Contacts of the helix formed by residues 275 - 289 (chain B) in PDB entry 1XDM
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 275 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273B GLY 3.8 1.2 + - - -
274B MET* 1.3 77.0 - - - +
276B GLU* 1.3 66.1 + - - +
277B GLU* 3.1 9.7 + - - +
278B ASP* 2.6 36.6 + - - +
279B ALA* 2.9 21.4 + - - +
304B ALA* 4.9 0.2 - - - -
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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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274B MET 3.9 0.6 + - - -
275B SER* 1.3 72.4 - - - +
277B GLU* 1.3 55.1 + - - +
279B ALA* 3.6 3.3 + - - +
280B THR* 2.8 32.1 + - - -
304B ALA* 3.0 33.8 - - - +
305B LEU 4.0 1.7 - - - +
307B ALA* 3.3 21.0 + - + +
308B SER* 2.7 53.0 + - - -
330B ARG* 3.3 30.7 + - - +
334B ASN* 4.5 1.0 + - - +
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Residues in contact with GLU 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B SER* 3.0 8.2 - - - +
276B GLU* 1.3 78.1 - - - +
278B ASP* 1.3 61.8 + - - +
280B THR* 3.0 6.6 + - - -
281B LEU* 2.9 40.0 + - + +
330B ARG* 3.7 18.8 + - - +
342B TYR* 2.5 30.0 + - - -
344B HIS* 2.9 35.4 - - + +
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Residues in contact with ASP 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B PRO* 5.5 1.6 - - - +
274B MET* 4.2 11.9 - - + -
275B SER* 2.6 33.5 + - - +
277B GLU* 1.3 72.6 - - - +
279B ALA* 1.3 67.8 + - - +
280B THR 2.9 1.6 - - - -
281B LEU* 3.7 20.2 - - - +
282B ASN* 2.9 37.7 + - - +
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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
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232B MET* 4.2 0.9 - - - +
271B SER* 3.5 20.0 - - - -
274B MET* 3.5 15.1 - - + +
275B SER 2.9 16.1 + - - +
276B GLU 3.8 3.1 - - - +
278B ASP* 1.3 76.2 - - - +
280B THR* 1.3 57.3 + - - +
282B ASN 4.1 0.2 - - - -
283B LEU* 3.1 18.2 + - - +
301B TYR* 2.6 46.1 + - + -
304B ALA* 3.6 7.6 - - + -
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Residues in contact with THR 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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276B GLU 2.8 14.0 + - - -
277B GLU 3.0 8.2 + - - -
278B ASP 2.9 1.4 - - - -
279B ALA* 1.3 75.9 - - - +
281B LEU* 1.3 54.6 + - - -
282B ASN 3.2 1.3 - - - -
284B ASN* 2.7 36.4 + - - +
330B ARG* 2.8 15.9 + - - +
333B ALA 3.8 7.6 - - - +
334B ASN* 2.7 19.8 + - - +
337B ALA* 3.3 17.1 - - + +
342B TYR* 3.6 39.7 - - + -
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Residues in contact with LEU 281 (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 PRO* 3.9 18.3 - - + +
277B GLU* 2.9 41.5 + - + +
278B ASP* 3.7 22.7 - - - +
280B THR* 1.3 72.4 - - - +
282B ASN* 1.3 60.6 + - - +
284B ASN* 3.6 4.4 - - - +
285B ALA* 2.7 36.5 + - - +
342B TYR* 3.8 23.1 - - + -
344B HIS* 4.0 18.6 - - + -
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Residues in contact with ASN 282 (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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232B MET* 3.6 19.0 - - + -
234B THR* 4.9 1.8 - - - +
245B PRO* 3.5 23.1 - - - +
248B VAL* 3.0 35.6 - - + +
274B MET* 3.8 18.2 - - - -
278B ASP* 2.9 24.8 + - - +
281B LEU* 1.3 76.8 - - - +
283B LEU* 1.3 59.3 + - - +
284B ASN 3.2 1.6 - - - -
285B ALA* 4.0 5.4 - - - -
286B ILE* 2.9 37.0 + - - +
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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
----------------------------------------------------------
232B MET* 4.2 4.0 - - + +
269B PHE* 4.6 8.1 - - + -
279B ALA 3.1 20.1 + - - +
280B THR* 3.2 0.6 + - - -
282B ASN* 1.3 74.3 - - - +
284B ASN* 1.3 66.8 + - - +
286B ILE* 4.5 3.8 - - + -
287B ASN* 3.3 10.2 + - - +
297B LEU* 3.0 31.2 - - + +
298B SER* 3.3 35.0 - - - +
299B PHE* 3.4 28.0 - - + +
301B TYR* 3.5 6.3 - - + +
334B ASN* 4.2 9.4 - - - +
337B ALA* 3.0 23.0 - - + +
338B ALA 4.5 1.6 - - - +
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Residues in contact with ASN 284 (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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280B THR 2.7 19.4 + - - +
281B LEU* 3.6 5.8 - - - +
283B LEU* 1.3 74.7 - - - +
285B ALA* 1.3 59.2 + - - +
287B ASN* 2.5 28.2 + - - +
288B LEU* 3.1 25.7 + - - +
337B ALA* 3.2 13.9 - - - +
340B GLY* 2.8 28.9 + - - +
342B TYR* 2.8 49.4 + - + +
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Residues in contact with ALA 285 (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 PRO* 3.0 39.5 - - + +
246B GLU* 4.4 9.9 - - - +
249B ALA* 3.6 4.9 - - + -
281B LEU 2.7 22.9 + - - +
282B ASN* 3.8 3.4 - - - +
284B ASN* 1.3 73.4 - - - +
286B ILE* 1.3 56.0 + - - +
288B LEU* 2.6 31.8 + - - +
289B CYS* 3.0 10.4 + - - -
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Residues in contact with ILE 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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232B MET* 3.9 24.0 - - + -
248B VAL 4.7 0.7 - - - +
249B ALA* 3.2 31.6 - - + +
252B THR* 3.9 6.7 - - + +
253B VAL* 3.5 26.0 - - + +
269B PHE* 3.7 40.2 - - + -
282B ASN* 2.9 26.7 + - + +
283B LEU* 4.1 6.1 - - + +
285B ALA* 1.3 72.2 - - - +
287B ASN* 1.3 59.5 + - - +
288B LEU 3.6 0.2 + - - -
289B CYS* 3.8 5.9 - - - +
293B LYS* 4.1 2.8 - - - +
297B LEU* 3.9 26.4 - - + +
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Residues in contact with ASN 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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283B LEU 3.3 8.8 + - - +
284B ASN 2.5 18.5 + - - +
286B ILE* 1.3 75.8 - - - +
288B LEU* 1.3 58.8 + - - +
289B CYS 3.6 0.2 - - - -
293B LYS* 3.4 17.2 + - - +
297B LEU* 2.9 42.6 + - - +
337B ALA 3.2 7.5 - - - +
338B ALA* 2.7 35.0 + - - +
339B LYS 4.8 1.2 - - - -
340B GLY* 4.0 8.0 - - - +
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Residues in contact with LEU 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 ASN* 3.1 31.5 + - - +
285B ALA* 2.6 17.4 + - - +
287B ASN* 1.3 75.0 - - - +
289B CYS* 1.3 63.7 + - - +
290B PRO* 3.2 7.4 - - - +
293B LYS* 4.1 3.3 + - - +
339B LYS 5.1 1.6 - - - +
340B GLY* 3.8 22.7 - - - +
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Residues in contact with CYS 289 (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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246B GLU 5.7 0.9 - - - +
249B ALA* 4.7 5.2 - - + +
250B MET* 3.6 22.9 - - - -
253B VAL* 3.9 22.7 - - + -
285B ALA 3.0 9.5 + - - +
286B ILE* 3.8 16.2 - - - +
287B ASN 3.6 1.4 - - - -
288B LEU* 1.3 74.0 - - - +
290B PRO* 1.3 59.7 - - - +
291B LEU* 2.6 49.4 + - - -
293B LYS* 3.0 20.6 + - - +
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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