Contacts of the helix formed by residues 268 - 281 (chain A) in PDB entry 1X0X
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 268 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152A ILE* 3.9 9.2 - - - -
263A THR 3.9 0.4 + - - -
264A THR* 2.9 21.6 + - - -
266A TYR 3.9 0.2 - - - -
267A GLY* 1.3 81.2 - - - +
269A ARG* 1.3 66.0 + - - -
270A ASN 3.3 2.2 - - - -
271A ARG* 3.3 6.3 + - - +
272A LYS* 3.2 20.5 + - - +
1002A SO4 3.6 15.5 - - - -
1004A SO4 4.7 1.2 + - - -
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Residues in contact with ARG 269 (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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13A ASN* 4.6 3.6 - - - -
267A GLY 4.1 0.6 + - - +
268A GLY* 1.3 69.0 - - - -
270A ASN* 1.3 64.9 + - - +
272A LYS* 3.1 14.9 + - - +
273A VAL* 3.1 27.2 + - - +
292A LEU* 4.2 25.8 - - + -
295A GLN* 2.9 42.7 - - - +
296A LYS 3.7 16.8 + - - +
297A LEU* 4.0 4.3 - - + -
298A GLN* 5.4 0.4 - - - +
1002A SO4 2.7 39.1 + - - +
1005A SO4 5.7 1.3 - - - -
2001A NAD 3.3 67.8 + - - -
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Residues in contact with ASN 270 (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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205A ASN* 3.3 27.8 - - - +
208A ALA* 4.3 9.9 - - + -
209A VAL* 4.0 5.8 - - + +
269A ARG* 1.3 78.4 - - - +
271A ARG* 1.3 58.1 + - - +
273A VAL* 4.3 0.5 - - - +
274A ALA* 3.0 31.4 + - - +
297A LEU* 3.4 23.7 - - - +
298A GLN 3.7 4.9 + - - +
299A GLY* 2.9 38.1 + - - +
300A PRO* 3.5 6.5 - - - +
1002A SO4 3.0 30.2 + - - +
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Residues in contact with ARG 271 (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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208A ALA* 3.7 14.5 + - - +
212A GLY* 3.6 19.4 - - - +
215A ASP* 3.0 29.7 + - - +
224A LYS* 3.9 1.8 - - - +
264A THR 3.8 13.9 - - - +
265A CYS 3.1 25.8 - - - +
266A TYR 3.7 21.0 + - - -
267A GLY* 4.8 1.0 - - - -
268A GLY* 3.3 10.1 + - - +
269A ARG 3.2 0.6 - - - -
270A ASN* 1.3 75.2 - - - +
272A LYS* 1.3 78.8 + - - +
275A GLU* 3.0 52.2 + - - +
1004A SO4 3.3 28.3 + - - -
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Residues in contact with LYS 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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268A GLY 3.2 7.3 + - - +
269A ARG* 3.1 16.4 + - - +
271A ARG* 1.3 94.3 - - - +
273A VAL* 1.3 62.2 + - - +
275A GLU* 3.3 4.2 + - - +
276A ALA* 3.2 19.6 + - - +
279A ARG* 5.4 0.3 + - - -
291A LEU* 4.1 26.8 + - + -
292A LEU* 4.0 25.7 - - + +
1004A SO4 3.3 38.7 + - - +
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Residues in contact with VAL 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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269A ARG 3.1 14.1 + - - +
272A LYS* 1.3 75.4 - - - +
274A ALA* 1.3 64.1 + - - +
276A ALA* 3.3 2.8 + - - +
277A PHE* 2.9 20.4 + - - +
284A ILE* 4.4 11.2 - - + +
287A LEU* 3.6 31.3 - - + +
288A GLU 4.4 0.2 - - - +
291A LEU* 4.3 16.6 - - + -
292A LEU* 3.8 35.4 - - + -
297A LEU* 3.6 28.9 - - + -
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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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209A VAL* 3.1 43.5 - - + +
212A GLY* 3.8 6.3 - - - -
213A PHE* 3.4 13.8 - - + -
270A ASN 3.0 21.1 + - - +
271A ARG 3.7 4.5 - - - +
273A VAL* 1.3 78.4 - - - +
275A GLU* 1.3 62.2 + - - +
277A PHE* 3.1 8.5 + - - +
278A ALA* 3.1 16.6 + - - +
284A ILE* 6.3 2.0 - - - -
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Residues in contact with GLU 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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212A GLY 3.1 14.3 + - - +
215A ASP* 3.9 7.7 - - + +
216A GLY* 3.5 26.5 - - - +
271A ARG* 3.0 41.6 + - - +
272A LYS 3.3 5.1 + - - +
274A ALA* 1.3 76.0 - - - +
276A ALA* 1.3 63.4 + - - +
278A ALA* 3.0 6.2 + - - +
279A ARG* 3.0 54.1 + - - +
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Residues in contact with ALA 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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272A LYS 3.2 6.5 + - - +
273A VAL 3.3 8.2 + - - +
275A GLU* 1.3 79.3 - - - +
277A PHE* 1.3 57.5 - - - +
279A ARG* 3.5 25.5 - - - +
280A THR* 2.8 39.2 + - + +
287A LEU* 3.8 11.4 - - + -
291A LEU* 3.8 26.0 - - + -
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Residues in contact with PHE 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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213A PHE* 3.8 17.0 - + + -
273A VAL 2.9 13.4 + - - +
274A ALA* 3.2 12.6 - - - +
275A GLU 3.1 0.4 - - - -
276A ALA* 1.3 77.1 - - - +
278A ALA* 1.3 66.8 + - - +
280A THR* 4.4 0.9 - - - -
281A GLY* 3.2 26.2 + - - -
282A LYS 3.2 27.1 - - - -
283A SER* 4.7 1.8 - - - -
284A ILE* 3.7 33.4 - - + -
287A LEU* 3.5 9.8 - - + +
328A VAL* 3.3 41.7 - - + -
329A CYS* 4.5 6.7 - - - -
332A GLY* 6.4 0.4 - - - -
333A GLN 5.6 0.7 - - - -
335A VAL* 4.9 6.0 - - + +
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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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213A PHE* 4.0 6.5 - - + +
216A GLY* 3.7 28.8 - - - +
217A LEU* 5.1 1.1 - - + +
274A ALA 3.1 10.9 + - - +
275A GLU 3.0 9.6 + - - +
277A PHE* 1.3 82.4 - - - +
279A ARG* 1.3 60.3 + - - +
281A GLY* 4.9 0.9 + - - -
335A VAL* 3.9 40.3 - - + +
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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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216A GLY* 4.0 17.0 - - - +
272A LYS 5.4 0.2 + - - -
275A GLU* 3.0 44.0 + - - +
276A ALA* 3.2 27.7 + - - +
278A ALA* 1.3 81.0 - - - +
280A THR* 1.3 75.5 + - + +
281A GLY 3.7 0.2 - - - -
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Residues in contact with THR 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 ALA* 2.8 31.9 + - + +
279A ARG* 1.3 94.5 - - + +
281A GLY* 1.3 57.8 + - - +
282A LYS* 3.0 41.7 + - + +
287A LEU* 4.0 5.6 - - + +
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Residues in contact with GLY 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 PHE* 3.2 21.5 + - - -
278A ALA 4.8 0.6 + - - -
279A ARG 3.7 1.2 - - - -
280A THR* 1.3 77.7 + - - +
282A LYS* 1.3 65.6 + - - +
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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
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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