Contacts of the helix formed by residues 276 - 289 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274C GLY 3.8 1.0 + - - -
275C GLN* 1.3 76.8 - - - +
277C GLU* 1.3 67.5 + - - +
278C GLU* 3.0 6.1 + - - +
279C GLU* 3.0 32.3 + - - +
280C ALA* 2.9 21.3 + - - +
305C ALA* 4.9 1.1 - - - -
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Residues in contact with GLU 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276C SER* 1.3 73.4 - - - +
278C GLU* 1.3 61.5 + - + +
280C ALA* 3.8 2.9 + - - +
281C SER* 2.9 14.2 + - - -
305C ALA* 3.5 24.9 - - - +
306C LEU 4.0 2.8 - - - -
308C ALA* 3.3 24.9 + - + +
309C SER* 2.8 50.1 + - - -
331C ARG* 2.8 52.2 + - - +
335C ASN* 4.9 0.2 + - - -
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Residues in contact with GLU 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276C SER* 3.1 5.4 + - - +
277C GLU* 1.3 76.9 - - + +
279C GLU* 1.3 58.1 + - - +
280C ALA 3.1 1.6 - - - -
281C SER* 2.9 4.0 + - - -
282C PHE* 2.7 74.7 + - + -
331C ARG* 2.5 35.0 + - - -
343C TYR* 3.1 13.5 + - - -
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Residues in contact with GLU 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249C ILE* 5.9 2.1 - - - +
274C GLY 4.7 1.0 - - - +
275C GLN* 3.5 26.3 - - + +
276C SER* 3.0 35.4 + - - +
278C GLU* 1.3 76.1 - - - +
280C ALA* 1.3 58.8 + - - +
282C PHE* 3.9 5.7 - - - +
283C ASN* 3.0 44.4 + - - +
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Residues in contact with ALA 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233C MET* 4.1 0.2 - - - +
272C SER* 4.4 2.2 - - - -
275C GLN* 3.6 20.3 + - + +
276C SER 2.9 15.7 + - - +
277C GLU 3.9 1.8 - - - +
279C GLU* 1.3 77.7 - - - +
281C SER* 1.3 57.5 + - - +
283C ASN* 3.9 0.7 - - - +
284C LEU* 2.8 26.9 + - - +
302C TYR* 3.1 40.6 + - + -
305C ALA* 3.8 14.8 - - + -
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Residues in contact with SER 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277C GLU 2.9 14.7 + - - -
278C GLU* 2.9 8.8 + - - -
280C ALA* 1.3 78.3 - - - +
282C PHE* 1.3 57.7 + - - +
284C LEU* 4.5 0.2 - - - -
285C ASN* 2.9 31.6 + - - +
331C ARG* 3.0 17.7 + - - -
334C VAL* 3.7 19.0 - - - +
335C ASN* 2.7 26.6 + - - -
338C ALA* 3.3 7.9 - - - +
343C TYR* 4.4 8.5 - - - -
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Residues in contact with PHE 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246C PRO* 4.5 14.5 - - + +
278C GLU* 2.7 54.9 + - + +
279C GLU* 3.9 5.4 - - - +
281C SER* 1.3 73.0 - - - +
283C ASN* 1.3 63.6 + - - +
285C ASN* 3.2 7.8 + - - +
286C ALA* 2.8 31.0 + - - +
343C TYR* 3.8 21.8 - + - -
344C GLU 6.0 3.4 - - - -
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Residues in contact with ASN 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233C MET* 3.7 19.8 - - - +
235C THR* 5.2 0.7 - - - +
246C PRO* 3.1 33.1 - - - +
249C ILE* 3.8 28.9 - - + +
250C ALA* 4.6 0.2 - - - +
275C GLN* 2.7 21.3 - - - +
279C GLU* 3.0 26.8 + - - +
280C ALA 3.9 0.4 - - - +
282C PHE* 1.3 77.1 - - - +
284C LEU* 1.3 63.6 + - - +
286C ALA* 3.2 5.6 + - - +
287C ILE* 2.9 29.5 + - - +
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Residues in contact with LEU 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233C MET* 4.1 5.5 - - + +
270C PHE* 4.2 13.7 - - + -
280C ALA 2.8 22.3 + - - +
281C SER* 3.8 3.1 - - - +
283C ASN* 1.3 71.3 - - - +
285C ASN* 1.3 64.5 + - - +
287C ILE* 3.1 9.1 + - + +
288C ASN* 3.0 22.0 + - - +
298C LEU 3.3 25.8 - - - +
299C THR 3.8 12.8 - - - +
300C PHE* 3.7 41.7 - - + -
302C TYR* 3.5 9.6 - - + +
335C ASN* 4.0 14.4 - - - +
338C ALA* 3.7 14.1 - - + +
339C ALA* 4.1 3.4 - - - +
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Residues in contact with ASN 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281C SER 2.9 19.1 + - - +
282C PHE* 3.4 6.5 - - - +
284C LEU* 1.3 75.6 - - - +
286C ALA* 1.3 64.0 - - - +
288C ASN* 2.9 14.7 + - - +
289C ARG* 3.0 45.4 + - - +
338C ALA* 3.2 14.7 - - + +
341C GLY* 3.0 14.2 + - - -
343C TYR* 2.9 52.8 + - + +
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Residues in contact with ALA 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246C PRO* 3.2 38.1 - - + +
247C GLU* 4.1 14.1 - - - +
250C ALA* 3.5 7.7 - - + +
282C PHE 2.8 16.8 + - - +
283C ASN 3.5 7.0 - - - +
285C ASN* 1.3 73.6 - - - +
287C ILE* 1.3 58.8 + - - +
289C ARG* 2.9 25.8 + - - +
290C CYS* 3.0 10.2 + - - -
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Residues in contact with ILE 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233C MET* 4.0 24.5 - - + -
249C ILE* 5.3 1.1 - - + -
250C ALA* 3.4 25.4 - - - +
253C THR* 3.8 13.9 - - + +
254C VAL* 3.8 9.7 - - + +
270C PHE* 3.8 35.0 - - + -
283C ASN* 2.9 19.6 + - + +
284C LEU* 3.2 9.6 - - + +
286C ALA* 1.3 75.7 - - - +
288C ASN* 1.3 58.5 + - - +
290C CYS* 3.0 24.9 + - - +
294C ARG* 3.6 6.9 - - - -
298C LEU* 3.4 29.8 - - + -
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Residues in contact with ASN 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284C LEU* 3.0 14.3 + - - +
285C ASN 2.9 4.5 + - - +
287C ILE* 1.3 73.4 - - - +
289C ARG* 1.3 59.7 + - - +
294C ARG* 2.8 33.9 + - - +
298C LEU* 2.8 39.7 + - - +
338C ALA 2.9 19.9 + - - +
339C ALA* 3.2 22.0 - - - +
340C GLN* 3.9 4.9 - - - +
341C GLY* 3.4 22.7 + - - +
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Residues in contact with ARG 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247C GLU* 5.0 9.7 + - - -
285C ASN* 3.0 26.8 + - - +
286C ALA* 2.9 15.3 + - - +
288C ASN* 1.3 79.8 - - - +
290C CYS* 1.3 66.6 + - - +
291C PRO* 3.5 5.5 - - - +
294C ARG* 4.3 0.4 - - - -
341C GLY* 2.8 32.9 + - - +
344C GLU* 5.2 7.7 + - - -
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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