Contacts of the helix formed by residues 293 - 304 (chain A) in PDB entry 5UQ9
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 LEU 293 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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289A CYS 3.5 15.7 - - - +
290A LEU* 3.4 15.2 + - + +
291A SER 3.1 1.6 - - - -
292A SER* 1.3 78.3 - - - +
294A LYS* 1.3 65.0 + - - +
295A ASP 3.5 2.2 - - - -
296A GLU* 3.9 28.7 - - + +
297A ARG* 3.0 31.2 + - + +
277B PRO* 4.2 13.7 - - + -
340B MET* 3.7 30.3 - - + -
344B GLN* 6.2 0.4 - - - +
433B TYR* 5.0 1.6 - - + -
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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 ARG* 3.8 29.1 - - - +
256A ASP* 2.4 29.8 + - - +
257A SER* 5.1 1.8 - - - -
291A SER 3.6 4.7 + - - +
292A SER 3.1 7.4 + - - +
293A LEU* 1.3 75.9 - - - +
295A ASP* 1.3 67.6 + - - +
297A ARG* 3.1 27.9 + - - +
298A ILE* 3.0 46.9 + - + +
436B GLU* 3.2 23.3 - - - +
437B MET* 3.9 7.0 - - - -
458B LEU* 3.0 30.3 - - - +
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Residues in contact with ASP 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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255A ARG* 5.2 5.1 + - - -
293A LEU 3.5 0.2 - - - -
294A LYS* 1.3 81.6 - - - +
296A GLU* 1.3 61.5 + - - +
298A ILE* 3.4 28.4 + - - +
299A GLN* 3.4 13.5 + - - +
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Residues in contact with GLU 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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293A LEU* 3.4 36.4 + - + +
294A LYS 3.2 1.0 - - - -
295A ASP* 1.3 78.3 - - - +
297A ARG* 1.3 57.7 + - - +
299A GLN* 3.7 5.2 + - - +
300A ALA* 3.1 25.1 + - - +
340B MET* 4.4 2.0 - - - +
343B ARG* 3.5 24.1 + - - +
387B GLN* 4.1 7.7 - - + +
388B ASN* 2.7 21.5 + - - -
391B LEU* 5.8 3.5 - - + +
433B TYR* 2.5 36.6 + - + +
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Residues in contact with ARG 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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256A ASP* 3.3 23.8 + - - -
290A LEU* 3.1 25.4 + - - +
291A SER* 3.1 22.8 + - - +
293A LEU* 3.0 16.6 + - + +
294A LYS* 3.1 17.3 + - - +
296A GLU* 1.3 73.3 - - - +
298A ILE* 1.3 61.7 + - - +
300A ALA* 3.7 1.0 - - - +
301A SER* 2.9 30.8 + - - -
432B GLY 3.4 20.9 - - - -
433B TYR* 3.3 33.1 - - + +
435B HIS 2.7 32.5 + - - +
436B GLU* 3.2 18.6 + - - -
438B LEU* 3.5 21.3 - - - +
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Residues in contact with ILE 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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294A LYS* 3.0 40.9 + - + +
295A ASP* 3.7 23.6 - - - +
296A GLU 3.4 0.2 - - - -
297A ARG* 1.3 76.6 - - - +
299A GLN* 1.3 60.8 + - - +
301A SER* 2.7 21.9 + - - -
302A LYS* 3.6 8.5 + - - +
436B GLU* 3.8 33.7 - - + +
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Residues in contact with GLN 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 ASP 3.4 9.6 + - - +
296A GLU* 3.7 7.6 + - + +
297A ARG 3.3 0.2 - - - -
298A ILE* 1.3 77.3 - - - +
300A ALA* 1.3 64.4 + - - +
302A LYS* 3.2 29.1 + - - +
303A LYS* 3.4 35.3 + - - +
391B LEU* 4.3 21.6 - - + +
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Residues in contact with ALA 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 GLU 3.1 18.8 + - - +
297A ARG 3.3 1.3 + - - +
299A GLN* 1.3 78.3 - - - +
301A SER* 1.3 56.7 + - - +
304A LEU* 2.9 40.7 + - + +
391B LEU* 4.3 12.5 - - + +
433B TYR* 3.4 46.7 - - + +
434B ARG* 4.5 1.6 - - - -
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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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297A ARG 2.9 12.1 + - - -
298A ILE* 2.7 23.6 + - - -
300A ALA* 1.3 77.7 - - - +
302A LYS* 1.3 59.1 + - - +
303A LYS 3.6 0.2 + - - -
304A LEU 3.6 12.0 - - - +
434B ARG 3.2 25.5 + - - -
436B GLU* 3.5 28.0 + - - +
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Residues in contact with LYS 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 ILE 3.6 8.3 + - - +
299A GLN* 3.2 25.7 + - - +
300A ALA 3.2 0.6 - - - -
301A SER* 1.3 82.4 + - - +
303A LYS* 1.3 81.9 + - + +
304A LEU 5.0 0.2 - - - -
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Residues in contact with LYS 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 GLN* 3.4 28.4 + - - +
300A ALA 3.3 1.4 + - - -
302A LYS* 1.3 105.6 - - + +
304A LEU* 1.3 62.7 + - - +
305A LYS* 3.9 1.7 + - - +
391B LEU* 4.3 24.0 - - + +
396B LYS* 3.4 44.9 + - + +
400B GLU* 5.0 1.9 - - - +
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Residues in contact with LEU 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 ALA* 2.9 19.7 + - + +
301A SER* 3.6 15.2 - - - +
302A LYS 5.0 0.2 - - - -
303A LYS* 1.3 78.2 - - - +
305A LYS* 1.3 60.0 + - - +
390B LEU* 3.2 35.0 - - + +
391B LEU* 4.6 3.6 - - + -
396B LYS* 3.7 25.1 - - + +
399B VAL* 6.2 1.3 - - + -
430B TYR* 3.8 34.5 - - + +
433B TYR* 4.0 29.6 - - + -
434B ARG* 4.1 17.9 + - + +
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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