Contacts of the strand formed by residues 338 - 345 (chain B) in PDB entry 1YCH
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 VAL 338 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305B ARG 2.9 14.2 + - - +
306B ALA* 3.2 4.8 - - - -
307B VAL 3.0 22.5 + - - -
336B ASN* 5.8 2.0 - - - +
337B LYS* 1.3 80.2 - - - +
339B GLY* 1.3 62.8 + - - +
364B ILE* 3.6 4.1 - - - +
365B GLU* 3.5 13.5 - - - +
367B ILE* 3.2 36.3 - - + -
393B ILE* 4.7 12.1 - - + -
396B ARG* 3.9 30.3 - - + +
397B ILE* 4.2 15.0 - - + -
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Residues in contact with GLY 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B ALA* 5.5 0.2 - - - -
307B VAL 3.3 13.7 - - - -
308B LEU* 4.9 3.4 - - - -
338B VAL* 1.3 78.7 - - - +
340B LEU* 1.3 63.6 + - - +
359B LEU* 5.3 0.7 - - - -
364B ILE* 3.6 11.6 - - - +
365B GLU 2.9 11.1 + - - -
366B LEU* 3.6 6.9 - - - -
367B ILE* 2.9 29.0 + - - +
393B ILE* 5.5 1.1 - - - -
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Residues in contact with LEU 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273B LEU* 3.6 34.1 - - + -
307B VAL 3.4 5.9 + - - -
308B LEU* 3.3 15.9 - - + +
309B VAL 3.0 24.3 + - - -
339B GLY* 1.3 73.2 - - - +
341B ALA* 1.3 66.0 + - - +
342B PHE* 4.6 2.4 - - + -
359B LEU* 3.8 10.8 - - - +
366B LEU* 5.1 5.4 - - - +
367B ILE* 3.6 25.1 - - + +
368B ALA* 3.9 17.3 - - + +
371B GLY* 4.6 0.2 - - - -
372B PRO* 3.7 23.3 - - + -
389B LEU* 3.8 15.7 - - + -
393B ILE* 4.2 13.0 - - + -
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Residues in contact with ALA 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309B VAL 3.2 7.2 - - - +
340B LEU* 1.3 77.2 - - - +
342B PHE* 1.3 61.5 + - - +
352B GLN* 3.0 29.1 + - - +
355B LEU* 3.6 28.7 - - + -
356B GLU* 4.1 14.3 - - + +
359B LEU* 4.2 9.4 - - + +
366B LEU* 5.3 1.6 - - - +
368B ALA 5.9 0.2 + - - -
371B GLY* 3.5 2.7 - - - -
372B PRO* 3.3 19.9 - - - +
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Residues in contact with PHE 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257B ILE* 4.0 13.2 - - + -
259B TYR* 3.9 8.7 - - + -
266B THR* 3.4 39.3 - - + -
269B MET* 4.1 8.5 - - + -
270B ALA* 3.9 24.0 - - + -
273B LEU* 3.5 23.8 - - + -
308B LEU* 4.2 8.3 - - + -
309B VAL 3.3 16.7 + - - -
310B GLY* 3.1 23.2 - - - -
311B SER 3.0 23.7 + - - +
340B LEU* 4.7 2.7 - - + -
341B ALA* 1.3 79.8 - - - +
343B GLY* 1.3 60.8 + - - +
352B GLN* 3.6 8.5 - - - +
355B LEU* 3.7 4.7 - - - +
372B PRO* 3.3 28.9 - - + +
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Residues in contact with GLY 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266B THR* 4.0 13.7 - - - -
269B MET* 3.6 9.8 - - - +
311B SER 3.3 13.2 - - - -
342B PHE* 1.3 81.2 - - - +
344B ALA* 1.3 61.6 + - - -
352B GLN* 4.0 2.1 + - - +
372B PRO 3.3 4.4 + - - -
373B THR* 3.3 13.8 + - - -
374B VAL 3.2 17.7 + - - -
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Residues in contact with ALA 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265B SER* 3.9 13.0 - - - -
266B THR* 3.4 8.7 + - - +
269B MET* 3.7 14.6 - - + +
311B SER 4.1 0.2 - - - +
312B PRO* 3.2 20.4 - - - +
313B THR* 3.5 6.6 + - - +
343B GLY* 1.3 76.6 - - - -
345B TYR* 1.3 67.2 + - - +
373B THR* 5.1 0.2 + - - -
374B VAL* 3.1 16.8 - - + +
376B TRP 4.2 0.9 - - - +
711B FMN 3.6 28.5 - - - +
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Residues in contact with TYR 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313B THR* 3.9 5.8 - - + -
344B ALA* 1.3 77.5 - - - +
346B GLY* 1.3 61.1 + - - +
347B TRP 3.6 29.2 - - - -
348B GLY 5.0 1.1 - - - -
349B GLY* 3.8 20.0 - - - -
373B THR* 3.3 38.3 - - + +
374B VAL 3.1 15.9 + - - -
375B GLN* 3.4 39.9 + - + +
376B TRP 2.9 23.4 + - - -
711B FMN 3.1 25.9 + - - +
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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
------------------------------------------------------------
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