Contacts of the helix formed by residues 276 - 289 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274H GLY 3.8 0.6 + - - -
275H GLN* 1.3 76.1 - - - +
277H GLU* 1.3 67.6 + - - +
278H GLU* 3.0 6.1 + - - +
279H GLU* 3.0 32.7 + - - +
280H ALA* 2.9 21.4 + - - +
305H ALA* 4.9 0.7 - - - -
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Residues in contact with GLU 277 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276H SER* 1.3 73.1 - - - +
278H GLU* 1.3 61.0 + - + +
280H ALA* 3.8 3.1 + - - +
281H SER* 2.9 14.2 + - - -
305H ALA* 3.5 23.9 - - - +
306H LEU 4.0 2.9 - - - +
308H ALA* 3.3 25.2 + - + +
309H SER* 2.8 49.6 + - - -
331H ARG* 2.8 52.8 + - - +
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Residues in contact with GLU 278 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276H SER* 3.1 5.2 + - - +
277H GLU* 1.3 78.0 - - + +
279H GLU* 1.3 57.0 + - - +
280H ALA 3.1 1.8 - - - -
281H SER* 2.9 3.8 + - - -
282H PHE* 2.7 75.0 + - + -
331H ARG* 2.5 35.6 + - - -
343H TYR* 3.1 13.9 + - - -
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Residues in contact with GLU 279 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274H GLY 4.7 1.2 - - - +
275H GLN* 3.5 26.8 - - - +
276H SER* 3.0 35.8 + - - +
278H GLU* 1.3 76.2 - - - +
280H ALA* 1.3 56.8 + - - +
282H PHE* 3.9 4.9 - - - +
283H ASN* 3.0 43.8 + - - +
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Residues in contact with ALA 280 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272H SER* 4.4 2.9 - - - -
275H GLN* 3.6 19.4 + - + +
276H SER 2.9 14.9 + - - +
277H GLU 3.9 2.5 - - - +
279H GLU* 1.3 76.6 - - - +
281H SER* 1.3 58.0 + - - +
283H ASN* 3.9 1.0 - - - +
284H LEU* 2.8 25.6 + - - +
302H TYR* 3.1 41.7 + - + -
305H ALA* 3.8 13.9 - - + -
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Residues in contact with SER 281 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277H GLU 2.9 14.6 + - - -
278H GLU* 2.9 8.6 + - - -
280H ALA* 1.3 77.6 - - - +
282H PHE* 1.3 56.9 + - - +
284H LEU* 4.5 0.2 - - - -
285H ASN* 2.9 31.4 + - - +
331H ARG* 3.0 17.9 + - - -
334H VAL* 3.7 19.2 - - - +
335H ASN* 2.7 26.6 + - - -
338H ALA* 3.3 7.7 - - - +
343H TYR* 4.4 9.6 - - - -
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Residues in contact with PHE 282 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246H PRO* 4.5 16.4 - - + +
278H GLU* 2.7 55.6 + - + +
279H GLU* 3.9 5.4 - - - +
281H SER* 1.3 72.0 - - - +
283H ASN* 1.3 64.0 + - - +
285H ASN* 3.2 7.2 + - - +
286H ALA* 2.8 30.2 + - - +
343H TYR* 3.8 21.1 - + - -
344H GLU 6.0 3.8 - - - -
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Residues in contact with ASN 283 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233H MET* 3.7 20.0 - - - +
235H THR* 5.2 1.0 - - - +
246H PRO* 3.1 32.7 - - - +
249H ILE* 3.8 29.3 - - + +
250H ALA* 4.6 0.3 - - - +
275H GLN* 2.7 20.9 - - - +
279H GLU* 3.0 27.1 + - - +
280H ALA 3.9 0.9 - - - +
282H PHE* 1.3 77.5 - - - +
284H LEU* 1.3 63.9 + - - +
286H ALA* 3.2 5.1 + - - +
287H ILE* 2.9 28.8 + - - +
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Residues in contact with LEU 284 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233H MET* 4.1 5.1 - - + +
270H PHE* 4.2 13.2 - - + -
280H ALA 2.8 22.7 + - - +
281H SER 3.8 3.1 - - - +
283H ASN* 1.3 72.7 - - - +
285H ASN* 1.3 64.8 + - - +
287H ILE* 3.1 8.5 + - + +
288H ASN* 3.0 22.3 + - - +
298H LEU 3.3 26.0 - - - +
299H THR 3.8 12.3 - - - +
300H PHE* 3.7 40.8 - - + -
302H TYR* 3.5 10.1 - - + +
335H ASN* 4.0 15.3 - - - +
338H ALA* 3.7 12.3 - - + +
339H ALA* 4.1 3.1 - - - +
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Residues in contact with ASN 285 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281H SER 2.9 19.3 + - - +
282H PHE* 3.4 7.0 - - - +
284H LEU* 1.3 76.3 - - - +
286H ALA* 1.3 65.0 + - - +
288H ASN* 2.9 14.0 + - - +
289H ARG* 3.0 45.9 + - - +
338H ALA* 3.2 15.1 - - + +
341H GLY* 3.0 13.7 + - - -
343H TYR* 2.9 52.9 + - + +
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Residues in contact with ALA 286 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246H PRO* 3.2 39.3 - - + +
247H GLU* 4.1 13.5 - - - +
250H ALA* 3.5 7.3 - - + +
282H PHE 2.8 16.7 + - - +
283H ASN 3.5 7.0 - - - +
285H ASN* 1.3 74.1 - - - +
287H ILE* 1.3 58.0 + - - +
289H ARG* 2.9 24.8 + - - +
290H CYS* 3.0 10.6 + - - -
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Residues in contact with ILE 287 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233H MET* 4.0 24.0 - - + -
249H ILE* 5.3 1.3 - - + -
250H ALA* 3.4 25.6 - - - -
253H THR* 3.8 13.7 - - + +
254H VAL* 3.8 10.1 - - + +
270H PHE* 3.8 35.0 - - + -
283H ASN* 2.9 19.0 + - + +
284H LEU* 3.1 11.2 + - + +
286H ALA* 1.3 75.8 - - - +
288H ASN* 1.3 59.0 + - - +
290H CYS* 3.0 25.6 + - - +
294H ARG* 3.6 6.8 - - - -
298H LEU* 3.4 28.9 - - + -
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Residues in contact with ASN 288 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319A ASP* 5.1 0.9 - - - +
320A ASN* 4.4 7.4 + - - -
284H LEU* 3.0 14.8 + - - +
285H ASN 2.9 4.4 + - - +
287H ILE* 1.3 73.1 - - - +
289H ARG* 1.3 59.8 + - - +
294H ARG* 2.8 33.5 + - - +
298H LEU* 2.8 40.5 + - - +
338H ALA 2.9 20.3 + - - +
339H ALA* 3.2 21.6 - - - +
340H GLN* 3.9 4.4 - - - +
341H GLY* 3.4 23.2 - - - +
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Residues in contact with ARG 289 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313A ALA* 4.8 23.6 + - - +
315A ARG* 4.0 8.3 - - - -
320A ASN* 3.4 29.6 - - - +
323A ALA* 4.9 11.9 - - - +
247H GLU* 5.0 9.1 + - - -
285H ASN* 3.0 26.6 + - - +
286H ALA* 2.9 14.4 + - - +
288H ASN* 1.3 79.3 - - - +
290H CYS* 1.3 67.0 + - - +
291H PRO* 3.5 4.3 - - - +
341H GLY* 2.8 31.8 + - - +
344H GLU* 5.2 8.1 + - - -
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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