Contacts of the helix formed by residues 279 - 292 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B ALA* 3.6 17.2 - - - +
157B ALA* 6.0 0.2 - - - -
158B VAL* 3.6 10.0 - - - +
276B ILE* 3.1 23.7 + - - -
277B TYR 3.0 1.4 + - - -
278B THR* 1.3 81.2 + - - +
280B SER* 1.3 57.7 + - - +
281B LEU 3.4 1.6 - - - -
282B TYR* 3.2 4.8 + - - -
283B LEU* 2.8 30.5 + - - +
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Residues in contact with SER 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B HIS* 3.5 19.3 - - - -
234B VAL* 3.3 24.7 + - - -
270B ASN* 3.3 14.6 + - - +
274B GLY 4.7 0.3 + - - -
275B ASN* 2.8 24.3 + - - -
276B ILE* 3.0 20.9 + - - +
277B TYR 3.0 4.0 + - - -
279B GLY* 1.3 77.0 - - - +
281B LEU* 1.3 63.0 + - - +
283B LEU 3.3 0.3 + - - -
284B SER* 3.0 19.6 + - - -
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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
----------------------------------------------------------
111B SCY 6.0 1.6 - - - +
231B CYS* 3.5 26.5 - - + +
232B PHE* 3.3 31.2 - - - +
233B HIS* 3.9 16.8 + - + +
278B THR 4.7 2.5 + - - +
279B GLY 3.4 0.6 - - - -
280B SER* 1.3 76.7 - - - +
282B TYR* 1.3 92.3 + - + +
284B SER* 3.3 3.3 + - - -
285B LEU* 2.9 22.3 + - - +
302B LEU* 4.3 9.2 - - + -
303B PHE 3.8 3.6 - - - +
304B SER* 3.5 36.6 - - - +
314B TYR* 4.5 5.2 - - + +
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Residues in contact with TYR 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ILE* 5.2 0.2 - - + -
8B ILE* 3.9 2.2 - - + +
114B ALA* 3.7 24.7 - - + -
115B THR* 2.8 31.5 + - - -
118B ILE* 3.6 18.1 - - + +
137B ALA* 5.5 0.4 - - + -
158B VAL* 3.8 24.2 - - + -
160B MET* 3.5 24.0 - - + -
278B THR 3.8 16.2 - - - -
279B GLY* 3.2 4.8 + - - +
281B LEU* 1.3 96.2 - - + +
283B LEU* 1.3 64.8 + - - +
284B SER 3.2 0.9 - - - -
285B LEU* 3.3 22.4 + - + +
286B ILE* 3.1 26.5 + - - +
302B LEU* 4.8 0.7 - - + -
304B SER* 5.1 0.7 - - - -
314B TYR* 2.7 29.1 + - - -
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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
----------------------------------------------------------
10B PHE* 3.8 46.2 - - + -
12B VAL* 5.5 0.2 - - + -
158B VAL* 4.0 6.5 - - + +
269B TYR* 4.1 11.4 - - + -
270B ASN* 3.8 24.2 - - - +
273B VAL* 4.2 30.1 - - + -
274B GLY 5.1 1.3 - - - +
276B ILE* 4.0 22.4 - - + -
279B GLY 2.8 16.1 + - - +
280B SER 3.7 4.3 - - - +
282B TYR* 1.3 76.7 - - - +
284B SER* 1.3 58.2 + - - +
286B ILE* 3.2 5.6 + - + +
287B SER* 3.0 25.1 + - - -
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Residues in contact with SER 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B CYS* 3.5 6.7 - - - -
232B PHE 3.9 7.3 + - - -
234B VAL* 3.9 16.6 - - - +
266B ALA* 2.6 41.7 + - - +
267B VAL* 4.5 0.5 - - - +
270B ASN* 3.5 8.7 - - - -
280B SER 3.0 13.7 + - - -
281B LEU 3.3 9.9 - - - -
283B LEU* 1.3 76.9 - - - +
285B LEU* 1.3 60.0 + - - +
287B SER 3.2 0.5 + - - -
288B LEU* 2.9 29.1 + - - +
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Residues in contact with LEU 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ILE* 3.8 20.4 - - + -
8B ILE* 4.4 6.7 - - + -
169B LEU* 3.7 33.9 - - + -
231B CYS* 3.5 14.6 - - + -
281B LEU 2.9 13.3 + - - +
282B TYR* 3.5 26.2 - - + +
283B LEU 3.2 0.4 - - - -
284B SER* 1.3 76.6 - - - +
286B ILE* 1.3 62.9 + - - +
288B LEU* 3.2 4.6 + - + +
289B LEU* 2.9 36.7 + - + +
300B ILE* 4.3 17.9 - - + -
302B LEU* 4.2 22.7 - - + -
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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
----------------------------------------------------------
8B ILE* 3.5 36.6 - - + -
9B ASN* 3.8 18.2 - - - +
10B PHE* 3.7 27.4 - - + -
158B VAL* 4.1 3.8 - - + -
269B TYR* 3.9 10.1 - - + -
282B TYR 3.1 15.5 + - - +
283B LEU* 3.2 9.4 + - - +
285B LEU* 1.3 77.0 - - - +
287B SER* 1.3 61.7 + - - +
289B LEU* 3.4 8.0 + - - +
290B GLU* 3.0 33.5 + - + +
331B HIS* 3.7 27.6 - - + +
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Residues in contact with SER 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B ASP 2.7 19.7 + - - -
266B ALA 3.2 18.8 - - - -
268B ASP* 3.4 1.6 + - - +
269B TYR* 3.1 40.7 + - - -
283B LEU 3.0 12.1 + - - -
284B SER* 3.4 1.6 - - - -
286B ILE* 1.3 77.3 - - - +
288B LEU* 1.3 56.3 + - - +
291B ASN* 2.8 47.5 + - - +
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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
----------------------------------------------------------
229B SER* 3.8 18.4 - - - +
230B LEU 4.2 7.9 - - - +
231B CYS* 4.2 9.6 - - + -
262B GLY 3.6 22.2 - - - +
265B ASP* 3.7 8.4 + - + -
266B ALA* 4.0 6.5 - - + -
284B SER 2.9 16.1 + - - +
285B LEU* 3.5 6.5 - - + +
287B SER* 1.3 77.4 - - - +
289B LEU* 1.3 62.8 - - - +
292B ARG* 3.0 56.4 + - + +
294B LEU* 4.2 9.7 - - + +
300B ILE* 3.9 35.4 - - + -
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Residues in contact with LEU 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ILE* 6.3 0.4 - - + -
8B ILE* 4.7 10.1 - - + -
168B ILE* 3.7 24.0 - - + -
169B LEU* 4.2 11.4 - - + -
285B LEU* 2.9 39.4 + - + +
286B ILE* 3.8 7.9 - - - +
288B LEU* 1.3 76.0 - - - +
290B GLU* 1.3 58.4 + - - +
292B ARG 3.5 1.8 - - - +
294B LEU* 5.5 3.1 - - + -
300B ILE* 4.4 10.5 - - + -
318B LEU* 3.4 33.7 - - + -
322B TYR* 3.8 12.2 + - + +
323B LYS* 2.8 23.9 + - - -
326B LEU* 3.4 26.4 - - + +
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Residues in contact with GLU 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B TYR* 2.6 36.8 + - - +
286B ILE* 3.0 20.8 + - + +
287B SER 4.2 0.7 - - - +
289B LEU* 1.3 81.2 - - + +
291B ASN* 1.3 62.3 + - - +
292B ARG 3.5 0.2 - - - -
323B LYS* 3.3 13.5 + - - +
326B LEU* 3.9 19.9 - - + +
327B ASP 3.5 5.7 + - - -
328B GLN* 3.4 51.2 + - + +
331B HIS* 2.5 41.6 + - - +
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Residues in contact with ASN 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B ASP* 3.9 26.3 - - - +
268B ASP* 3.4 27.5 + - + +
269B TYR* 3.6 18.0 + - - -
287B SER* 2.8 46.5 + - - +
290B GLU* 1.3 75.7 - - - +
292B ARG* 1.3 59.0 + - - +
328B GLN* 4.5 9.0 + - - +
332B LYS* 6.0 1.0 - - - -
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Residues in contact with ARG 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B ALA 4.5 3.8 + - - -
229B SER* 4.7 0.9 - - - -
258B ARG* 3.7 27.3 + - - +
261B SER* 2.8 33.7 + - - -
262B GLY* 3.8 12.5 - - - -
265B ASP* 2.8 40.7 + - - +
288B LEU* 3.0 35.1 + - + +
289B LEU 3.5 4.3 - - - +
291B ASN* 1.3 78.0 - - - +
293B ASP* 1.3 62.9 + - - +
294B LEU* 3.5 34.0 + - + +
322B TYR* 4.3 0.2 + - - -
323B LYS* 2.7 30.1 + - - -
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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
------------------------------------------------------------
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