Contacts of the helix formed by residues 288 - 300 (chain A) in PDB entry 1U2X
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 ASP 288 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250A THR* 4.6 12.4 + - - +
286A VAL* 3.3 5.0 - - + +
287A GLN* 1.3 77.4 - - - +
289A ARG* 1.3 61.5 + - - +
290A LYS* 3.0 18.5 + - - +
291A LEU* 2.9 38.5 + - + +
292A ARG* 2.8 28.2 + - - +
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Residues in contact with ARG 289 (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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287A GLN 3.3 4.4 + - - +
288A ASP* 1.3 73.1 + - - +
290A LYS* 1.3 57.9 + - - +
292A ARG* 3.4 31.6 + - - +
293A LYS* 3.0 28.2 + - - +
318A SER* 2.2 44.3 + - - -
319A VAL* 3.7 23.1 - - + +
323A ARG* 3.5 17.8 - - - +
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Residues in contact with LYS 290 (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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250A THR* 6.5 0.7 - - + -
288A ASP* 3.0 9.9 + - - +
289A ARG* 1.3 78.1 - - - +
291A LEU* 1.3 60.8 + - - +
293A LYS* 3.3 8.4 + - + +
294A LYS* 3.0 46.3 + - + +
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Residues in contact with LEU 291 (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 ARG* 4.9 2.9 - - - +
245A TYR 4.7 0.2 - - - +
246A GLN 4.5 7.6 - - - +
248A LEU* 3.3 38.1 - - + +
249A ARG* 4.9 4.9 - - - +
250A THR* 5.2 6.1 - - - +
258A ALA* 3.6 30.5 - - + -
262A LEU* 5.0 0.9 - - + -
286A VAL* 4.0 15.0 - - + -
288A ASP* 2.9 26.3 + - + +
290A LYS* 1.3 73.1 - - - +
292A ARG* 1.3 65.0 + - - +
294A LYS* 3.1 10.9 + - + +
295A ILE* 3.0 39.7 + - + +
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Residues in contact with ARG 292 (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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283A PHE* 4.2 11.4 - - + -
286A VAL* 2.9 41.1 + - + +
287A GLN* 3.7 15.4 + - - +
288A ASP 2.8 15.8 + - - +
289A ARG* 3.5 30.8 - - - +
291A LEU* 1.3 75.7 - - - +
293A LYS* 1.3 57.4 + - - +
295A ILE* 3.4 4.9 + - - +
296A ILE* 3.0 44.2 + - + +
315A GLN* 3.0 64.7 + - - +
316A ILE* 4.5 0.7 - - - +
318A SER* 4.5 0.6 - - - -
319A VAL* 3.9 18.6 - - + +
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Residues in contact with LYS 293 (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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289A ARG 3.0 17.9 + - - +
290A LYS* 3.5 9.4 - - + +
291A LEU 3.2 0.2 - - - -
292A ARG* 1.3 74.7 - - - +
294A LYS* 1.3 59.8 + - + +
296A ILE* 3.5 7.7 + - + +
297A THR* 3.0 49.5 + - - +
319A VAL* 3.9 36.2 + - + +
320A LEU* 4.4 17.0 - - + +
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Residues in contact with LYS 294 (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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250A THR* 6.3 3.4 - - - -
258A ALA* 4.3 18.6 - - + -
259A ASN* 3.4 36.0 + - - +
262A LEU* 3.6 15.0 - - + -
290A LYS* 3.0 33.3 + - + +
291A LEU* 3.1 12.5 + - + +
293A LYS* 1.3 76.6 - - + +
295A ILE* 1.3 59.7 + - - +
297A THR* 3.4 3.1 + - - -
298A ASN* 2.8 41.6 + - - +
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Residues in contact with ILE 295 (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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245A TYR* 3.6 52.5 - - + +
246A GLN* 4.3 0.7 - - - -
248A LEU* 5.0 0.4 - - + -
262A LEU* 4.4 14.8 - - + -
281A VAL* 6.4 0.4 - - + -
283A PHE* 4.1 21.3 - - + -
286A VAL* 4.0 21.5 - - + -
291A LEU* 3.0 40.3 + - + +
292A ARG* 3.7 4.3 - - - +
294A LYS* 1.3 77.7 - - - +
296A ILE* 1.3 57.3 + - - +
299A ILE* 2.9 45.1 + - + +
300A LEU* 3.8 1.4 + - + +
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Residues in contact with ILE 296 (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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283A PHE* 3.9 17.7 - - + -
292A ARG* 3.0 29.0 + - + +
293A LYS* 3.7 6.5 - - + +
295A ILE* 1.3 79.5 - - - +
297A THR* 1.3 64.6 + - - +
300A LEU* 3.3 16.3 + - + +
301A PRO* 3.2 21.7 - - - +
316A ILE* 4.1 18.6 - - + -
319A VAL* 3.3 31.9 - - + -
320A LEU* 4.3 13.0 - - + -
349A LEU* 3.9 32.3 - - + -
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Residues in contact with THR 297 (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 LYS* 3.0 36.3 + - - +
294A LYS* 3.7 5.6 - - - -
296A ILE* 1.3 83.5 - - - +
298A ASN* 1.3 69.8 + - - +
301A PRO* 3.8 14.8 - - - +
349A LEU* 5.7 1.6 - - - -
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Residues in contact with ASN 298 (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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259A ASN* 4.5 9.8 + - - +
262A LEU* 3.8 37.3 - - + +
263A ARG* 5.0 0.9 + - - +
266A LYS* 2.9 60.0 + - + +
269A ILE* 4.9 0.2 - - - +
294A LYS* 2.8 39.7 + - - +
297A THR* 1.3 84.1 - - - +
299A ILE* 1.4 60.4 + - + +
301A PRO* 4.7 0.4 - - - -
302A PHE* 4.6 6.8 - - - +
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Residues in contact with ILE 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A TYR* 3.7 34.5 - - + +
262A LEU* 4.0 16.8 - - + -
265A ALA* 3.7 31.0 - - + -
266A LYS* 4.8 1.6 - - + -
269A ILE* 4.1 14.1 - - + -
281A VAL* 3.7 33.2 - - + -
295A ILE* 2.9 21.3 + - + +
297A THR 3.4 0.2 - - - -
298A ASN* 1.4 86.4 - - + +
300A LEU* 1.3 67.3 + - + +
301A PRO* 3.6 2.2 - - - -
302A PHE* 3.1 20.1 + - - +
303A VAL* 3.6 7.4 + - - +
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Residues in contact with LEU 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A VAL* 4.0 24.5 - - + -
283A PHE* 4.2 26.7 - - + -
295A ILE* 4.7 1.1 - - + +
296A ILE* 3.3 22.9 + - + +
299A ILE* 1.3 82.9 - - + +
301A PRO* 1.4 67.1 - - + +
302A PHE 3.0 1.6 + - - -
303A VAL* 3.4 9.7 + - - +
306A VAL* 3.9 31.9 - - + -
316A ILE* 4.5 11.7 - - + -
345A ILE* 5.5 1.3 - - + -
349A LEU* 3.9 26.9 - - + -
351A PHE* 3.3 29.9 - - + +
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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