Contacts of the strand formed by residues 329 - 338 (chain A) in PDB entry 1YTS
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 ALA 329 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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320A GLN* 3.2 3.8 - - - +
321A VAL* 2.8 36.1 + - + +
323A LEU* 4.4 10.2 - - + +
328A MET* 1.3 73.5 - - - +
330A ASP* 1.3 61.7 + - - +
331A MET* 3.7 22.6 + - + +
349A VAL* 4.0 13.7 - - + -
350A HIS 3.3 6.5 - - - +
351A VAL* 4.5 2.2 - - + +
371A LEU* 3.9 16.8 - - + -
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Residues in contact with ASP 330 (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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303A ARG* 5.3 4.2 + - - -
317A MET* 3.5 22.2 - - + -
319A GLN 3.7 4.3 - - - -
320A GLN* 3.1 32.6 + - - +
328A MET* 4.5 5.8 - - - +
329A ALA* 1.3 74.8 - - - +
331A MET* 1.4 59.5 + - - +
332A TYR* 3.5 24.9 + - + +
349A VAL 3.7 0.3 - - - -
350A HIS* 2.8 42.9 + - + +
352A GLY* 5.2 6.4 - - - -
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Residues in contact with MET 331 (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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317A MET* 3.4 8.1 - - - +
318A THR* 2.7 44.7 + - - +
319A GLN* 2.9 38.3 + - - +
321A VAL* 3.6 26.9 - - + -
329A ALA* 3.7 16.8 - - + +
330A ASP* 1.4 68.6 - - - +
332A TYR* 1.3 60.9 + - - +
348A VAL 3.4 10.3 - - - +
349A VAL* 4.1 14.8 - - + -
371A LEU* 3.6 29.4 - - + -
375A THR* 5.1 7.2 - - - -
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Residues in contact with TYR 332 (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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302A PHE* 3.8 17.5 - + - +
303A ARG* 3.6 37.7 + - + -
315A SER* 3.8 17.9 - - - +
316A LYS 2.9 14.4 - - - +
317A MET* 3.9 28.2 - - + +
318A THR* 4.4 2.3 + - - +
330A ASP* 3.5 41.9 + - + +
331A MET* 1.3 73.4 - - - +
333A THR* 1.3 65.5 + - - +
334A LEU* 5.2 0.2 - - + -
347A PRO* 3.8 3.5 - - - +
348A VAL* 3.1 50.0 + - + +
350A HIS* 4.2 11.2 + - + -
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Residues in contact with THR 333 (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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314A GLU 3.6 1.0 - - - +
315A SER* 3.3 4.9 + - - -
316A LYS* 2.8 44.6 + - + +
318A THR* 3.6 19.2 - - - +
332A TYR* 1.3 76.3 + - - +
334A LEU* 1.3 64.9 + - - +
335A THR* 4.1 8.2 + - - +
345A SER* 3.2 26.9 - - - +
346A VAL 3.3 11.4 - - - +
347A PRO* 4.9 3.7 - - + +
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Residues in contact with LEU 334 (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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271A PHE* 4.1 25.8 - - + -
274A LEU* 4.7 6.5 - - + -
282A LEU* 4.7 11.4 - - + -
301A TYR* 4.7 0.7 - - + -
302A PHE* 3.5 45.5 - - + +
313A VAL* 4.1 8.7 - - + -
314A GLU 3.3 4.0 - - - +
315A SER* 3.8 17.0 - - - +
332A TYR* 4.2 0.4 - - + -
333A THR* 1.3 73.7 - - - +
335A THR* 1.3 61.9 + - - +
336A ILE* 4.0 10.5 + - + +
344A ILE 3.8 0.2 - - - +
345A SER* 3.1 2.6 - - - -
346A VAL* 2.7 45.9 + - + +
348A VAL* 3.8 17.5 - - + +
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Residues in contact with THR 335 (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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312A THR 3.8 0.5 - - - +
313A VAL* 3.2 6.8 - - - +
314A GLU* 2.9 50.7 + - - +
316A LYS* 6.2 0.3 - - - +
333A THR* 4.4 7.8 + - - +
334A LEU* 1.3 75.6 + - - +
336A ILE* 1.4 58.0 + - - +
337A ARG* 4.2 21.7 - - - +
343A THR* 3.8 25.1 - - + -
344A ILE 3.4 4.7 - - - +
345A SER* 4.1 13.2 + - - +
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Residues in contact with ILE 336 (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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271A PHE* 4.2 24.0 - - + +
274A LEU* 4.0 22.0 - - + -
275A ALA* 4.4 21.3 - - + -
311A ILE* 3.7 27.6 - - + -
312A THR 3.7 2.7 - - - -
313A VAL* 4.6 2.7 - - + -
334A LEU* 4.3 11.4 - - + +
335A THR* 1.4 74.7 - - - +
337A ARG* 1.3 63.5 + - - +
338A GLU* 6.0 0.4 - - + -
342A LYS 4.6 1.0 - - - +
343A THR* 3.5 5.7 - - - +
344A ILE* 2.7 35.9 + - + +
346A VAL* 3.7 30.3 - - + -
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Residues in contact with ARG 337 (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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311A ILE* 3.3 3.8 - - - +
312A THR* 2.8 51.7 + - + +
314A GLU* 3.0 33.3 + - - +
335A THR* 4.3 19.3 - - - +
336A ILE* 1.3 83.2 - - - +
338A GLU* 1.3 62.2 + - - +
343A THR* 4.2 27.4 + - + +
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Residues in contact with GLU 338 (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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272A ARG* 3.1 39.8 + - - -
310A SER* 3.1 29.5 + - - +
311A ILE* 3.9 12.1 - - + +
336A ILE* 6.0 1.1 - - + -
337A ARG* 1.3 76.6 - - - +
339A ALA* 1.3 73.3 + - + +
340A GLY 3.3 0.9 + - - -
341A GLN* 3.2 49.4 + - + +
342A LYS 6.0 0.2 + - - -
343A THR* 5.8 0.2 - - - +
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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