
282F PHE* 3.9 5.1 - - - +
283F ASN* 3.0 45.6 + - - +
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Residues in contact with ALA 280 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233F MET* 4.1 0.2 - - - +
272F SER* 4.4 2.2 - - - -
275F GLN* 3.6 20.8 + - + +
276F SER 2.9 15.3 + - - +
277F GLU 3.9 1.8 - - - +
279F GLU* 1.3 77.9 - - - +
281F SER* 1.3 56.8 + - - +
283F ASN* 3.9 0.7 - - - +
284F LEU* 2.8 26.3 + - - +
302F TYR* 3.1 42.3 + - + -
305F ALA* 3.8 15.3 - - + -
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Residues in contact with SER 281 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277F GLU 2.9 15.5 + - - -
278F GLU* 2.9 8.6 + - - -
280F ALA* 1.3 78.3 - - - +
282F PHE* 1.3 57.8 + - - +
284F LEU* 4.5 0.2 - - - -
285F ASN* 2.9 31.4 + - - +
331F ARG* 3.0 17.2 + - - -
334F VAL* 3.7 18.8 - - - +
335F ASN* 2.7 26.8 + - - -
338F ALA* 3.3 7.9 - - - +
343F TYR* 4.4 8.7 - - - -
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Residues in contact with PHE 282 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246F PRO* 4.5 16.1 - - + +
278F GLU* 2.7 55.3 + - + +
279F GLU* 3.9 5.4 - - - +
281F SER* 1.3 72.4 - - - +
283F ASN* 1.3 64.4 + - - +
285F ASN* 3.2 7.0 + - - +
286F ALA* 2.8 30.5 + - - +
343F TYR* 3.8 20.9 - + - -
344F GLU 6.0 3.6 - - - -
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Residues in contact with ASN 283 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233F MET* 3.7 20.0 - - - +
235F THR* 5.2 1.0 - - - +
246F PRO* 3.1 33.7 - - - +
249F ILE* 3.8 29.0 - - + +
250F ALA* 4.6 0.3 + - - +
275F GLN* 2.7 21.5 - - - +
279F GLU* 3.0 27.3 + - - +
280F ALA 3.9 0.7 - - - +
282F PHE* 1.3 77.8 - - - +
284F LEU* 1.3 63.9 + - - +
286F ALA* 3.2 6.0 + - - +
287F ILE* 2.9 29.5 + - - +
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Residues in contact with LEU 284 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233F MET* 4.1 5.5 - - + +
270F PHE* 4.2 14.1 - - + -
280F ALA 2.8 22.7 + - - +
281F SER* 3.8 3.6 - - - +
283F ASN* 1.3 71.8 - - - +
285F ASN* 1.3 64.7 + - - +
287F ILE* 3.1 9.5 + - + +
288F ASN* 3.0 21.8 + - - +
298F LEU 3.3 26.0 - - - +
299F THR 3.8 11.9 - - - +
300F PHE* 3.7 42.2 - - + -
302F TYR* 3.5 9.2 - - + +
335F ASN* 4.0 14.6 - - - +
338F ALA* 3.7 13.0 - - + +
339F ALA* 4.1 3.4 - - - +
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Residues in contact with ASN 285 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281F SER 2.9 18.6 + - - +
282F PHE* 3.4 7.0 - - - +
284F LEU* 1.3 76.8 - - - +
286F ALA* 1.3 64.8 + - - +
288F ASN* 2.9 14.2 + - - +
289F ARG* 3.0 44.6 + - - +
338F ALA* 3.2 14.8 - - + +
341F GLY* 3.0 13.7 + - - -
343F TYR* 2.9 52.0 + - + +
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Residues in contact with ALA 286 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246F PRO* 3.2 39.3 - - + +
247F GLU* 4.1 14.1 - - - +
250F ALA* 3.5 7.5 - - + +
282F PHE 2.8 17.0 + - - +
283F ASN 3.4 7.0 - - - +
285F ASN* 1.3 73.6 - - - +
287F ILE* 1.3 58.5 + - - +
289F ARG* 2.9 25.3 + - - +
290F CYS* 3.0 10.6 + - - -
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Residues in contact with ILE 287 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233F MET* 4.0 23.8 - - + -
249F ILE* 5.5 1.1 - - + -
250F ALA* 3.4 25.6 - - - -
253F THR* 3.8 13.5 - - + +
254F VAL* 3.8 9.9 - - + +
270F PHE* 3.8 36.6 - - + -
283F ASN* 2.9 19.0 + - + +
284F LEU* 3.1 9.8 + - + +
286F ALA* 1.3 75.5 - - - +
288F ASN* 1.3 57.5 + - - +
290F CYS* 3.0 25.3 + - - +
294F ARG* 3.6 7.1 - - - -
298F LEU* 3.4 29.6 - - + -
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Residues in contact with ASN 288 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284F LEU* 3.0 15.2 + - - +
285F ASN 2.9 4.0 + - - +
287F ILE* 1.3 73.2 - - - +
289F ARG* 1.3 58.0 + - - +
294F ARG* 2.8 33.5 + - - +
298F LEU* 2.8 39.6 + - - +
338F ALA 2.9 19.9 + - - +
339F ALA* 3.2 21.4 - - - +
340F GLN* 3.9 5.0 - - - +
341F GLY* 3.4 23.0 - - - +
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Residues in contact with ARG 289 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247F GLU* 5.0 9.5 + - - -
285F ASN* 3.0 27.2 + - - +
286F ALA* 2.9 14.0 + - - +
288F ASN* 1.3 80.5 - - - +
290F CYS* 1.3 68.2 + - - +
291F PRO* 3.5 6.1 - - - +
341F GLY* 2.8 31.3 + - - +
344F GLU* 5.2 8.2 + - - -
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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