Contacts of the helix formed by residues 279 - 292 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C ALA* 3.6 17.4 - - - +
157C ALA* 6.0 0.2 - - - -
158C VAL* 3.6 9.8 - - - +
276C ILE* 3.1 23.2 + - - -
277C TYR 3.0 1.6 + - - -
278C THR* 1.3 80.8 + - - +
280C SER* 1.3 57.8 + - - +
281C LEU 3.4 1.6 - - - -
282C TYR* 3.2 4.8 + - - -
283C LEU* 2.9 30.3 + - - +
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Residues in contact with SER 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233C HIS* 3.3 22.0 - - - -
234C VAL* 3.3 22.2 + - - -
270C ASN* 3.3 14.8 + - - +
274C GLY 4.8 0.3 + - - -
275C ASN* 2.8 24.8 + - - -
276C ILE* 3.0 21.3 + - - +
277C TYR 3.0 3.7 + - - -
279C GLY* 1.3 76.8 - - - +
281C LEU* 1.3 63.1 + - - +
283C LEU 3.3 0.3 + - - -
284C SER* 3.0 19.8 + - - -
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Residues in contact with LEU 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C SCY 6.0 1.6 - - - +
231C CYS* 3.5 26.7 - - + +
232C PHE* 3.3 31.2 - - - +
233C HIS* 3.8 17.9 + - + +
278C THR 4.6 2.5 + - - +
279C GLY 3.4 0.6 - - - -
280C SER* 1.3 77.3 - - - +
282C TYR* 1.3 91.8 + - + +
284C SER* 3.3 3.1 + - - -
285C LEU* 2.9 22.5 + - - +
302C LEU* 4.4 9.4 - - + -
303C PHE 3.8 2.7 - - - +
304C SER* 3.6 36.3 - - - +
314C TYR* 4.5 5.2 - - + +
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Residues in contact with TYR 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C ILE* 3.9 2.2 - - + +
114C ALA* 3.7 24.5 - - + -
115C THR* 2.8 30.7 + - - -
118C ILE* 3.6 18.2 - - + +
137C ALA* 5.4 0.4 - - + -
158C VAL* 3.8 24.5 - - + -
160C MET* 3.5 24.5 - - + -
278C THR 3.8 16.4 - - - -
279C GLY* 3.2 4.8 + - - +
281C LEU* 1.3 98.0 - - + +
283C LEU* 1.3 63.0 + - - +
284C SER 3.2 0.9 - - - -
285C LEU* 3.3 23.0 + - + +
286C ILE* 3.1 26.5 + - - +
302C LEU* 4.8 0.7 - - + -
304C SER* 5.1 0.7 - - - -
314C TYR* 2.7 28.5 + - - -
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Residues in contact with LEU 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C PHE* 3.7 45.5 - - + -
12C VAL* 5.5 0.2 - - + -
158C VAL* 4.0 6.5 - - + +
269C TYR* 4.1 11.9 - - + -
270C ASN* 3.7 24.9 - - - +
273C VAL* 4.2 30.1 - - + -
274C GLY 5.0 1.3 - - - +
276C ILE* 4.0 22.0 - - + -
279C GLY 2.9 16.4 + - - +
280C SER 3.3 4.2 + - - +
282C TYR* 1.3 76.5 - - - +
284C SER* 1.3 58.4 + - - +
286C ILE* 3.2 5.6 + - + +
287C SER* 2.9 25.8 + - - -
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Residues in contact with SER 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231C CYS* 3.6 6.7 - - - -
232C PHE 3.9 14.0 + - - -
234C VAL* 3.9 10.1 - - - +
266C ALA* 2.6 41.7 + - - +
267C VAL* 4.5 0.5 - - - +
270C ASN* 3.5 8.5 - - - -
280C SER 3.0 13.1 + - - -
281C LEU 3.3 9.4 - - - -
283C LEU* 1.3 77.1 - - - +
285C LEU* 1.3 60.2 + - - +
287C SER 3.2 0.5 + - - -
288C LEU* 2.8 29.6 + - - +
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Residues in contact with LEU 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C ILE* 3.8 19.1 - - + -
8C ILE* 4.4 7.2 - - + -
169C LEU* 3.8 32.8 - - + -
231C CYS* 3.5 17.2 - - + -
281C LEU 2.9 13.1 + - - +
282C TYR* 3.5 26.5 - - + +
283C LEU 3.2 0.4 - - - -
284C SER* 1.3 77.2 - - - +
286C ILE* 1.3 62.8 + - - +
288C LEU* 3.3 4.9 + - + +
289C LEU* 2.9 42.6 + - + +
300C ILE* 4.4 14.6 - - + -
302C LEU* 4.2 20.0 - - + -
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Residues in contact with ILE 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C ILE* 3.5 36.3 - - + -
9C ASN* 3.8 18.2 - - - +
10C PHE* 3.7 27.8 - - + -
158C VAL* 4.1 3.8 - - + -
269C TYR* 3.9 11.0 - - + -
282C TYR 3.1 15.2 + - - +
283C LEU* 3.2 9.2 + - - +
285C LEU* 1.3 76.6 - - - +
287C SER* 1.3 62.3 + - - +
289C LEU* 3.4 8.4 + - - +
290C GLU* 3.0 33.9 + - - +
326C LEU* 6.6 0.2 - - + -
331C HIS* 3.7 26.5 - - + +
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Residues in contact with SER 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265C ASP 2.6 20.0 + - - -
266C ALA 3.2 18.4 - - - -
268C ASP* 3.4 1.0 + - - +
269C TYR* 3.1 40.6 + - - -
283C LEU 2.9 12.5 + - - -
284C SER* 3.4 1.3 - - - -
286C ILE* 1.3 77.6 - - - +
288C LEU* 1.3 56.3 + - - +
291C ASN* 2.8 47.8 + - - +
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Residues in contact with LEU 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229C SER* 3.8 18.8 - - - +
230C LEU 4.1 7.9 - - - +
231C CYS* 4.1 9.4 - - + -
262C GLY 3.7 21.5 - - - +
265C ASP* 3.7 8.7 + - + -
266C ALA* 4.0 6.7 - - + -
284C SER 2.8 15.8 + - - +
285C LEU* 3.6 7.2 - - + +
287C SER* 1.3 76.9 - - - +
289C LEU* 1.3 63.7 + - - +
292C ARG* 3.0 56.3 + - + +
294C LEU* 4.2 9.8 - - + +
300C ILE* 3.9 34.8 - - + -
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Residues in contact with LEU 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C ILE* 6.4 0.2 - - + -
8C ILE* 4.6 10.3 - - + -
168C ILE* 3.8 22.9 - - + -
169C LEU* 4.3 9.6 - - + -
285C LEU* 2.9 39.2 + - + +
286C ILE* 3.8 8.7 - - - +
288C LEU* 1.3 76.4 - - - +
290C GLU* 1.3 58.3 + - - +
292C ARG 3.5 2.6 - - - +
294C LEU* 5.5 3.1 - - + -
300C ILE* 4.5 9.6 - - + -
318C LEU* 3.5 33.4 - - + -
322C TYR* 3.8 12.8 + - + -
323C LYS* 2.8 23.2 + - - -
326C LEU* 3.4 25.7 - - + +
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Residues in contact with GLU 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269C TYR* 2.6 37.6 + - - +
286C ILE* 3.0 20.9 + - + +
287C SER 4.3 0.7 - - - +
289C LEU* 1.3 80.8 - - + +
291C ASN* 1.3 62.8 + - - +
292C ARG 3.4 0.4 - - - -
293C ASP* 5.9 0.3 - - - -
323C LYS* 3.3 13.9 + - - +
326C LEU* 3.9 18.6 - - + +
327C ASP 3.6 5.0 + - - -
328C GLN* 3.2 51.2 + - + +
331C HIS* 2.4 41.8 + - - -
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Residues in contact with ASN 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265C ASP* 3.9 26.4 - - - +
268C ASP* 3.4 29.2 + - + +
269C TYR* 3.6 17.7 - - - -
287C SER* 2.8 43.8 + - - +
290C GLU* 1.3 75.9 - - - +
292C ARG* 1.3 59.0 + - - +
293C ASP* 5.3 2.1 - - - -
328C GLN* 4.3 9.2 + - - +
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Residues in contact with ARG 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228C ALA 4.5 3.6 + - - -
229C SER* 4.8 0.7 - - - -
258C ARG* 3.7 27.5 + - - +
261C SER* 2.8 34.5 + - - -
262C GLY* 3.8 12.0 - - - -
265C ASP* 2.8 40.7 + - - +
288C LEU* 3.0 36.5 + - + +
289C LEU 3.5 5.0 - - - +
291C ASN* 1.3 78.7 - - - +
293C ASP* 1.3 70.6 + - - +
294C LEU* 3.5 31.4 + - + +
322C TYR* 4.3 0.2 + - - -
323C LYS* 2.8 23.6 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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