Contacts of the helix formed by residues 293 - 304 (chain A) in PDB entry 1YV5
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 293 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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291A ARG 4.9 2.9 - - - +
292A ALA* 1.3 74.3 - - - +
294A PRO* 1.3 71.2 - - + +
295A GLU* 3.6 8.9 + - - +
296A GLN* 2.9 40.2 + - - +
297A TYR* 2.8 26.2 + - - +
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Residues in contact with PRO 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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292A ALA 4.7 0.4 - - - +
293A THR* 1.3 88.6 - - + +
295A GLU* 1.3 58.8 + - - +
297A TYR* 3.6 9.7 + - + +
298A GLN* 3.5 25.6 + - - +
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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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293A THR* 3.1 9.4 + - - +
294A PRO* 1.3 77.9 - - - +
296A GLN* 1.3 65.4 + - + +
298A GLN* 3.2 9.1 + - - +
299A ILE* 3.2 25.7 + - + +
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Residues in contact with GLN 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A ARG 4.3 0.5 - - - +
292A ALA* 3.6 16.7 - - + -
293A THR* 2.9 45.8 + - - +
295A GLU* 1.3 76.0 - - + +
297A TYR* 1.3 66.7 + - - +
299A ILE* 3.2 16.4 + - + +
300A LEU* 3.1 18.7 + - - +
318A LEU* 3.2 38.8 - - + +
321A GLU* 4.4 14.8 - - - +
322A LEU* 3.9 20.3 - - - +
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Residues in contact with TYR 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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197A VAL* 5.3 2.4 - - - +
199A LEU* 3.6 31.4 - - + +
200A VAL* 4.4 14.8 - - - +
289A LEU* 3.6 26.0 - - + -
292A ALA* 3.9 9.3 - - + +
293A THR 2.8 18.8 + - - +
294A PRO* 3.8 11.0 - - + +
295A GLU 3.3 0.2 - - - -
296A GLN* 1.3 73.5 - - - +
298A GLN* 1.3 65.4 + - + +
300A LEU* 3.3 8.2 + - - +
301A LYS* 2.8 53.3 + - + +
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Residues in contact with GLN 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 PRO 3.5 12.3 + - - +
295A GLU* 3.2 10.4 + - - +
296A GLN 3.2 0.6 - - - -
297A TYR* 1.3 88.4 - - + +
299A ILE* 1.3 60.5 + - - +
301A LYS* 3.6 36.4 - - - +
302A GLU* 2.8 33.1 + - - +
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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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295A GLU* 3.2 16.7 + - + +
296A GLN* 3.2 22.3 + - + +
298A GLN* 1.3 77.3 - - - +
300A LEU* 1.3 63.5 + - - +
302A GLU* 4.8 1.8 - - - -
303A ASN* 2.7 43.2 + - + +
314A ARG* 4.5 21.8 - - + +
315A VAL* 5.5 0.7 - - - -
318A LEU* 4.3 17.9 - - + -
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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
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199A LEU* 4.1 12.1 - - + -
285A VAL* 3.8 16.2 - - + -
288A CYS* 3.9 27.6 - - - -
289A LEU* 3.7 31.2 - - + -
292A ALA* 5.7 1.1 - - + -
296A GLN 3.1 9.2 + - - +
297A TYR* 3.4 9.4 - - - +
299A ILE* 1.3 77.6 - - - +
301A LYS* 1.3 62.1 + - - +
303A ASN* 5.0 1.6 - - - -
304A TYR* 2.8 47.8 + - + +
315A VAL* 3.8 30.7 - - + -
318A LEU* 4.2 7.2 - - + -
319A TYR* 4.3 3.8 - - + +
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Residues in contact with LYS 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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197A VAL* 4.1 37.6 - - + +
199A LEU* 3.8 13.4 - - + +
297A TYR* 2.8 32.2 + - + +
298A GLN* 3.2 39.4 + - - +
300A LEU* 1.3 78.5 - - - +
302A GLU* 1.3 61.0 + - - +
303A ASN 3.5 0.2 + - - -
304A TYR* 4.4 6.3 + - - +
306A GLN* 4.6 2.3 + - - -
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Residues in contact with GLU 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 GLN 2.8 18.3 + - - +
299A ILE* 3.9 4.0 - - - +
301A LYS* 1.3 78.1 - - - +
303A ASN* 1.3 66.4 + - - +
306A GLN* 2.9 18.0 + - - -
311A LYS* 4.0 8.0 - - - +
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Residues in contact with ASN 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 ILE* 4.5 2.4 - - - +
299A ILE* 2.7 36.4 + - - +
302A GLU* 1.3 88.4 - - - +
304A TYR* 1.3 66.7 + - - +
305A GLY 3.7 1.2 + - - -
306A GLN* 3.9 9.5 + - - +
311A LYS* 3.3 49.2 - - - +
312A VAL 4.6 0.2 + - - -
314A ARG* 3.3 40.5 + - + +
315A VAL* 3.8 14.0 - - + +
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Residues in contact with TYR 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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197A VAL* 5.9 2.4 - - - +
199A LEU* 4.6 7.6 - - + -
202A PHE* 3.7 14.6 - + - -
275A ASP 3.6 10.1 + - - -
276A ILE* 3.9 30.4 - - + +
279A ASN* 3.2 37.8 - - - +
280A LYS 2.6 29.6 + - - -
282A SER* 4.1 8.1 - - - -
285A VAL* 3.8 15.1 - - + +
300A LEU* 2.8 35.5 + - + +
301A LYS* 4.5 4.1 - - - +
303A ASN* 1.3 75.0 - - - +
305A GLY* 1.3 66.7 + - - +
306A GLN* 3.5 11.4 + - - +
315A VAL* 4.0 15.6 - - + +
319A TYR* 3.4 21.7 + - - -
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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