Contacts of the strand formed by residues 254 - 259 (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 LYS 254 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252B LYS* 2.6 25.3 + - + +
253B ALA* 1.3 76.0 - - - +
255B ALA* 1.3 66.5 + - - +
256B VAL* 4.6 4.0 - - + -
282B CYS* 4.0 2.5 - - - -
283B GLU* 3.3 40.6 - - + +
285B LYS* 4.1 16.8 - - + +
300B GLU* 2.6 51.7 + - - +
303B ASP* 3.8 26.1 + - - +
304B ALA* 3.5 11.6 - - + -
305B ARG* 2.9 26.3 + - - +
306B ALA* 3.4 4.3 + - - +
397B ILE* 4.2 1.6 - - - +
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Residues in contact with ALA 255 (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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254B LYS* 1.3 78.3 - - - +
256B VAL* 1.3 64.2 + - - +
277B LEU* 3.6 42.0 - - + -
282B CYS* 4.3 1.3 - - - -
283B GLU 2.9 9.3 + - - +
284B VAL* 3.4 6.6 - - + +
285B LYS* 3.0 24.3 + - - +
306B ALA* 3.4 20.2 - - + -
308B LEU* 4.7 2.7 - - + -
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Residues in contact with VAL 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B LYS* 4.6 3.1 - - + -
255B ALA* 1.3 75.7 - - - +
257B ILE* 1.3 68.0 + - - +
258B ALA* 4.5 2.9 - - + +
285B LYS* 3.5 11.0 - - + -
287B PHE* 4.0 21.1 - - + -
297B VAL* 4.3 8.1 - - + -
300B GLU* 3.7 41.5 - - + +
301B ILE* 4.0 24.9 - - + +
304B ALA* 4.2 5.6 - - + -
306B ALA 3.0 10.7 + - - +
307B VAL* 3.5 5.8 - - + +
308B LEU* 2.9 25.5 + - - +
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Residues in contact with ILE 257 (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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256B VAL* 1.3 76.9 - - - +
258B ALA* 1.3 56.4 + - - +
259B TYR* 4.5 4.9 - - + -
270B ALA* 3.9 30.7 - - + +
273B LEU* 4.5 5.6 - - + -
274B MET* 3.9 25.1 - - + +
277B LEU* 4.0 17.0 - - + -
284B VAL* 4.0 10.3 - - + -
285B LYS 3.0 10.0 + - - +
286B LEU* 3.5 8.8 - - + +
287B PHE* 2.8 32.6 + - - +
308B LEU* 3.3 22.2 - - + +
342B PHE* 4.0 27.6 - - + -
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Residues in contact with ALA 258 (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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256B VAL* 4.1 4.4 + - + -
257B ILE* 1.3 73.5 - - - +
259B TYR* 1.3 63.4 + - - +
287B PHE* 3.4 7.6 - - + +
289B LEU* 3.9 24.5 - - + -
297B VAL* 4.6 13.9 - - + -
301B ILE* 6.3 0.4 - - + -
307B VAL* 6.3 0.7 - - + -
308B LEU 2.9 8.1 + - - +
309B VAL* 3.2 9.3 - - + +
310B GLY 3.0 20.4 + - - -
325B LEU* 4.3 19.5 - - + -
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Residues in contact with TYR 259 (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* 4.5 3.8 - - + -
258B ALA* 1.3 80.0 - - - +
260B ASP* 1.3 83.0 + - - +
261B THR* 3.7 15.5 - - + -
266B THR* 4.4 5.6 - - + -
267B GLU* 3.2 53.1 + - + +
270B ALA* 4.2 13.2 - - + -
286B LEU* 3.4 31.9 - - + +
287B PHE 3.1 18.1 + - - -
288B LYS* 3.5 25.9 - - + +
289B LEU* 2.9 35.1 + - - +
309B VAL* 5.4 0.2 - - - -
310B GLY 3.3 22.4 - - - +
322B VAL* 4.7 0.2 - - - -
342B PHE* 3.9 10.5 - - + -
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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