Contacts of the helix formed by residues 270 - 287 (chain A) in PDB entry 1XRB
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 VAL 270 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A ALA* 4.8 3.4 - - + -
117A GLY 4.2 10.2 + - - +
118A ASP* 3.8 25.1 - - + +
119A GLN 4.8 1.1 - - - +
122A MSE 3.8 16.2 - - + -
268A SER 3.4 7.6 + - - +
269A LYS* 1.3 71.2 - - - +
271A ASP* 1.4 67.2 + - - +
272A ARG 3.0 0.3 + - - -
273A SER* 3.8 10.5 - - - +
274A ALA* 2.9 41.8 + - + +
300A TYR* 4.2 17.5 - - + -
337A PRO* 4.2 34.1 - - + -
340A LEU* 4.6 2.0 - - + -
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Residues in contact with ASP 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A ASP* 4.1 7.4 - - - +
119A GLN 4.5 2.3 - - - +
120A GLY* 5.3 1.4 - - - -
122A MSE 3.6 24.5 - - - +
260A GLY* 4.1 17.4 + - - +
261A ALA 4.2 2.5 - - - +
262A PHE* 3.2 20.7 - - - -
265A LYS* 3.6 27.3 + - + +
269A LYS* 3.2 4.0 - - + +
270A VAL* 1.4 77.8 + - - +
272A ARG* 1.3 57.8 + - - +
275A ALA* 3.5 8.1 - - - +
384A PO4 4.7 1.0 + - - -
385A PO4 3.6 7.1 + - - -
411A MG 2.3 31.2 - - - -
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Residues in contact with ARG 272 (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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24A ASP* 2.7 44.2 + - - -
27A LEU* 3.3 7.5 - - - +
261A ALA 4.5 0.8 + - - +
262A PHE* 3.2 45.5 + - + +
265A LYS* 2.9 35.8 + - + +
266A ASP 5.1 0.2 - - - +
267A PRO* 5.0 7.0 - - + -
269A LYS* 3.0 10.7 + - + +
270A VAL 3.4 0.2 - - - -
271A ASP* 1.3 78.5 - - - +
273A SER* 1.3 64.3 + - - +
275A ALA* 3.2 6.1 - - - +
276A TYR* 2.9 74.4 + - + -
351A TYR* 3.5 15.8 - - + +
354A THR* 3.3 11.5 - - - +
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Residues in contact with SER 273 (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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267A PRO* 2.9 30.9 + - - -
268A SER 4.6 0.2 - - - -
269A LYS 3.0 12.5 + - - -
270A VAL* 3.8 10.6 - - - +
272A ARG* 1.3 76.3 - - - +
274A ALA* 1.3 52.4 + - - +
276A TYR* 3.3 9.3 + - - +
277A ALA* 2.8 35.1 + - - +
340A LEU* 4.2 15.6 - - - +
341A ILE* 4.9 2.5 - - - +
344A LEU* 5.0 1.2 - - - +
346A LEU* 3.9 21.7 - - - +
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Residues in contact with ALA 274 (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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122A MSE 3.3 20.5 - - + +
270A VAL* 2.9 22.4 + - + +
273A SER* 1.3 75.0 + - - +
275A ALA* 1.3 52.4 + - - +
277A ALA* 3.3 8.1 + - - +
278A ALA* 2.7 35.5 + - - +
298A VAL* 4.2 4.8 - - + +
300A TYR* 3.5 35.4 - - + +
340A LEU* 4.4 4.2 - - - +
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Residues in contact with ALA 275 (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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122A MSE 3.7 16.8 - - + +
123A PHE 4.9 8.4 - - - +
262A PHE* 3.5 22.7 - - + -
270A VAL 3.9 0.4 + - - -
271A ASP 3.5 15.3 - - - +
272A ARG 3.2 10.5 + - - +
274A ALA* 1.3 75.5 - - - +
276A TYR* 1.3 66.8 + - - +
278A ALA* 3.1 5.2 + - - +
279A ARG* 3.0 23.4 + - - +
360A PHE* 4.1 7.1 - - + -
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Residues in contact with TYR 276 (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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262A PHE* 3.9 22.0 - + - -
272A ARG* 2.9 56.9 + - + -
273A SER* 3.5 11.0 - - - +
275A ALA* 1.3 77.5 - - + +
277A ALA* 1.3 62.5 + - - +
279A ARG* 3.2 1.7 + - - +
280A TYR* 3.0 21.7 + - - +
344A LEU* 4.3 4.5 - - + -
346A LEU* 5.0 7.6 - - + -
351A TYR* 3.8 10.5 - + - -
354A THR* 3.7 5.5 + - - +
359A HIS* 2.9 18.4 - + - -
360A PHE* 3.6 24.2 - + - -
367A TRP* 3.4 57.6 - + + +
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Residues in contact with ALA 277 (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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273A SER 2.8 19.9 + - - +
274A ALA* 3.4 5.8 - - - +
276A TYR* 1.3 70.9 - - - +
278A ALA* 1.3 58.3 + - - +
280A TYR* 3.1 7.6 - - + +
281A VAL* 2.8 30.6 + - - +
335A LEU* 4.2 10.5 - - + -
340A LEU* 3.7 29.6 - - + -
343A MSE 5.1 2.9 - - + -
344A LEU* 3.6 19.9 - - + +
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Residues in contact with ALA 278 (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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122A MSE 5.1 0.4 - - - -
123A PHE* 4.3 4.3 - - - +
124A GLY* 3.7 24.0 - - - +
274A ALA 2.7 21.5 + - - +
275A ALA* 3.1 5.6 + - - +
277A ALA* 1.3 71.1 - - - +
279A ARG* 1.3 64.0 + - - +
281A VAL* 3.2 7.2 + - - +
282A ALA* 3.1 23.9 + - - +
296A ILE* 4.0 16.5 - - + +
298A VAL* 4.8 15.3 - - + -
335A LEU* 6.0 0.7 - - - -
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Residues in contact with ARG 279 (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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124A GLY* 3.9 3.8 - - - -
125A TYR 2.8 38.1 + - - +
126A ALA* 3.5 6.7 - - - +
132A VAL 2.9 23.0 + - - -
133A LEU 3.0 21.0 + - - -
134A MSE 3.3 23.2 - - - +
251A TYR* 3.4 23.1 - - - +
275A ALA 3.0 11.3 + - - +
276A TYR 3.5 7.6 - - - +
278A ALA* 1.3 74.7 - - - +
280A TYR* 1.3 56.2 + - - +
282A ALA* 3.3 1.0 + - - +
283A LYS* 2.8 46.1 + - - +
360A PHE* 3.8 17.4 - - + +
367A TRP* 4.3 6.7 - - + +
368A GLU* 2.6 44.1 + - - +
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Residues in contact with TYR 280 (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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276A TYR 3.0 12.0 + - - +
277A ALA* 3.1 13.2 - - - +
279A ARG* 1.3 76.3 - - - +
281A VAL* 1.3 66.7 + - + +
283A LYS* 4.0 1.9 - - + +
284A ASN* 3.1 30.6 + - - +
333A PHE* 3.8 25.6 - + - -
343A MSE 4.0 17.0 + - + -
344A LEU* 3.8 16.6 - - + +
366A PRO 3.9 2.2 - - - -
367A TRP* 3.1 33.6 + - + +
369A LYS* 2.8 49.1 + - + -
371A ASP* 2.5 23.5 + - - -
372A LYS* 2.5 16.1 + - + -
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Residues in contact with VAL 281 (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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277A ALA 2.8 24.9 + - - +
278A ALA* 3.2 4.6 + - - +
280A TYR* 1.3 71.6 - - + +
282A ALA* 1.3 67.5 + - - +
284A ASN* 3.0 2.6 + - - +
285A ILE* 2.9 25.2 + - + +
296A ILE* 3.5 31.4 - - + -
329A VAL* 3.9 25.8 - - + -
333A PHE* 3.7 47.3 - - + -
335A LEU* 4.3 13.5 - - + -
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Residues in contact with ALA 282 (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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125A TYR* 3.7 30.1 - - - +
126A ALA* 3.6 9.4 - - + +
278A ALA 3.1 12.6 + - - +
279A ARG 3.8 3.8 - - - +
281A VAL* 1.3 79.5 - - - +
283A LYS* 1.3 62.7 + - - +
285A ILE* 3.2 2.7 + - - +
286A VAL* 3.2 20.4 + - - +
294A CYS* 3.7 18.4 - - - +
296A ILE* 4.1 15.9 - - + -
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Residues in contact with LYS 283 (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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126A ALA* 3.7 8.9 - - - +
132A VAL 3.8 4.9 - - - -
133A LEU* 4.0 24.1 - - + +
279A ARG* 2.8 36.7 + - - +
280A TYR* 4.1 4.7 - - + +
282A ALA* 1.3 70.8 - - - +
284A ASN* 1.3 64.5 + - - +
286A VAL* 4.0 1.3 - - - +
287A ALA* 2.9 27.1 + - - +
363A GLU* 2.7 35.4 + - - -
367A TRP 5.0 0.4 - - - +
368A GLU* 2.6 63.7 + - - +
369A LYS 5.9 0.2 - - - +
370A THR* 4.0 16.6 - - + -
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Residues in contact with ASN 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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280A TYR* 3.1 23.6 + - - +
281A VAL 3.0 8.1 + - - +
283A LYS* 1.3 76.6 - - - +
285A ILE* 1.3 63.3 + - - +
287A ALA* 3.0 4.7 + - - +
288A ALA* 3.0 24.3 + - - +
333A PHE* 4.2 15.5 - - + -
369A LYS 3.2 21.1 - - - +
370A THR* 2.9 18.8 + - - +
372A LYS* 3.1 14.0 - - - +
373A ALA* 2.9 33.8 - - - +
376A LEU* 4.0 7.4 - - + -
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Residues in contact with ILE 285 (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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281A VAL* 2.9 24.4 + - + +
282A ALA 3.2 6.7 + - - +
284A ASN* 1.3 75.2 - - - +
286A VAL* 1.3 61.3 + - + +
288A ALA* 3.4 4.5 + - - +
290A LEU* 3.1 41.3 + - + +
291A ALA* 4.5 8.5 - - + -
294A CYS* 3.8 34.8 - - + -
296A ILE* 4.1 2.2 - - + -
312A VAL* 5.1 3.4 - - + -
325A LEU* 4.4 21.1 - - + -
329A VAL* 3.7 29.2 - - + -
333A PHE* 5.3 0.2 - - + -
376A LEU* 3.8 21.7 - - + +
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Residues in contact with VAL 286 (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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126A ALA* 4.0 11.0 - - + -
127A THR 4.2 0.4 - - - -
128A ASN* 4.0 10.5 - - + +
133A LEU* 3.5 26.6 - - + +
282A ALA 3.2 15.0 + - - +
283A LYS 4.1 2.0 - - - +
285A ILE* 1.3 72.7 - - + +
287A ALA* 1.3 66.6 + - - +
288A ALA 3.1 1.8 - - - -
289A GLY* 3.0 13.5 + - - -
291A ALA 3.7 20.2 - - - +
292A ASP 3.6 16.8 - - - +
293A ARG* 4.1 11.0 - - - +
294A CYS* 3.9 22.9 - - + -
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Residues in contact with ALA 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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133A LEU* 4.9 10.5 - - + +
283A LYS* 2.9 19.7 + - + +
284A ASN* 3.5 4.7 - - - +
286A VAL* 1.3 79.1 - - - +
288A ALA* 1.3 60.6 + - - +
289A GLY 3.2 1.1 + - - -
370A THR* 3.5 26.5 - - + -
373A ALA* 4.7 10.9 - - + +
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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