Contacts of the strand formed by residues 283 - 288 (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 GLU 283 (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* 5.9 2.3 - - - +
253D ALA 3.1 14.5 + - - +
254D LYS* 3.3 26.6 - - + +
255D ALA 2.9 25.3 + - - -
281D GLY 4.3 0.2 + - - -
282D CYS* 1.3 74.4 - - - +
284D VAL* 1.3 70.6 + - - +
285D LYS* 3.9 23.3 + - - -
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Residues in contact with VAL 284 (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* 3.4 5.2 - - + +
257D ILE* 3.1 31.6 - - + -
274D MET* 3.7 29.9 - - + +
277D LEU* 3.6 34.5 - - + -
278D VAL* 3.8 20.0 - - + +
282D CYS 3.7 2.2 + - - +
283D GLU* 1.3 85.1 - - - +
285D LYS* 1.3 75.1 + - - +
286D LEU 4.3 0.7 + - - +
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Residues in contact with LYS 285 (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* 4.7 12.3 - - + +
255D ALA 3.0 9.9 + - - +
256D VAL* 3.5 8.8 - - + +
257D ILE 2.9 25.8 + - - +
283D GLU* 3.9 21.5 + - - +
284D VAL* 1.3 81.0 - - - +
286D LEU* 1.3 60.3 + - - +
287D PHE* 4.0 22.2 - - + -
300D GLU* 3.1 48.4 + - + +
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Residues in contact with LEU 286 (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* 3.5 15.7 - - + +
259D TYR* 3.1 40.6 - - + +
267D GLU* 6.4 1.1 - - + -
270D ALA* 4.8 14.8 - - + +
271D HIS* 5.0 4.3 - - + +
274D MET* 3.7 38.4 - - + -
284D VAL* 4.1 2.8 + - + -
285D LYS* 1.3 73.9 - - - +
287D PHE* 1.3 69.6 + - - +
288D LYS* 4.3 1.7 + - + +
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Residues in contact with PHE 287 (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* 3.9 30.5 - - + -
257D ILE 2.8 13.0 + - - +
258D ALA* 3.4 6.0 - - + -
259D TYR* 3.1 26.9 + - - -
285D LYS* 4.0 21.8 - - + -
286D LEU* 1.3 83.6 - - - +
288D LYS* 1.3 61.2 + - - +
289D LEU* 3.3 2.2 + - + +
292D SER* 3.7 20.9 - - - +
296D ASP* 4.3 8.1 - - + -
297D VAL* 3.6 41.1 - - + -
300D GLU* 3.8 24.5 - - + -
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Residues in contact with LYS 288 (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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26C GLY* 5.6 6.1 - - - -
27C PRO* 5.4 1.6 - - - +
259D TYR* 3.5 27.2 - - + +
260D ASP* 3.3 28.7 + - - +
261D THR* 4.9 7.1 + - - -
264D LEU* 6.3 1.3 - - - -
267D GLU* 4.2 16.2 - - - +
286D LEU* 4.3 2.7 + - + +
287D PHE* 1.3 70.3 - - - +
289D LEU* 1.3 61.5 + - - +
290D SER* 3.9 14.0 + - - +
291D VAL* 3.2 31.8 + - + +
292D SER* 2.8 19.4 + - - -
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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