Contacts of the helix formed by residues 290 - 304 (chain A) in PDB entry 5LUQ
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 TYR 290 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246A ARG* 3.8 34.5 + - - -
286A LEU* 3.2 44.9 - - + -
289A ASN* 1.3 112.2 + - + +
291A VAL* 1.3 60.4 + - - +
292A SER 3.2 1.1 - - - -
293A LEU* 3.4 42.2 - - + -
294A PHE* 2.8 33.1 + - - +
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Residues in contact with VAL 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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286A LEU 3.4 3.4 + - - -
287A LEU* 3.2 32.1 - - + +
288A ASP* 3.2 24.3 - - - +
290A TYR* 1.3 78.5 - - - +
292A SER* 1.3 67.4 + - - +
294A PHE* 3.4 19.3 - - - -
295A GLU* 3.7 13.5 - - - +
337A LYS 5.1 1.6 - - - +
340A TYR* 4.7 18.6 - - + -
341A PHE* 3.7 36.3 - - + +
344A GLN* 4.6 8.9 - - - +
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Residues in contact with SER 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A ASN 4.3 7.8 + - - -
290A TYR* 4.1 0.2 - - - +
291A VAL* 1.3 85.3 - - - +
293A LEU* 1.3 64.3 + - - +
295A GLU* 3.8 2.7 - - - +
296A VAL* 2.9 37.8 + - - +
344A GLN* 5.3 6.5 - - - -
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Residues in contact with LEU 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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246A ARG* 4.2 21.1 - - + +
250A ASN* 4.4 15.7 - - - +
253A LEU* 6.0 1.3 - - + -
286A LEU* 5.8 0.7 - - + -
289A ASN 4.4 2.2 - - - +
290A TYR* 3.4 51.3 + - + -
292A SER* 1.3 79.6 + - - +
294A PHE* 1.3 69.7 + - + +
296A VAL* 3.0 11.1 - - + +
297A LEU* 2.9 47.3 + - + +
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Residues in contact with PHE 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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283A SER* 5.9 2.9 - - - -
286A LEU* 3.8 24.7 - - + -
287A LEU* 3.6 25.6 - - + -
290A TYR* 2.8 31.3 + - + +
291A VAL* 3.4 16.2 - - - -
293A LEU* 1.3 73.3 - - + +
295A GLU* 1.3 68.7 + - + +
297A LEU* 3.0 17.7 - - + +
298A LEU* 2.9 52.9 + - + +
319A PHE* 4.3 26.0 - + + -
320A LEU* 5.1 2.9 - - + -
323A VAL* 5.3 2.2 - - + -
341A PHE* 3.1 38.6 - + - -
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Residues in contact with GLU 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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291A VAL 3.7 9.1 - - - +
292A SER* 3.7 4.1 + - - +
293A LEU 3.4 0.2 - - - -
294A PHE* 1.3 88.9 - - + +
296A VAL* 1.3 60.1 + - + +
298A LEU* 3.6 14.6 - - + -
299A LYS* 2.7 64.0 + - + +
316A LEU* 5.1 2.5 - - + +
341A PHE* 2.8 42.3 - - + +
344A GLN* 3.5 17.9 - - - +
345A PHE* 3.0 22.7 - - - -
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Residues in contact with VAL 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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253A LEU* 5.0 8.5 - - + -
292A SER* 2.9 21.3 + - - +
293A LEU* 3.0 26.2 + - + +
295A GLU* 1.3 77.9 - - + +
297A LEU* 1.3 61.3 + - + +
299A LYS* 4.4 3.6 - - + +
300A TRP* 2.8 41.9 + - + +
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Residues in contact with LEU 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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246A ARG* 4.8 2.2 - - + +
249A PHE* 3.3 55.9 - - + -
250A ASN* 4.5 5.8 - - - +
253A LEU* 3.5 31.3 - - + +
265A TYR* 2.8 19.1 + - - +
293A LEU* 2.9 44.8 + - + +
294A PHE* 3.0 24.5 - - + +
296A VAL* 1.3 76.1 - - - +
298A LEU* 1.3 79.2 + - + +
300A TRP* 4.2 0.2 - - - +
301A CYS* 3.0 14.7 + - - +
319A PHE* 6.0 1.3 - - + -
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Residues in contact with LEU 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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249A PHE* 4.9 1.8 - - + -
265A TYR* 3.8 6.5 - - + +
294A PHE* 2.9 51.0 + - + +
295A GLU* 3.5 9.6 - - + +
297A LEU* 1.3 92.5 - - + +
299A LYS* 1.3 66.7 + - + +
301A CYS* 2.9 4.9 + - - +
302A ALA* 2.9 18.2 + - - +
312A ALA* 4.1 13.4 - - - +
315A ALA* 3.6 30.7 - - + -
316A LEU* 3.6 37.0 - - + +
319A PHE* 4.1 11.0 - - + -
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Residues in contact with LYS 299 (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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295A GLU* 2.7 61.9 + - + +
296A VAL* 4.7 3.4 - - + +
298A LEU* 1.3 76.7 - - + +
300A TRP* 1.3 57.6 + - - +
302A ALA* 2.7 31.4 + - + +
303A HIS* 3.0 25.0 + - + +
316A LEU* 5.2 7.2 - - + -
344A GLN* 5.4 4.6 + - - +
345A PHE* 4.7 2.4 - - + -
348A ILE* 3.5 30.2 - - + +
360A SER* 6.2 2.7 - - - -
363A ILE* 5.2 14.6 - - + -
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Residues in contact with TRP 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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252A VAL* 3.7 29.8 - - + -
253A LEU* 3.5 29.2 - - + -
254A LYS 4.9 10.5 - - - -
255A ALA* 5.2 5.6 - - + -
265A TYR* 6.1 1.1 - + - -
296A VAL* 2.8 29.5 + - + +
297A LEU 4.2 0.9 - - - +
299A LYS* 1.3 77.3 - - - +
301A CYS* 1.3 68.5 + - + +
303A HIS* 3.4 9.1 + - + +
304A THR* 2.8 46.0 + - + -
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Residues in contact with CYS 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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265A TYR* 3.3 38.1 - - + -
297A LEU 3.0 14.3 + - - +
298A LEU* 2.9 13.5 + - - +
300A TRP* 1.3 80.0 - - + +
302A ALA* 1.3 56.4 + - - +
304A THR* 2.7 37.5 + - - +
306A VAL* 4.6 9.5 - - - +
308A LEU 4.0 21.5 - - - -
309A LYS* 5.3 0.7 - - - -
311A ALA* 4.8 0.2 - - - -
312A ALA* 4.3 11.9 - - + -
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Residues in contact with ALA 302 (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 LEU 2.9 5.7 + - - -
299A LYS* 2.7 28.2 + - + +
301A CYS* 1.3 71.5 - - - +
303A HIS* 1.3 64.6 + - + +
304A THR 4.2 3.5 - - - +
309A LYS* 4.9 12.4 - - - +
312A ALA* 3.5 25.6 - - + -
316A LEU* 6.4 0.2 - - + -
359A LEU* 5.2 15.0 - - + +
360A SER* 5.3 2.9 - - - +
363A ILE* 4.9 15.3 - - + -
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Residues in contact with HIS 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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299A LYS* 3.0 25.3 + - + +
300A TRP* 3.9 10.8 - - + +
301A CYS 2.8 0.4 + - - -
302A ALA* 1.3 83.8 + - + +
304A THR* 1.3 66.0 + - - +
305A ASN* 3.4 3.5 + - - +
357A LYS* 5.1 12.4 + - + +
360A SER* 3.8 24.0 - - - -
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Residues in contact with THR 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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262A LEU* 4.8 7.9 - - + -
300A TRP* 2.8 46.2 + - + -
301A CYS* 2.7 21.6 + - - +
302A ALA 4.2 0.5 - - - +
303A HIS* 1.3 73.5 - - - +
305A ASN* 1.3 63.1 + - - +
306A VAL* 2.9 34.8 + - + +
309A LYS* 4.1 9.4 - - - +
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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