Contacts of the helix formed by residues 279 - 292 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D ALA* 3.6 17.4 - - - +
157D ALA* 6.0 0.2 - - - -
158D VAL* 3.6 8.8 - - - +
276D ILE* 3.1 23.3 + - - -
277D TYR 3.0 1.4 - - - -
278D THR* 1.3 81.4 + - - +
280D SER* 1.3 58.6 + - - +
281D LEU 3.4 1.1 - - - -
282D TYR* 3.2 5.3 + - - -
283D LEU* 2.9 30.1 + - - +
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Residues in contact with SER 280 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233D HIS* 3.3 23.6 - - - -
234D VAL* 3.3 21.4 + - - -
270D ASN* 3.3 13.8 + - - +
274D GLY 4.8 0.5 + - - -
275D ASN* 2.8 25.1 + - - -
276D ILE* 3.1 19.6 + - - +
277D TYR 3.0 4.3 + - - -
279D GLY* 1.3 75.0 - - - +
281D LEU* 1.3 64.5 + - - +
283D LEU 3.3 0.3 + - - -
284D SER* 3.0 20.6 + - - -
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Residues in contact with LEU 281 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111D SCY 6.1 1.3 - - - +
231D CYS* 3.5 25.1 - - - +
232D PHE* 3.3 31.6 - - - +
233D HIS* 3.9 14.7 + - + +
278D THR 4.6 2.1 + - - +
279D GLY 3.4 0.2 - - - -
280D SER* 1.3 78.8 - - - +
282D TYR* 1.3 92.4 + - + +
284D SER* 3.3 3.8 + - - -
285D LEU* 2.9 22.5 + - - +
302D LEU* 4.3 11.0 - - + -
303D PHE 3.8 2.9 - - - +
304D SER* 3.6 35.9 - - - +
314D TYR* 4.4 5.2 - - + +
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Residues in contact with TYR 282 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D ILE* 5.2 0.4 - - + -
8D ILE* 4.0 1.9 - - + +
114D ALA* 3.7 24.0 - - + -
115D THR* 2.8 31.4 + - - -
118D ILE* 3.7 18.1 - - + +
137D ALA* 5.4 0.7 - - + -
158D VAL* 3.8 23.3 - - + -
160D MET* 3.5 23.6 - - + -
278D THR 3.8 16.8 - - - -
279D GLY* 3.2 5.1 + - - +
281D LEU* 1.3 94.9 - - + +
283D LEU* 1.3 63.6 + - - +
284D SER 3.2 1.6 - - - -
285D LEU* 3.3 18.3 + - + +
286D ILE* 3.1 26.9 + - - +
302D LEU* 4.7 3.8 - - + -
304D SER* 5.2 0.7 - - - -
314D TYR* 2.7 29.3 + - - -
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Residues in contact with LEU 283 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D PHE* 3.8 46.0 - - + -
158D VAL* 3.9 6.7 - - + +
269D TYR* 4.0 13.2 - - + -
270D ASN* 3.9 23.6 - - - +
273D VAL* 4.2 30.1 - - + -
274D GLY 5.1 1.3 - - - +
276D ILE* 4.0 22.7 - - + -
279D GLY 2.9 16.3 + - - +
280D SER 3.7 3.6 - - - +
282D TYR* 1.3 75.7 - - - +
284D SER* 1.3 59.7 + - - +
286D ILE* 3.2 5.2 + - + +
287D SER* 3.0 25.1 + - - -
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Residues in contact with SER 284 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231D CYS* 3.6 6.4 - - - -
232D PHE 3.9 14.6 + - - -
234D VAL* 4.0 9.7 - - - +
266D ALA* 2.7 41.6 + - - +
267D VAL* 4.5 0.7 - - - +
270D ASN* 3.5 8.5 + - - -
280D SER 3.0 14.1 + - - -
281D LEU 3.3 10.5 - - - -
283D LEU* 1.3 76.6 - - - +
285D LEU* 1.3 59.7 + - - +
287D SER 3.2 0.5 + - - -
288D LEU* 2.9 28.8 + - - +
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Residues in contact with LEU 285 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D ILE* 3.8 20.0 - - + -
8D ILE* 4.3 9.6 - - + -
169D LEU* 3.8 31.4 - - + -
231D CYS* 3.5 15.2 - - + -
281D LEU 2.9 14.2 + - - +
282D TYR* 3.5 25.8 - - + +
283D LEU 3.2 0.4 - - - -
284D SER* 1.3 77.0 - - - +
286D ILE* 1.3 62.4 + - - +
288D LEU* 3.3 3.5 + - + +
289D LEU* 3.0 41.4 + - + +
300D ILE* 4.3 14.8 - - + -
302D LEU* 4.3 23.3 - - + -
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Residues in contact with ILE 286 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D ILE* 3.5 36.6 - - + -
9D ASN* 3.8 19.1 - - - +
10D PHE* 3.8 26.5 - - + -
158D VAL* 4.1 3.1 - - + -
269D TYR* 4.0 8.7 - - + -
282D TYR 3.1 15.9 + - - +
283D LEU* 3.5 8.7 - - - +
285D LEU* 1.3 75.0 - - - +
287D SER* 1.3 63.5 + - - +
289D LEU* 3.3 8.6 + - - +
290D GLU* 3.0 53.4 + - + +
326D LEU* 6.3 0.9 - - + -
331D HIS* 3.7 14.4 - - + +
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Residues in contact with SER 287 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265D ASP 2.7 20.4 + - - -
266D ALA 3.2 19.9 + - - -
268D ASP* 3.4 0.3 - - - +
269D TYR* 3.1 41.5 + - - -
270D ASN* 4.4 0.2 - - - -
283D LEU 3.0 13.2 + - - -
284D SER* 3.2 2.0 + - - -
286D ILE* 1.3 76.9 - - - +
288D LEU* 1.3 56.3 + - - +
291D ASN* 2.9 47.7 + - - +
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Residues in contact with LEU 288 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229D SER* 3.8 19.1 - - - +
230D LEU 4.3 1.6 - - - +
231D CYS* 4.2 14.8 - - + -
262D GLY 3.7 21.8 - - - +
265D ASP* 3.7 7.6 + - + -
266D ALA* 3.9 7.0 - - + -
284D SER 2.9 16.1 + - - +
285D LEU* 3.6 5.8 - - + +
287D SER* 1.3 77.2 - - - +
289D LEU* 1.3 62.5 + - - +
292D ARG* 3.0 57.2 + - + +
294D LEU* 4.2 7.4 - - + +
300D ILE* 3.9 37.7 - - + -
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Residues in contact with LEU 289 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D ILE* 6.3 0.4 - - + -
8D ILE* 4.7 9.2 - - + -
168D ILE* 3.9 20.9 - - + -
169D LEU* 4.2 8.7 - - + -
285D LEU* 3.0 41.2 + - + +
286D ILE* 3.7 8.1 - - - +
288D LEU* 1.3 76.4 - - - +
290D GLU* 1.3 57.9 + - - +
292D ARG 3.5 3.2 - - - +
294D LEU* 5.4 3.4 - - + -
300D ILE* 4.3 16.6 - - + -
318D LEU* 3.6 32.1 - - + -
322D TYR* 3.8 11.9 - - + -
323D LYS* 2.9 22.5 + - - -
326D LEU* 3.5 26.4 - - + +
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Residues in contact with GLU 290 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269D TYR* 2.6 36.0 + - - +
286D ILE* 3.0 21.6 + - + +
287D SER 4.4 0.7 - - - +
289D LEU* 1.3 80.8 - - + +
291D ASN* 1.3 60.3 + - - +
292D ARG 3.4 0.7 - - - -
323D LYS* 3.3 15.7 + - - +
326D LEU* 3.8 18.9 - - + +
327D ASP 3.4 7.3 + - - -
328D GLN* 3.4 49.6 + - + +
331D HIS* 2.7 39.5 + - - +
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Residues in contact with ASN 291 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265D ASP* 3.7 27.2 - - + +
268D ASP* 3.3 27.1 + - + +
269D TYR* 3.5 17.4 - - - -
287D SER* 2.9 41.2 + - - +
290D GLU* 1.3 77.7 - - - +
292D ARG* 1.3 58.9 + - - +
293D ASP* 5.3 2.0 - - - -
328D GLN* 4.1 12.3 + - - +
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Residues in contact with ARG 292 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228D ALA 4.5 4.6 + - - -
229D SER* 4.8 0.7 - - - -
258D ARG* 3.6 30.5 + - - +
261D SER* 3.1 31.1 + - - -
262D GLY* 3.8 11.4 - - - -
265D ASP* 2.7 38.1 + - - +
288D LEU* 3.0 37.6 + - + +
289D LEU* 3.5 5.5 - - - +
291D ASN* 1.3 78.5 - - - +
293D ASP* 1.3 67.5 + - - +
294D LEU* 3.4 32.0 + - + +
322D TYR* 4.2 0.5 + - - -
323D LYS* 2.9 23.0 + - - -
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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