Contacts of the strand formed by residues 306 - 310 (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 ALA 306 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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254D LYS 3.4 2.4 + - - -
255D ALA* 3.4 10.8 - - + -
256D VAL 3.1 23.4 + - - -
304D ALA* 3.7 2.9 - - - +
305D ARG* 1.3 81.0 - - - +
307D VAL* 1.3 69.3 + - - +
308D LEU* 4.2 5.4 - - + -
338D VAL* 3.1 9.2 - - + +
339D GLY* 5.5 0.2 - - - -
393D ILE* 3.7 17.9 - - + -
397D ILE* 3.1 28.3 - - + -
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Residues in contact with VAL 307 (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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256D VAL* 3.5 8.1 - - + +
258D ALA* 6.3 1.3 - - + -
301D ILE* 4.0 45.8 - - + -
304D ALA* 4.9 2.7 - - + -
306D ALA* 1.3 82.8 - - - +
308D LEU* 1.3 62.2 + - - +
309D VAL* 4.0 13.4 + - + -
325D LEU* 5.7 0.9 - - + -
329D LEU* 4.2 17.9 - - + -
334D PRO* 6.1 0.2 - - + -
337D LYS* 4.3 18.4 - - + -
338D VAL 2.9 10.4 + - - +
339D GLY* 3.3 19.3 - - - -
340D LEU 3.4 3.6 + - - +
359D LEU* 4.7 4.7 - - + +
364D ILE* 4.5 12.9 - - + +
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Residues in contact with LEU 308 (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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255D ALA* 4.3 3.4 - - + -
256D VAL 2.9 14.8 + - - +
257D ILE* 3.3 30.2 - - + +
258D ALA* 2.9 25.1 + - - +
273D LEU* 4.0 14.8 - - + -
277D LEU* 4.2 16.2 - - + -
306D ALA* 4.2 13.0 - - + -
307D VAL* 1.3 83.2 - - - +
309D VAL* 1.3 61.7 + - - +
339D GLY* 5.8 0.4 - - - -
340D LEU* 3.3 50.0 - - + +
342D PHE* 4.1 5.8 - - + -
393D ILE* 3.5 16.6 - - + -
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Residues in contact with VAL 309 (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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258D ALA* 3.1 11.2 - - + +
289D LEU* 5.3 0.2 - - + -
307D VAL* 4.3 10.3 - - + -
308D LEU* 1.3 78.2 - - - +
310D GLY* 1.3 62.8 + - - +
322D VAL* 3.8 28.5 - - + -
325D LEU* 4.1 24.7 - - + -
326D LEU* 4.1 8.7 - - + -
329D LEU* 5.1 0.4 - - + -
340D LEU 3.0 7.7 + - - -
341D ALA* 3.3 6.9 - - - -
342D PHE* 3.2 20.9 + - - -
355D LEU* 3.8 16.0 - - + +
359D LEU* 4.2 29.8 - - + -
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Residues in contact with GLY 310 (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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258D ALA 3.0 10.9 + - - -
259D TYR* 3.2 24.7 - - - +
260D ASP 3.5 2.1 + - - -
266D THR* 3.9 1.6 - - - -
309D VAL* 1.3 75.1 - - - +
311D SER* 1.3 67.0 + - - -
322D VAL* 4.0 6.1 - - - +
342D PHE* 3.2 32.6 - - - -
355D LEU* 4.3 2.0 - - - -
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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