Contacts of the strand formed by residues 254 - 259 (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 LYS 254 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252D LYS* 2.6 22.3 + - + +
253D ALA* 1.3 74.1 - - - +
255D ALA* 1.3 67.2 + - - +
256D VAL* 4.6 7.0 - - + -
282D CYS* 4.9 1.1 - - - -
283D GLU* 3.3 40.2 - - + +
285D LYS* 4.7 5.8 - - + +
300D GLU* 2.5 46.9 + - - +
303D ASP* 3.4 26.9 + - - +
304D ALA* 3.4 23.5 - - + +
305D ARG* 3.0 25.8 + - - -
306D ALA 3.4 3.3 + - - -
397D ILE* 4.0 5.9 - - - +
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Residues in contact with ALA 255 (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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254D LYS* 1.3 78.8 - - - +
256D VAL* 1.3 64.5 + - - +
257D ILE* 4.1 1.1 - - + -
277D LEU* 4.2 32.5 - - + -
282D CYS* 5.3 1.1 - - + -
283D GLU 2.9 9.8 + - - +
284D VAL* 3.4 7.2 - - + +
285D LYS* 3.0 23.6 + - - +
304D ALA* 4.2 0.2 - - - -
306D ALA* 3.4 24.7 - - + -
308D LEU* 4.3 4.5 - - + -
397D ILE* 4.3 1.6 - - + -
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Residues in contact with VAL 256 (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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254D LYS* 4.6 2.0 - - + -
255D ALA* 1.3 77.2 - - - +
257D ILE* 1.3 67.4 + - - +
258D ALA* 4.5 3.1 - - + +
285D LYS* 3.5 9.6 - - + -
287D PHE* 3.9 25.8 - - + -
297D VAL* 4.5 6.5 - - + -
300D GLU* 3.8 41.1 - - + +
301D ILE* 4.0 21.3 - - + +
304D ALA* 4.0 7.2 - - + -
306D ALA 3.1 8.6 + - - +
307D VAL* 3.5 6.4 - - + +
308D LEU* 2.9 26.5 + - - +
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Residues in contact with ILE 257 (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 4.2 3.6 - - - +
256D VAL* 1.3 75.1 - - - +
258D ALA* 1.3 61.7 + - - +
259D TYR* 4.6 3.8 - - + -
270D ALA* 4.2 21.8 - - + +
273D LEU* 5.3 3.1 - - + -
274D MET* 4.6 6.7 - - + -
277D LEU* 4.0 19.3 - - + -
284D VAL* 3.1 36.1 - - + -
285D LYS 2.9 9.6 + - - +
286D LEU* 4.3 8.9 - - + +
287D PHE* 2.8 28.6 + - - +
308D LEU* 3.3 25.6 - - + +
342D PHE* 3.9 29.6 - - + -
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Residues in contact with ALA 258 (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* 4.0 4.6 + - + -
257D ILE* 1.3 72.7 - - - +
259D TYR* 1.3 61.4 + - - +
287D PHE* 3.4 7.9 - - + +
289D LEU* 4.0 24.0 - - + -
297D VAL* 4.5 12.8 - - + -
301D ILE* 6.4 0.4 - - + -
307D VAL* 6.3 1.3 - - + -
308D LEU 2.9 7.9 + - - +
309D VAL* 3.1 9.2 - - + +
310D GLY 3.0 20.4 + - - -
325D LEU* 4.1 21.3 - - + -
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Residues in contact with TYR 259 (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* 4.6 3.1 - - + -
258D ALA* 1.3 78.1 - - - +
260D ASP* 1.3 92.0 + - - +
261D THR* 4.3 3.1 - - + -
266D THR* 4.4 3.1 - - + -
267D GLU* 2.8 59.6 + - + +
270D ALA* 4.0 16.6 - - + -
286D LEU* 3.1 34.3 - - + +
287D PHE 3.1 16.4 + - - -
288D LYS* 3.5 20.9 - - + +
289D LEU* 2.9 37.0 + - - +
310D GLY* 3.2 26.5 - - - +
322D VAL* 4.7 0.2 - - - -
342D PHE* 4.1 7.2 - - + -
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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