Contacts of the helix formed by residues 289 - 302 (chain C) in PDB entry 1UU1
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 GLU 289 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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288C MET* 1.3 73.0 - - - +
290C LYS* 1.3 74.6 + - + +
291C GLU* 3.2 41.8 + - + +
292C GLU* 2.9 18.7 + - + +
293C LYS* 2.9 23.9 + - - +
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Residues in contact with LYS 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288C MET 3.9 0.2 + - - -
289C GLU* 1.3 82.3 - - + +
291C GLU* 1.3 64.7 + - - +
293C LYS* 3.7 23.9 - - - +
294C GLU* 3.0 45.8 + - - +
311C ARG* 4.2 26.1 + - - +
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Residues in contact with GLU 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289C GLU* 3.3 33.0 + - + +
290C LYS* 1.3 81.0 - - - +
292C GLU* 1.3 94.5 + - - +
294C GLU* 4.1 4.0 - - - +
295C ARG* 3.2 38.9 + - + +
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Residues in contact with GLU 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274C TYR* 5.4 3.5 - - - -
287C PHE 4.3 2.1 - - - +
288C MET* 3.2 24.6 - - + +
289C GLU* 2.9 32.9 + - - +
291C GLU* 1.3 99.7 - - - +
293C LYS* 1.3 80.7 + - - +
295C ARG* 3.1 15.0 + - - +
296C LEU* 3.0 16.7 + - - +
334C PHE* 3.5 16.8 - - + -
335C LYS* 4.4 25.3 + - - +
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Residues in contact with LYS 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288C MET* 3.3 30.5 - - + +
289C GLU 2.9 19.5 + - - +
290C LYS* 3.7 28.2 - - - +
291C GLU 3.3 0.2 - - - -
292C GLU* 1.3 76.9 - - - +
294C GLU* 1.3 66.1 + - - +
296C LEU* 2.9 10.7 + - - +
297C LEU* 2.8 34.6 + - + +
309C SER* 3.8 16.9 + - - +
310C PHE 2.6 33.3 + - - +
311C ARG* 3.3 17.4 + - - +
313C GLY* 4.1 17.3 - - - +
314C VAL* 4.0 2.0 - - + -
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Residues in contact with GLU 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290C LYS* 3.0 39.6 + - - +
291C GLU* 4.2 4.5 - - - +
293C LYS* 1.3 84.5 - - - +
295C ARG* 1.3 60.4 + - - +
297C LEU* 3.5 19.2 - - + +
298C GLU* 2.8 29.6 + - - +
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Residues in contact with ARG 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291C GLU* 3.2 37.2 + - - +
292C GLU* 3.1 14.5 + - - +
294C GLU* 1.3 76.0 - - - +
296C LEU* 1.3 57.9 + - - +
298C GLU* 3.5 6.3 - - - +
299C HIS* 2.9 29.5 + - - +
334C PHE* 3.2 44.9 + - + -
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Residues in contact with LEU 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288C MET* 3.8 28.7 - - + -
292C GLU 3.0 10.7 + - - +
293C LYS* 2.9 13.9 + - - +
295C ARG* 1.3 75.9 - - - +
297C LEU* 1.3 69.2 + - + +
299C HIS* 3.0 7.0 + - - +
300C LEU* 2.8 57.6 + - + +
307C VAL* 5.5 0.2 - - + -
314C VAL* 4.5 10.5 - - + -
316C ILE* 5.9 1.3 - - + -
330C GLU* 5.6 1.1 - - + +
331C LEU* 4.2 24.5 - - + -
334C PHE* 3.1 31.8 - - + -
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Residues in contact with LEU 297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293C LYS* 2.8 26.1 + - + +
294C GLU* 3.5 21.3 - - + +
296C LEU* 1.3 80.0 - - + +
298C GLU* 1.3 60.9 + - - +
300C LEU* 3.3 5.7 + - + +
301C ARG* 3.0 33.0 + - + +
307C VAL* 3.9 22.7 - - + +
309C SER* 3.7 30.3 - - - +
314C VAL* 3.6 25.8 - - + -
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Residues in contact with GLU 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294C GLU 2.8 21.5 + - - +
295C ARG* 3.5 7.6 - - - +
297C LEU* 1.3 70.2 - - - +
299C HIS* 1.3 67.7 + - - +
301C ARG* 3.0 41.1 + - - +
302C THR* 3.2 27.2 + - + +
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Residues in contact with HIS 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295C ARG 2.9 18.6 + - - +
296C LEU* 3.0 10.5 + - - +
298C GLU* 1.3 79.0 - - - +
300C LEU* 1.3 65.0 + - + +
302C THR* 2.6 34.6 + - - -
303C LYS* 3.5 23.9 + - + +
330C GLU* 2.9 37.9 + - + +
333C VAL* 5.4 3.8 - - + -
334C PHE* 4.1 22.5 - + + -
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Residues in contact with LEU 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296C LEU* 2.8 52.3 + - + +
297C LEU* 3.6 5.8 - - + +
299C HIS* 1.3 73.6 - - + +
301C ARG* 1.3 64.6 + - - +
303C LYS* 3.0 10.2 + - + +
305C VAL* 2.8 58.0 + - + +
307C VAL* 3.7 37.0 - - + -
316C ILE* 6.0 1.6 - - + -
327C ILE* 4.8 8.7 - - + -
330C GLU* 4.5 22.7 - - + -
331C LEU* 5.2 3.6 - - + -
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Residues in contact with ARG 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C ASP* 4.4 7.3 - - - +
297C LEU* 3.0 29.4 + - - +
298C GLU* 3.0 35.8 + - - +
300C LEU* 1.3 77.4 - - - +
302C THR* 1.3 57.3 + - - +
304C ASN* 2.8 25.5 + - - +
305C VAL 4.0 9.4 - - - +
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Residues in contact with THR 302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A ASP* 4.0 0.9 - - - +
189A LYS* 2.8 24.8 + - - +
298C GLU* 3.2 30.4 + - + +
299C HIS* 2.6 32.3 + - + -
301C ARG* 1.3 77.5 - - + +
303C LYS* 1.3 60.6 + - - +
304C ASN* 3.3 1.1 - - - -
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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
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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