Contacts of the helix formed by residues 267 - 283 (chain A) in PDB entry 3UGM
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 267 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232A TRP* 4.5 3.4 - - - -
262A LYS 4.1 0.2 + - - -
263A ILE 2.9 16.8 + - - -
266A ARG* 1.3 79.9 - - - +
268A GLY* 1.3 66.1 + - - +
270A THR* 3.4 11.1 - - - +
271A ALA* 3.4 17.5 + - - +
298A ALA 3.3 17.1 + - - -
299A SER 4.2 0.6 - - - -
300A ASN 3.2 14.3 - - - +
301A ASN* 5.1 1.7 - - - +
0B T 4.9 0.2 + - - -
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Residues in contact with GLY 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A GLN* 6.4 1.6 - - - -
232A TRP* 4.2 12.3 - - - -
233A SER* 3.6 12.3 - - - -
237A ALA* 4.3 5.2 - - - -
263A ILE 3.5 5.7 + - - +
264A ALA 3.6 13.8 + - - -
265A LYS 4.6 1.1 + - - -
266A ARG 3.4 2.4 - - - -
267A GLY* 1.3 79.8 - - - +
269A VAL* 1.3 63.9 + - - -
270A THR 2.9 7.5 + - - -
272A MET* 3.2 18.4 + - - +
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Residues in contact with VAL 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A TRP* 4.5 1.8 - - + -
233A SER* 3.2 19.5 + - - +
236A ARG* 3.1 71.1 - - + +
237A ALA* 3.7 11.7 - - - +
240A ALA* 3.9 8.0 - - + +
268A GLY* 1.3 70.6 - - - -
270A THR* 1.3 62.7 + - - +
272A MET* 3.3 5.9 + - - +
273A GLU* 2.9 49.9 + - - +
-1B A 4.3 4.5 - - - +
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Residues in contact with THR 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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232A TRP* 4.1 13.8 - - + -
267A GLY 3.4 13.5 - - - +
268A GLY 2.9 0.4 - - - -
269A VAL* 1.3 79.5 - - - +
271A ALA* 1.3 80.1 + - - +
273A GLU* 3.1 19.1 + - - +
274A ALA 3.2 9.4 + - - -
303A GLY* 4.9 0.7 - - - -
304A LYS* 3.7 35.2 + - + +
-1B A 3.9 13.5 + - - -
0B T 2.8 37.4 + - - +
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Residues in contact with ALA 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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263A ILE* 4.7 3.4 - - + +
267A GLY* 3.4 18.8 - - - +
268A GLY 3.2 1.8 + - - -
270A THR* 1.3 82.5 - - - +
272A MET* 1.3 64.3 + - - +
274A ALA* 3.1 4.0 + - - +
275A VAL* 3.0 28.1 + - - +
298A ALA* 3.4 34.8 - - + +
303A GLY* 3.8 11.7 - - - -
304A LYS* 3.9 10.8 - - - +
307A LEU* 4.9 0.7 - - + -
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Residues in contact with MET 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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237A ALA* 2.7 43.3 - - + +
240A ALA* 3.7 6.1 - - + -
241A LEU* 3.5 40.6 - - - +
244A ASP* 4.8 6.1 - - + -
260A LEU* 4.7 5.8 - - + +
263A ILE* 5.0 10.5 - - + +
264A ALA* 3.6 24.7 - - + -
268A GLY 3.2 6.5 + - - +
269A VAL* 3.6 8.7 - - - +
270A THR 3.2 0.4 - - - -
271A ALA* 1.3 79.6 - - - +
273A GLU* 1.3 54.9 + - - +
275A VAL* 3.2 13.5 + - + +
276A HIS* 2.8 42.4 + - + +
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Residues in contact with GLU 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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236A ARG* 5.5 1.6 + - - -
240A ALA* 5.1 4.4 - - + +
269A VAL* 2.9 36.3 + - + +
270A THR* 3.1 12.7 + - - +
272A MET* 1.3 72.6 - - - +
274A ALA* 1.3 58.1 + - - +
275A VAL 2.9 10.8 + - - -
276A HIS* 3.6 12.1 + - + -
277A ALA* 3.2 24.2 + - - +
304A LYS* 5.4 5.6 + - - +
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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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270A THR 3.2 2.4 + - - -
271A ALA 3.1 8.6 + - - +
273A GLU* 1.3 76.6 - - - +
275A VAL* 1.3 60.2 + - - +
277A ALA* 4.5 4.5 - - - -
278A SER* 3.1 29.7 - - - -
304A LYS* 3.6 41.9 - - + +
307A LEU* 4.1 11.7 - - + +
308A GLU* 4.6 13.0 - - - +
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Residues in contact with VAL 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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244A ASP* 4.6 9.2 - - - +
255A LEU* 4.6 18.6 - - + -
260A LEU* 6.2 0.9 - - + -
263A ILE* 4.5 9.4 - - + -
271A ALA 3.0 17.8 + - - +
272A MET* 3.7 7.6 - - + +
273A GLU 2.9 3.2 + - - -
274A ALA* 1.3 77.1 - - - +
276A HIS* 1.3 53.5 + - - +
277A ALA 2.5 15.7 + - - -
278A SER* 3.0 0.9 + - - -
279A ARG* 2.9 36.2 + - + +
282A LEU* 5.1 5.6 - - + -
294A VAL* 4.9 15.0 - - + -
298A ALA* 4.1 13.7 - - + -
307A LEU* 3.7 21.5 - - + -
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Residues in contact with HIS 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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240A ALA* 3.4 29.6 + - + -
243A THR* 3.6 23.7 - - + +
244A ASP* 3.2 43.7 + - + +
247A GLU* 3.3 22.3 - - + +
253A LEU* 5.7 0.4 - - + -
272A MET* 2.8 37.5 + - + -
273A GLU* 3.6 11.5 + - + -
275A VAL* 1.3 72.2 - - - +
277A ALA* 1.3 58.4 + - - +
279A ARG* 3.8 18.6 + - - +
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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 GLU 3.2 17.4 + - - +
274A ALA* 4.3 4.9 - - - -
275A VAL 2.5 4.6 + - - -
276A HIS* 1.3 75.8 - - - +
278A SER* 1.3 56.7 + - - +
279A ARG* 2.6 37.2 + - - +
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Residues in contact with SER 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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274A ALA* 3.1 19.0 + - - -
275A VAL 3.0 2.7 + - - -
277A ALA* 1.3 76.9 - - - +
279A ARG* 1.3 63.0 + - - +
280A ASN 3.4 1.8 - - - -
281A ALA* 3.1 19.4 + - - +
282A LEU* 3.2 20.9 + - - +
307A LEU* 5.0 3.5 - - - +
308A GLU* 4.5 13.5 + - - -
311A GLN* 3.2 22.2 + - - -
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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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247A GLU* 4.2 13.8 + - - -
253A LEU* 4.4 13.5 - - + -
254A GLN* 4.3 21.7 - - + +
275A VAL* 2.9 23.4 + - + +
276A HIS* 3.8 23.7 + - - +
277A ALA* 2.6 34.0 + - - +
278A SER* 1.3 71.6 - - - +
280A ASN* 1.3 106.4 + - - +
282A LEU* 3.0 14.7 + - - +
283A THR* 2.8 29.6 + - - -
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Residues in contact with ASN 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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254A GLN* 4.4 6.2 + - - -
278A SER 3.4 0.4 - - - -
279A ARG* 1.3 119.3 + - - +
281A ALA* 1.3 62.8 + - - +
283A THR* 3.3 18.7 + - - +
286A PRO* 3.7 13.9 - - - +
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Residues in contact with ALA 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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278A SER* 3.1 17.5 + - - +
279A ARG* 5.3 0.2 - - - +
280A ASN* 1.3 78.5 - - - +
282A LEU* 1.3 59.3 + - - +
286A PRO* 3.5 25.7 - - - +
288A ASN* 3.3 1.6 - - - +
311A GLN* 2.8 33.3 + - - +
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Residues in contact with LEU 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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274A ALA 5.2 0.4 - - - +
275A VAL* 5.1 7.6 - - + -
278A SER* 3.2 26.2 - - - +
279A ARG* 3.0 10.9 + - + +
281A ALA* 1.3 79.2 - - - +
283A THR* 1.3 60.3 + - - +
287A LEU 2.6 26.5 - - - +
288A ASN* 2.8 33.3 - - + +
289A LEU* 4.1 16.3 - - + +
294A VAL* 4.3 29.6 - - + -
307A LEU* 4.1 27.1 - - + -
310A VAL* 6.1 0.2 - - + -
311A GLN* 3.5 22.4 - - + +
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Residues in contact with THR 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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254A GLN* 2.4 39.1 + - - +
279A ARG 2.8 11.8 + - - -
280A ASN* 3.3 13.1 + - - +
282A LEU* 1.3 81.1 - - - +
286A PRO* 3.9 22.4 - - - +
287A LEU* 4.1 13.3 - - - +
289A LEU 5.6 0.8 - - - +
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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