Contacts of the helix formed by residues 299 - 317 (chain A) in PDB entry 1UOU
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 PRO 299 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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278A GLY* 3.6 24.0 - - - -
279A ARG* 4.2 17.3 - - + +
289A GLU* 3.8 29.2 - - + +
292A LEU* 5.2 2.5 - - + -
298A GLY* 1.3 87.2 - - - +
300A PRO* 1.3 72.5 - - + +
301A ASP* 3.4 15.7 - - - +
302A LEU* 3.3 11.6 + - + +
303A ARG* 3.3 19.7 + - - +
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Residues in contact with PRO 300 (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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298A GLY 3.7 4.2 - - - +
299A PRO* 1.3 88.0 - - + +
301A ASP* 1.3 58.8 + - - +
303A ARG* 3.9 8.3 - - + +
304A ASP* 3.0 29.5 + - - +
471A LEU* 3.7 16.2 - - + +
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Residues in contact with ASP 301 (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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275A LYS* 5.8 1.6 - - - +
276A PRO 4.0 4.3 - - - +
277A LEU* 3.4 22.8 - - + +
278A GLY* 2.8 26.7 + - - +
299A PRO* 3.4 18.5 - - - +
300A PRO* 1.3 73.8 - - - +
302A LEU* 1.3 69.2 + - - +
304A ASP* 3.4 1.9 + - - +
305A LEU* 3.1 19.1 + - - +
470A PRO 5.6 2.5 - - - +
471A LEU* 4.2 3.7 - - + +
472A PRO* 3.8 27.8 - - + +
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Residues in contact with LEU 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A LYS* 3.9 27.6 - - + +
125A VAL* 4.1 11.4 - - + +
128A VAL* 5.0 1.3 - - + -
277A LEU* 3.9 28.3 - - + -
278A GLY* 4.8 3.1 - - - -
289A GLU* 4.0 32.3 - - + +
290A ALA* 4.7 1.1 - - - -
293A CYS* 3.8 29.6 - - + -
298A GLY* 5.7 0.2 - - - -
299A PRO* 3.3 19.9 + - + +
301A ASP* 1.3 84.2 + - - +
303A ARG* 1.3 63.0 + - - +
305A LEU* 3.5 1.4 + - - +
306A VAL* 3.1 34.2 + - + +
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Residues in contact with ARG 303 (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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293A CYS* 4.3 15.6 + - - -
296A GLY* 3.8 21.1 + - - -
297A ALA 5.1 9.6 + - - +
298A GLY 5.8 0.2 - - - +
299A PRO 3.3 13.3 + - - +
300A PRO* 3.9 8.7 - - + +
302A LEU* 1.3 79.5 - - - +
304A ASP* 1.3 61.9 + - - +
306A VAL* 3.3 3.4 + - - +
307A THR* 3.1 29.6 + - + +
331A ALA* 3.6 25.5 + - - +
334A LEU* 4.2 20.6 - - + +
335A ASP* 3.0 40.8 + - - -
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Residues in contact with ASP 304 (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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300A PRO 3.0 20.1 + - - +
301A ASP* 3.7 4.9 - - - +
302A LEU 3.3 0.2 - - - -
303A ARG* 1.3 77.4 - - - +
305A LEU* 1.3 59.0 + - - +
307A THR* 3.2 8.1 + - - -
308A THR* 2.7 45.3 + - - +
471A LEU* 4.1 30.3 - - + +
472A PRO* 3.4 26.6 - - - +
474A ALA* 6.1 0.7 - - - +
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Residues in contact with LEU 305 (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 VAL* 3.8 11.7 - - + -
233A ASP* 3.8 15.9 - - - +
235A LYS* 3.8 12.3 - - - +
271A THR* 4.1 23.8 - - + +
273A MET* 4.2 8.5 - - - -
277A LEU* 3.8 26.5 - - + -
301A ASP 3.1 14.4 + - - +
302A LEU 4.1 2.2 - - - +
304A ASP* 1.3 79.8 - - - +
306A VAL* 1.3 60.6 + - - +
308A THR* 4.2 9.0 - - + -
309A LEU* 3.0 56.4 + - + +
472A PRO* 4.9 11.7 - - + -
473A PHE 5.5 0.7 - - - +
474A ALA* 5.4 3.1 - - + -
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Residues in contact with VAL 306 (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 VAL* 4.3 18.6 - - + +
128A VAL* 3.6 39.9 - - + -
129A LEU* 3.4 20.9 - - + +
132A ALA* 5.1 0.7 - - + -
293A CYS* 4.2 3.6 - - - -
302A LEU* 3.1 30.0 + - + +
303A ARG* 3.3 8.7 + - - +
305A LEU* 1.3 75.9 - - - +
307A THR* 1.3 59.4 + - - +
310A GLY* 3.0 24.3 + - - -
330A VAL* 3.9 13.1 - - + +
334A LEU* 4.1 9.9 - - + -
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Residues in contact with THR 307 (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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303A ARG* 3.1 21.2 + - + +
304A ASP* 3.2 14.7 + - - -
306A VAL* 1.3 71.8 - - - +
308A THR* 1.3 60.2 + - - +
311A GLY* 2.7 33.1 + - - -
327A ALA* 3.6 35.8 - - - +
330A VAL* 4.0 10.8 - - + -
331A ALA* 3.8 26.0 - - + +
334A LEU* 4.4 8.7 - - + -
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Residues in contact with THR 308 (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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304A ASP* 2.7 39.0 + - - -
305A LEU* 3.9 9.4 - - + -
307A THR* 1.3 77.3 + - - +
309A LEU* 1.3 64.1 + - + +
312A ALA* 3.0 16.7 + - + +
323A GLN* 2.7 33.5 + - - +
327A ALA* 4.6 1.7 - - - +
474A ALA* 4.1 25.4 - - + -
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Residues in contact with LEU 309 (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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115A LYS* 3.9 23.6 - - + +
125A VAL* 4.3 5.8 - - + -
129A LEU* 4.3 12.5 - - + +
231A VAL* 4.4 17.5 - - + +
233A ASP* 3.5 35.4 - - + +
269A ALA* 3.6 31.2 - - + -
271A THR* 5.2 0.4 - - + -
305A LEU* 3.0 37.3 + - + +
306A VAL 4.3 0.9 - - - +
308A THR* 1.3 81.6 - - + +
310A GLY* 1.3 59.3 + - - +
312A ALA* 3.6 6.8 - - + +
313A LEU* 3.2 24.8 + - - +
474A ALA* 6.2 0.2 - - + -
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Residues in contact with GLY 310 (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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129A LEU* 3.7 18.9 - - - +
133A LEU* 4.0 4.4 - - - +
306A VAL 3.0 17.3 + - - -
309A LEU* 1.3 73.5 - - - +
311A GLY* 1.3 61.8 + - - +
313A LEU* 3.2 8.0 + - - +
314A LEU* 2.9 34.5 + - - +
330A VAL* 3.8 12.3 - - - -
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Residues in contact with GLY 311 (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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307A THR 2.7 19.6 + - - -
308A THR 3.9 0.4 - - - -
310A GLY* 1.3 75.8 - - - +
312A ALA* 1.3 61.8 + - - +
314A LEU* 3.0 5.2 + - - +
315A TRP* 2.9 24.0 + - - +
323A GLN* 4.1 7.4 - - - -
326A GLY* 3.5 29.8 - - - -
327A ALA* 3.7 2.5 - - - -
330A VAL* 4.0 2.4 - - - +
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Residues in contact with ALA 312 (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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231A VAL* 4.4 10.7 - - + +
308A THR 3.0 19.0 + - - +
309A LEU* 3.6 10.1 - - + +
311A GLY* 1.3 72.7 - - - +
313A LEU* 1.3 57.0 - - - +
315A TRP* 3.4 11.8 + - - +
316A LEU* 2.9 29.8 + - - +
323A GLN* 3.4 18.0 + - - +
476A LEU* 4.4 25.5 - - + +
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Residues in contact with LEU 313 (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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113A VAL* 3.4 46.0 - - + -
114A ASP 3.6 23.8 - - - +
115A LYS* 4.6 5.4 - - + +
133A LEU* 3.5 21.1 - - + -
229A ALA* 4.0 20.6 - - + +
231A VAL* 3.9 21.1 - - + +
309A LEU 3.2 11.2 + - - +
310A GLY* 3.5 8.7 - - - +
311A GLY 3.1 0.8 - - - -
312A ALA* 1.3 75.7 - - - +
314A LEU* 1.3 62.1 + - - +
316A LEU* 3.5 2.1 + - + +
317A SER* 2.9 27.9 + - - -
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Residues in contact with LEU 314 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A VAL* 6.0 0.4 - - + -
133A LEU* 3.9 10.3 - - + -
136A CYS* 4.4 14.8 - - + +
138A CYS* 3.5 32.1 - - - -
310A GLY 2.9 14.8 + - - +
311A GLY 3.5 4.0 - - - +
313A LEU* 1.3 72.9 - - - +
315A TRP* 1.3 65.3 + - - +
317A SER* 2.9 9.2 + - - +
318A GLY 3.0 0.2 + - - -
319A HIS* 2.8 43.9 + - + +
320A ALA* 3.7 15.7 - - + +
326A GLY* 3.9 11.9 - - - +
329A ARG* 4.0 20.0 - - + -
330A VAL* 3.8 26.0 - - + -
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Residues in contact with TRP 315 (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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265A ARG* 4.8 12.8 + - - -
311A GLY 2.9 11.8 + - - +
312A ALA* 3.6 16.8 - - - +
314A LEU* 1.3 77.1 - - - +
316A LEU* 1.3 85.6 + - + +
318A GLY* 3.0 15.2 + - - -
320A ALA* 3.4 17.0 - - - +
321A GLY 3.5 27.0 + - - -
322A THR* 4.2 18.2 - - - +
323A GLN* 4.6 4.7 - - + +
476A LEU* 4.2 13.9 - - + -
478A LEU* 3.9 38.4 - - + -
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Residues in contact with LEU 316 (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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229A ALA* 3.9 18.1 - - + +
230A LEU 3.5 25.6 - - - +
231A VAL* 4.0 11.4 - - + -
265A ARG* 3.2 79.0 + - + +
266A VAL 5.2 1.3 - - - -
267A ALA* 4.0 22.2 - - + +
312A ALA 2.9 17.9 + - - +
313A LEU* 3.7 5.2 - - + +
315A TRP* 1.3 92.3 - - + +
317A SER* 1.3 61.0 + - - +
318A GLY* 3.5 0.3 + - - -
478A LEU* 5.4 2.2 - - + -
479A PRO* 5.5 2.2 - - + -
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Residues in contact with SER 317 (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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110A GLN* 3.4 27.3 + - - +
113A VAL* 3.7 26.8 - - - +
228A SER* 4.6 3.0 + - - -
229A ALA* 4.0 11.2 - - - +
313A LEU 2.9 19.5 + - - -
314A LEU* 2.9 14.7 + - - +
316A LEU* 1.3 76.0 - - - +
318A GLY* 1.3 57.9 + - - +
319A HIS* 3.2 22.8 + - - -
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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