Contacts of the helix formed by residues 279 - 292 (chain A) in PDB entry 1XPM
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 GLY 279 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A ALA* 3.6 17.8 - - - +
158A VAL* 3.6 9.2 - - - +
276A ILE* 3.0 25.1 + - - -
278A THR* 1.3 81.4 + - - +
280A SER* 1.3 58.7 + - - +
281A LEU 3.4 0.4 - - - -
282A TYR* 3.2 5.0 + - - -
283A LEU* 2.8 30.3 + - - +
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Residues in contact with SER 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A HIS* 3.3 22.0 - - - -
234A VAL* 3.3 22.8 + - - -
270A ASN* 3.4 13.8 + - - +
274A GLY 4.8 0.3 + - - -
275A ASN* 2.8 25.5 + - - -
276A ILE* 3.1 19.8 + - - +
277A TYR 3.1 4.2 + - - -
279A GLY* 1.3 75.4 - - - +
281A LEU* 1.3 63.7 + - - +
283A LEU* 3.3 0.6 + - - -
284A SER* 3.0 20.6 + - - -
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Residues in contact with LEU 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A SCY 6.1 0.9 - - - +
231A CYS* 3.6 25.4 - - - +
232A PHE* 3.3 30.5 - - - +
233A HIS* 3.9 15.1 + - + +
278A THR 4.6 2.3 + - - +
279A GLY 3.4 0.4 - - - -
280A SER* 1.3 78.8 - - - +
282A TYR* 1.3 92.7 + - + +
284A SER* 3.3 3.8 + - - -
285A LEU* 2.9 22.3 + - - +
302A LEU* 4.3 11.0 - - + -
303A PHE 3.8 3.1 - - - +
304A SER* 3.6 35.4 - - - +
314A TYR* 4.4 4.9 - - + +
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Residues in contact with TYR 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ILE* 5.2 0.4 - - + -
8A ILE* 4.0 1.9 - - + +
114A ALA* 3.6 24.5 - - + -
115A THR* 2.7 31.7 + - - -
118A ILE* 3.6 17.4 - - + +
137A ALA* 5.4 0.4 - - + -
158A VAL* 3.8 23.1 - - + -
160A MET* 3.5 23.8 - - + -
278A THR 3.8 16.8 - - - -
279A GLY* 3.2 5.4 + - - +
281A LEU* 1.3 95.9 - - + +
283A LEU* 1.3 63.8 + - - +
284A SER 3.2 1.6 - - - -
285A LEU* 3.3 17.6 + - + +
286A ILE* 3.1 26.9 + - - +
302A LEU* 4.7 3.8 - - + -
304A SER* 5.2 0.7 - - - -
314A TYR* 2.7 28.8 + - - -
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Residues in contact with LEU 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A PHE* 3.8 46.7 - - + -
158A VAL* 3.9 11.1 - - + +
269A TYR* 4.0 11.9 - - + -
270A ASN* 3.8 24.5 - - - +
273A VAL* 4.2 29.6 - - + -
274A GLY 5.1 1.6 - - - +
276A ILE* 4.1 18.2 - - + -
279A GLY 2.8 16.5 + - - +
280A SER 3.7 3.6 - - - +
282A TYR* 1.3 75.7 - - - +
284A SER* 1.3 59.1 + - - +
286A ILE* 3.2 5.5 + - + +
287A SER* 3.0 25.1 + - - -
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Residues in contact with SER 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A CYS* 3.6 6.6 - - - -
232A PHE 3.9 14.6 + - - -
234A VAL* 4.0 9.5 - - - +
263A TYR* 6.0 0.2 - - - -
266A ALA* 2.6 41.5 + - - +
267A VAL* 4.4 0.7 - - - +
270A ASN* 3.5 8.9 + - - -
280A SER 3.0 13.7 + - - -
281A LEU 3.3 10.3 - - - -
283A LEU* 1.3 75.9 - - - +
285A LEU* 1.3 59.3 + - - +
287A SER 3.2 0.2 + - - -
288A LEU* 2.8 29.1 + - - +
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Residues in contact with LEU 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ILE* 3.8 20.0 - - + -
8A ILE* 4.3 12.3 - - + -
169A LEU* 3.8 31.2 - - + -
231A CYS* 3.5 14.8 - - + -
281A LEU 2.9 14.2 + - - +
282A TYR* 3.5 21.8 - - + +
283A LEU 3.2 0.4 - - - -
284A SER* 1.3 77.2 - - - +
286A ILE* 1.3 62.3 + - - +
288A LEU* 3.2 4.5 + - + +
289A LEU* 2.9 38.5 + - + +
300A ILE* 4.3 17.9 - - + -
302A LEU* 4.2 24.0 - - + -
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Residues in contact with ILE 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ILE* 3.5 36.6 - - + -
9A ASN* 3.7 27.1 - - - +
10A PHE* 3.8 18.6 - - + -
158A VAL* 4.1 3.4 - - + -
269A TYR* 3.9 8.7 - - + -
282A TYR 3.1 15.4 + - - +
283A LEU* 3.5 8.7 - - - +
285A LEU* 1.3 75.4 - - - +
287A SER* 1.3 63.5 + - - +
289A LEU* 3.3 8.4 + - - +
290A GLU* 3.0 40.6 + - + +
326A LEU* 6.3 0.9 - - + -
331A HIS* 3.6 28.0 - - + +
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Residues in contact with SER 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A ASP 2.7 20.1 + - - -
266A ALA 3.2 19.3 - - - -
268A ASP 3.4 1.4 + - - -
269A TYR* 3.1 42.1 + - - -
283A LEU 3.0 13.2 + - - -
284A SER* 3.2 1.8 + - - -
286A ILE* 1.3 76.7 - - - +
288A LEU* 1.3 56.1 + - - +
291A ASN* 2.9 47.7 + - - +
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Residues in contact with LEU 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A SER* 3.8 19.1 - - - +
230A LEU 4.4 1.6 - - - +
231A CYS* 4.2 14.8 - - + -
262A GLY 3.7 19.1 - - - +
265A ASP* 3.7 3.8 + - + -
266A ALA* 3.9 11.0 - - + +
284A SER 2.8 16.3 + - - +
285A LEU* 3.6 6.1 - - + +
287A SER* 1.3 77.4 - - - +
289A LEU* 1.3 61.8 + - - +
292A ARG* 3.1 59.2 + - + +
294A LEU* 4.2 8.3 - - + +
300A ILE* 3.9 37.5 - - + -
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Residues in contact with LEU 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ILE* 6.3 0.4 - - + -
8A ILE* 4.6 10.3 - - + -
168A ILE* 3.8 22.2 - - + -
169A LEU* 4.2 13.2 - - + -
285A LEU* 2.9 39.4 + - + +
286A ILE* 3.7 7.9 - - - +
288A LEU* 1.3 76.6 - - + +
290A GLU* 1.3 57.6 + - - +
292A ARG 3.5 2.8 - - - +
294A LEU* 5.5 3.6 - - + -
300A ILE* 4.3 11.2 - - + -
318A LEU* 3.6 31.4 - - + -
322A TYR* 3.8 11.8 + - + -
323A LYS* 2.9 22.5 + - - -
326A LEU* 3.4 26.9 - - + +
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Residues in contact with GLU 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A TYR* 2.6 36.3 + - - +
286A ILE* 3.0 21.2 + - + +
287A SER 4.4 0.4 - - - +
289A LEU* 1.3 80.4 - - + +
291A ASN* 1.3 60.0 + - - +
292A ARG 3.4 0.7 - - - -
323A LYS* 3.3 15.9 + - - +
326A LEU* 3.7 19.9 - - + +
327A ASP 3.3 17.3 + - - -
328A GLN* 3.3 40.2 + - + +
331A HIS* 2.8 39.0 + - - -
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Residues in contact with ASN 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A ASP* 3.9 27.3 - - + +
268A ASP* 3.4 28.0 + - - +
269A TYR* 3.6 17.4 - - - -
287A SER* 2.9 41.2 + - - +
290A GLU* 1.3 77.1 - - - +
292A ARG* 1.3 58.7 + - - +
293A ASP* 5.3 2.3 - - - -
328A GLN* 4.2 11.1 + - - +
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Residues in contact with ARG 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A ALA 4.5 4.2 + - - -
229A SER* 4.8 0.7 - - - -
258A ARG* 3.6 28.9 + - - +
261A SER* 3.0 33.1 + - - -
262A GLY* 3.8 11.4 - - - -
265A ASP* 2.7 37.9 + - - +
288A LEU* 3.1 35.3 + - + +
289A LEU 3.5 4.9 - - - +
291A ASN* 1.3 78.7 - - - +
293A ASP* 1.3 71.9 + - - +
294A LEU* 3.5 34.2 + - + +
322A TYR* 4.2 0.3 + - - -
323A LYS* 2.8 24.3 + - - -
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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