Contacts of the helix formed by residues 298 - 306 (chain A) in PDB entry 1YDY
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 GLY 298 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297A THR* 1.3 75.2 - - - +
299A MET* 1.3 63.3 - - - +
300A VAL 3.6 0.4 - - - -
301A GLN* 3.3 14.5 + - - +
302A ASP* 3.0 24.2 + - - +
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Residues in contact with MET 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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236A ILE* 4.1 16.8 - - + -
261A MET 3.8 15.5 - - - +
262A PHE* 3.5 39.5 - - + -
267A MET* 4.6 14.5 - - + +
277A ILE* 5.4 3.6 - - + -
279A PRO* 3.8 21.8 - - + -
283A MET* 4.2 8.1 - - + +
284A LEU* 3.6 26.9 - - + -
297A THR* 3.2 12.3 + - - +
298A GLY* 1.3 74.2 - - - +
300A VAL* 1.3 64.5 + - - +
302A ASP* 3.3 6.0 + - - +
303A ALA* 2.8 28.8 + - + +
310A VAL* 6.1 0.2 - - + -
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Residues in contact with VAL 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A LEU* 3.5 40.5 - - + +
296A LEU* 6.0 3.8 - - + -
297A THR* 4.7 2.6 + - - -
298A GLY 3.4 0.6 + - - -
299A MET* 1.3 75.2 - - - +
301A GLN* 1.3 58.5 + - - +
303A ALA* 3.2 5.2 + - - +
304A GLN* 2.8 55.0 + - + +
310A VAL* 4.4 6.5 - - + -
338A ALA* 3.2 41.7 - - + +
340A VAL* 4.1 9.9 - - + -
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Residues in contact with GLN 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 THR 5.5 0.4 + - - +
298A GLY* 3.3 12.0 + - - +
299A MET 3.3 0.4 - - - -
300A VAL* 1.3 79.4 - - - +
302A ASP* 1.3 57.9 + - - +
304A GLN* 3.2 6.1 + - - +
305A GLN* 2.8 33.3 + - + +
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Residues in contact with ASP 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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263A LYS 4.6 4.3 - - - +
264A PRO* 5.0 1.7 - - - +
265A GLY* 4.3 16.3 + - - -
266A ALA* 4.3 1.0 + - - +
267A MET* 3.3 29.3 + - + +
268A LYS 5.2 0.2 + - - -
298A GLY 3.0 19.8 + - - +
299A MET* 3.7 5.6 - - - +
301A GLN* 1.3 75.7 - - - +
303A ALA* 1.3 64.2 + - - +
305A GLN* 2.9 33.9 + - - +
306A ASN* 3.0 27.8 + - - -
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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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267A MET* 3.8 19.9 - - + +
277A ILE* 3.5 17.3 - - + -
299A MET* 2.8 22.6 + - + +
300A VAL* 3.5 0.9 - - - +
302A ASP* 1.3 72.5 - - - +
304A GLN* 1.3 63.1 + - - +
306A ASN* 3.0 12.6 + - - +
307A LYS 3.4 0.2 + - - -
308A LEU* 3.1 22.7 + - + +
310A VAL* 3.4 28.3 - - + -
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Residues in contact with GLN 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 VAL* 2.8 41.8 + - + +
301A GLN* 4.0 5.4 - - - +
303A ALA* 1.3 69.8 - - - +
305A GLN* 1.3 64.6 + - - +
307A LYS* 3.1 14.7 + - - +
308A LEU 3.8 16.8 - - - +
310A VAL* 4.2 4.4 - - + +
338A ALA 4.5 1.9 - - - +
339A GLY* 3.2 22.3 + - - +
340A VAL* 4.3 0.6 - - - +
341A ASN* 3.0 30.1 + - - +
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Residues in contact with GLN 305 (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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301A GLN* 2.8 15.2 + - + +
302A ASP* 2.9 32.9 + - - +
304A GLN* 1.3 77.8 - - - +
306A ASN* 1.3 67.7 + - - +
307A LYS* 3.4 9.7 + - - +
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Residues in contact with ASN 306 (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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267A MET* 3.6 14.3 - - + +
268A LYS* 3.2 45.6 - - - +
271A ALA* 3.7 20.9 - - + +
302A ASP* 3.0 33.9 + - - +
303A ALA 3.0 9.2 + - - +
305A GLN* 1.3 88.4 - - - +
307A LYS* 1.3 68.7 + - - +
308A LEU* 3.3 3.6 + - + +
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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