Contacts of the strand formed by residues 338 - 345 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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305D ARG* 2.9 15.7 + - + +
306D ALA* 3.1 13.0 - - + -
307D VAL* 2.9 23.7 + - - +
336D ASN* 6.0 1.8 - - - +
337D LYS* 1.3 76.6 - - - +
339D GLY* 1.3 63.9 + - - +
364D ILE* 3.8 3.7 - - - +
365D GLU* 3.5 9.4 - - + +
367D ILE* 3.6 30.1 - - + -
393D ILE* 4.5 9.9 - - + -
396D ARG* 4.0 38.8 - - + +
397D ILE* 5.2 4.9 - - + -
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Residues in contact with GLY 339 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306D ALA* 5.5 0.4 - - - -
307D VAL 3.3 13.7 - - - -
308D LEU* 5.3 0.9 - - - -
338D VAL* 1.3 79.3 - - - +
340D LEU* 1.3 63.4 + - - +
359D LEU* 5.4 0.4 - - - -
364D ILE* 3.7 12.6 - - - +
365D GLU 2.8 13.5 + - - -
366D LEU* 3.5 7.1 - - - -
367D ILE* 2.8 34.6 + - - +
393D ILE* 5.3 2.0 - - - -
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Residues in contact with LEU 340 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273D LEU* 3.7 24.0 - - + -
307D VAL 3.4 6.4 + - - +
308D LEU* 3.3 32.4 - - + +
309D VAL 3.0 24.3 + - - -
339D GLY* 1.3 74.2 - - - +
341D ALA* 1.3 68.0 + - - +
342D PHE* 4.6 2.1 - - + -
359D LEU* 3.9 7.8 - - - +
366D LEU* 4.2 6.7 - - - +
367D ILE* 3.7 19.3 - - + -
368D ALA* 4.1 24.0 - - + +
372D PRO* 3.8 29.4 - - + -
389D LEU* 4.4 6.7 - - + -
393D ILE* 4.2 9.0 - - + -
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Residues in contact with ALA 341 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309D VAL 3.3 6.5 - - - +
340D LEU* 1.3 75.3 - - - +
342D PHE* 1.3 64.4 + - - +
352D GLN* 2.7 24.4 + - - +
355D LEU* 3.7 30.3 - - + -
356D GLU* 3.8 20.9 + - + -
359D LEU* 4.2 9.1 - - + +
366D LEU* 4.7 2.6 - - - +
368D ALA 5.8 0.2 + - - -
371D GLY* 3.6 2.1 - - - -
372D PRO* 3.5 13.7 - - - +
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Residues in contact with PHE 342 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257D ILE* 3.9 18.6 - - + -
259D TYR* 4.1 3.4 - - + -
266D THR* 3.5 35.4 - - + -
269D MET* 4.1 14.6 - - + -
270D ALA* 3.8 24.5 - - + -
273D LEU* 3.4 23.1 - - + -
308D LEU* 4.1 7.6 - - + -
309D VAL 3.2 12.3 + - - -
310D GLY* 3.2 22.9 - - - -
311D SER 3.1 21.8 + - - +
340D LEU* 4.6 4.0 - - + -
341D ALA* 1.3 78.3 - - - +
343D GLY* 1.3 61.1 + - - +
352D GLN* 3.4 10.9 + - - +
355D LEU* 3.7 3.6 - - - +
372D PRO* 3.3 27.8 - - + +
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Residues in contact with GLY 343 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266D THR* 4.0 10.8 - - - -
269D MET* 3.6 9.2 - - - +
311D SER 3.2 16.2 - - - -
342D PHE* 1.3 81.2 - - - +
344D ALA* 1.3 63.2 + - - -
345D TYR* 4.8 0.2 - - - -
352D GLN* 3.7 3.5 + - - +
372D PRO 3.3 4.0 + - - -
373D THR* 3.3 10.9 + - - -
374D VAL 3.3 17.7 + - - -
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Residues in contact with ALA 344 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265D SER* 3.9 22.7 - - - -
266D THR* 3.4 9.3 + - - +
269D MET* 3.9 7.9 - - + -
311D SER 4.2 0.2 - - - +
312D PRO* 3.2 20.8 - - - +
313D THR* 3.3 7.1 + - - +
343D GLY* 1.3 75.0 - - - -
345D TYR* 1.3 65.3 + - - +
374D VAL* 3.2 15.0 - - + +
376D TRP 4.4 3.1 - - - +
731D FMN 3.7 25.4 - - - +
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Residues in contact with TYR 345 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313D THR* 3.4 19.3 - - + -
344D ALA* 1.3 78.9 - - - +
346D GLY* 1.3 60.8 + - - +
347D TRP 3.5 31.2 - - - -
348D GLY 4.9 1.6 - - - -
349D GLY* 3.8 11.4 - - - -
373D THR* 3.1 32.8 - - + +
374D VAL 3.1 18.5 + - - -
375D GLN* 3.4 36.5 + - + +
376D TRP 2.8 24.3 + - - -
731D FMN 3.1 22.0 + - - +
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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