Contacts of the helix formed by residues 306 - 317 (chain A) in PDB entry 1YNU
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 SER 306 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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280A PHE 5.7 1.1 + - - -
304A LEU 3.8 2.2 + - - -
305A VAL* 1.3 75.3 - - - +
307A SER* 1.3 58.5 + - - +
308A GLN* 3.0 25.4 + - - +
309A THR* 3.1 17.4 + - - -
310A GLN* 2.9 24.9 + - - +
801A K 4.0 4.9 - - - -
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Residues in contact with SER 307 (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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79A LEU* 2.7 41.6 + - - +
80A ALA* 4.8 0.5 - - - -
82A PHE* 3.6 32.4 + - - -
88A LEU* 4.8 1.2 - - - +
305A VAL 3.2 5.4 + - - -
306A SER* 1.3 72.8 + - - +
308A GLN* 1.3 58.9 + - - +
310A GLN* 3.7 12.9 - - - +
311A HIS* 3.0 30.0 + - - +
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Residues in contact with GLN 308 (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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65A ALA 5.6 0.7 - - - +
66A ALA* 5.4 6.7 + - - +
68A PHE* 3.5 42.7 - - + -
79A LEU* 5.2 2.2 - - - -
306A SER* 3.0 13.0 + - - +
307A SER* 1.3 80.1 + - - +
309A THR* 1.3 68.3 + - - +
311A HIS* 3.3 5.7 + - - +
312A LEU* 3.1 24.1 + - + +
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Residues in contact with THR 309 (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 PHE* 3.8 31.0 + - + +
282A VAL* 3.7 30.5 - - + -
305A VAL* 4.3 4.5 - - + -
306A SER* 3.1 21.1 + - - -
308A GLN* 1.3 83.2 + - - +
310A GLN* 1.3 62.8 + - - +
312A LEU* 3.2 8.2 + - - +
313A LEU* 2.9 35.2 + - + +
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Residues in contact with GLN 310 (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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82A PHE* 4.9 6.3 + - - -
84A ASP 5.6 0.8 + - - -
87A GLY* 4.7 4.6 - - - -
88A LEU* 2.9 42.8 + - + +
91A PHE* 3.4 29.5 - - + -
116A LEU* 3.5 19.0 - - - +
304A LEU* 5.8 1.0 - - - +
305A VAL* 2.9 38.8 + - + +
306A SER 2.9 13.8 + - - +
307A SER* 3.7 16.2 - - - +
309A THR* 1.3 77.6 - - - +
311A HIS* 1.3 58.4 + - - +
314A SER* 3.0 28.6 + - - -
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Residues in contact with HIS 311 (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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65A ALA* 3.5 28.1 + - + -
69A LYS 3.7 21.6 + - - -
70A LYS* 4.3 14.5 - - + +
75A ILE* 3.3 31.6 - - + +
79A LEU* 3.7 27.6 - - + +
88A LEU* 3.9 13.4 - - + +
307A SER 3.0 17.0 + - - +
308A GLN 3.8 4.2 + - - +
310A GLN* 1.3 76.8 - - - +
312A LEU* 1.3 64.2 + - - +
314A SER* 3.2 14.3 + - - -
315A ALA* 3.2 16.0 + - + +
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Residues in contact with LEU 312 (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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59A LEU* 4.3 24.0 - - + -
65A ALA* 3.7 28.3 - - + +
66A ALA* 3.9 22.7 - - + +
280A PHE* 4.2 26.9 - - + -
308A GLN* 3.1 18.1 + - + +
309A THR* 3.6 7.0 - - - +
311A HIS* 1.3 76.9 + - - +
313A LEU* 1.3 69.5 + - + +
315A ALA* 3.1 6.6 + - - +
316A MET* 3.1 35.4 + - + +
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Residues in contact with LEU 313 (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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91A PHE* 3.5 20.0 - - + -
271A LEU* 3.5 29.4 - - + -
275A LEU* 5.2 4.0 - - + -
277A LEU* 3.9 27.1 - - + -
280A PHE* 4.5 5.4 - - + -
282A VAL* 3.7 21.8 - - + -
309A THR* 2.9 22.8 + - + +
312A LEU* 1.3 84.5 - - + +
314A SER* 1.3 56.9 + - - +
316A MET* 3.9 24.9 - - + -
317A LEU* 2.9 36.6 + - + +
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Residues in contact with SER 314 (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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88A LEU* 4.8 1.3 - - - -
90A ALA* 3.3 35.3 + - - +
91A PHE* 3.4 15.0 + - - -
94A ALA* 4.0 5.0 - - - +
310A GLN 3.0 19.8 + - - -
311A HIS* 3.3 15.2 - - - -
313A LEU* 1.3 80.1 - - - +
315A ALA* 1.3 55.0 - - - +
318A SER* 2.5 35.5 + - - -
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Residues in contact with ALA 315 (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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58A TRP* 4.0 15.7 - - + -
65A ALA* 3.8 23.3 - - + -
311A HIS* 3.2 7.7 + - + +
312A LEU 3.1 8.8 + - - +
314A SER* 1.3 78.4 - - - +
316A MET* 1.3 64.4 + - - +
318A SER* 3.1 14.3 + - - -
319A ASP* 3.4 8.8 + - - +
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Residues in contact with MET 316 (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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55A LEU* 3.7 35.9 - - + +
58A TRP* 3.2 43.3 - - + -
59A LEU* 3.5 27.4 - - + -
277A LEU* 5.8 1.8 - - - -
280A PHE* 6.4 0.4 - - - -
312A LEU* 3.1 20.5 + - + +
313A LEU* 4.0 26.2 - - + +
315A ALA* 1.3 76.6 - - - +
317A LEU* 1.3 62.8 + - + +
318A SER 3.1 4.3 + - - -
319A ASP* 3.2 14.2 + - - +
322A LEU* 3.7 23.0 - - + +
323A THR* 4.0 2.9 - - - +
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Residues in contact with LEU 317 (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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91A PHE* 4.2 10.3 - - + -
94A ALA* 3.9 33.0 - - + +
95A MET* 4.0 28.0 - - + -
98A PHE* 4.1 29.3 + - + +
271A LEU* 4.4 8.1 - - + -
275A LEU* 4.0 24.5 - - + -
313A LEU* 2.9 26.1 + - + +
316A MET* 1.3 79.1 - - + +
318A SER* 1.3 60.0 + - - +
319A ASP 3.5 0.4 - - - -
320A LYS* 4.6 11.1 + - - -
323A THR* 3.9 21.5 + - + +
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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