Contacts of the helix formed by residues 292 - 303 (chain A) in PDB entry 1QCY
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 THR 292 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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282A LEU* 3.9 31.3 - - + +
285A TYR* 3.4 39.5 - - + -
286A ASN* 3.9 15.9 + - - +
290A LEU 3.4 6.7 + - - +
291A SER* 1.3 72.7 + - - +
293A GLU* 1.3 69.0 + - - +
294A LYS 3.5 2.0 - - - -
295A PHE* 3.3 6.8 + - + +
296A VAL* 2.9 34.0 + - - +
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Residues in contact with GLU 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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291A SER* 3.5 17.0 - - - +
292A THR* 1.3 87.1 + - - +
294A LYS* 1.3 66.9 + - + +
296A VAL* 3.8 4.8 - - - +
297A GLU* 3.0 23.4 + - - +
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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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255A GLU* 3.7 21.5 - - - +
291A SER* 5.2 2.2 + - - +
292A THR 3.5 0.2 - - - -
293A GLU* 1.3 79.7 - - + +
295A PHE* 1.3 58.8 + - - +
297A GLU* 3.3 17.4 + - - +
298A GLU* 2.8 32.1 + - - +
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Residues in contact with PHE 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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252A THR* 3.7 9.2 - - + -
253A ASP* 3.3 12.8 - - - -
254A GLY 3.1 48.7 - - - -
255A GLU* 3.5 23.5 + - + +
280A ALA* 3.9 15.9 - - + -
281A ILE 3.5 21.1 - - - -
282A LEU* 4.1 15.7 - - + -
285A TYR* 3.9 27.4 - + + -
291A SER 5.4 0.2 + - - -
292A THR* 3.3 9.3 + - + +
293A GLU 3.3 0.2 - - - -
294A LYS* 1.3 78.0 - - - +
296A VAL* 1.3 64.4 + - - +
298A GLU* 3.0 4.6 + - + +
299A ILE* 3.0 41.5 + - + +
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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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280A ALA* 5.2 0.9 - - - -
282A LEU* 4.2 24.9 - - + -
292A THR* 2.9 22.5 + - - +
293A GLU* 3.8 4.7 - - - +
295A PHE* 1.3 75.7 - - + +
297A GLU* 1.3 59.7 + - - +
299A ILE* 3.4 2.5 + - - +
300A LYS* 2.9 48.0 + - + +
311A PHE* 3.8 28.9 - - + -
313A ASN* 4.0 21.3 - - - +
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Residues in contact with GLU 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 GLU 3.0 17.9 + - - +
294A LYS* 3.5 15.7 - - - +
296A VAL* 1.3 77.7 - - - +
298A GLU* 1.3 63.4 + - - +
300A LYS* 3.5 10.4 - - - +
301A SER* 3.1 22.5 + - - -
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Residues in contact with GLU 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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222A THR* 5.0 1.2 + - - +
255A GLU* 3.8 18.0 - - - +
256A SER* 2.7 46.8 + - - -
259A ASN* 3.7 16.9 + - + +
262A LEU* 3.5 20.4 - - + +
294A LYS 2.8 17.5 + - - +
295A PHE 3.4 5.4 - - - +
297A GLU* 1.3 76.3 - - - +
299A ILE* 1.3 74.7 + - + +
301A SER* 2.5 26.7 + - - +
302A ILE* 3.5 6.4 + - - +
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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
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222A THR* 5.3 2.9 - - + +
250A ILE* 5.4 0.4 - - + +
252A THR* 3.4 24.7 - - + -
254A GLY 4.4 4.5 - - - +
278A SER* 2.8 43.6 + - - +
279A ILE 4.0 11.4 - - - +
280A ALA* 3.8 14.1 - - + -
295A PHE* 3.0 39.5 + - + +
296A VAL 4.1 0.2 - - - +
298A GLU* 1.3 87.2 - - - +
300A LYS* 1.3 59.4 + - - +
302A ILE* 3.0 29.2 + - + +
311A PHE* 3.8 17.0 - - + -
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Residues in contact with LYS 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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296A VAL* 2.9 33.0 + - + +
297A GLU* 3.5 9.9 - - - +
299A ILE* 1.3 78.8 - - - +
301A SER* 1.3 61.8 + - - +
302A ILE 3.1 1.6 + - - -
303A ALA* 3.1 19.6 + - - +
307A THR* 4.1 24.9 + - + +
308A GLU* 6.4 1.8 - - - +
311A PHE* 3.6 41.1 - - + -
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Residues in contact with SER 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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262A LEU* 4.6 6.4 - - - +
266A ILE* 3.2 25.8 - - - +
276A ARG* 4.3 0.2 + - - -
297A GLU* 3.1 11.9 + - - -
298A GLU* 2.5 23.3 + - - +
300A LYS* 1.3 79.0 - - - +
302A ILE* 1.3 60.5 + - - +
303A ALA 3.4 4.9 - - - +
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Residues in contact with ILE 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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222A THR* 3.8 29.4 - - + -
226A THR* 5.1 2.2 - - + +
250A ILE* 3.2 37.5 - - + -
262A LEU* 4.3 15.5 - - + -
266A ILE* 3.6 20.0 - - + -
276A ARG* 2.5 37.6 + - + +
278A SER* 3.9 8.1 - - - -
298A GLU 3.7 9.9 - - - +
299A ILE* 3.0 32.8 + - + +
301A SER* 1.3 78.0 - - - +
303A ALA* 1.3 58.5 + - - +
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Residues in contact with ALA 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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276A ARG* 3.6 11.0 + - - -
278A SER* 3.4 18.8 + - - +
299A ILE 3.5 2.2 + - - -
300A LYS 3.1 15.6 + - - +
301A SER 4.0 4.3 - - - +
302A ILE* 1.3 82.4 - - - +
304A SER* 1.3 64.6 - - - +
305A GLU* 5.7 0.3 - - - +
307A THR* 4.6 8.5 + - + +
310A HIS* 3.8 26.5 - - + -
311A PHE* 3.9 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