Contacts of the strand formed by residues 283 - 288 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252C LYS* 4.9 8.5 - - - +
253C ALA 3.1 13.7 + - - +
254C LYS* 3.3 32.8 - - + +
255C ALA 2.8 26.9 + - - -
281C GLY 4.3 0.2 + - - -
282C CYS* 1.3 75.6 - - - +
284C VAL* 1.3 70.7 + - - +
285C LYS* 4.2 18.6 + - - -
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Residues in contact with VAL 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255C ALA* 3.4 10.5 - - + +
257C ILE* 4.1 17.3 - - + -
274C MET* 3.8 32.8 - - + +
277C LEU* 3.6 31.6 - - + -
278C VAL* 3.9 14.7 - - + +
282C CYS* 3.7 9.8 + - + +
283C GLU* 1.3 86.7 - - - +
285C LYS* 1.3 78.8 + - - +
286C LEU* 4.3 1.2 + - + -
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Residues in contact with LYS 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254C LYS* 4.7 9.9 - - + +
255C ALA 3.0 7.2 + - - +
256C VAL* 3.5 13.6 - - + -
257C ILE 3.0 26.0 + - - +
283C GLU* 4.2 20.5 + - - -
284C VAL* 1.3 78.8 + - - +
286C LEU* 1.3 60.0 + - - +
287C PHE* 3.7 22.7 - - + -
300C GLU* 3.9 37.9 - - + +
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Residues in contact with LEU 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257C ILE* 3.6 14.8 - - + +
259C TYR* 3.1 40.2 - - + +
267C GLU 6.1 0.4 - - - +
270C ALA* 4.7 16.2 - - + +
271C HIS* 5.0 4.7 - - - +
274C MET* 3.8 39.7 - - + -
284C VAL* 4.1 2.1 - - + -
285C LYS* 1.3 72.3 - - - +
287C PHE* 1.3 70.3 + - - +
288C LYS* 4.3 2.3 + - + +
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Residues in contact with PHE 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256C VAL* 4.1 22.2 - - + -
257C ILE 2.9 12.8 + - - +
258C ALA* 3.4 5.1 - - - -
259C TYR* 3.1 30.0 + - - -
285C LYS* 3.7 29.6 - - + -
286C LEU* 1.3 79.8 - - - +
288C LYS* 1.3 61.5 + - - +
289C LEU* 3.2 3.3 + - + -
292C SER* 3.7 21.1 - - - +
293C ASP 6.1 0.2 - - - -
296C ASP* 4.5 7.4 - - + -
297C VAL* 3.6 37.9 - - + -
300C GLU* 3.8 27.6 - - + -
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Residues in contact with LYS 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259C TYR* 3.5 31.9 - - + +
260C ASP* 3.5 30.2 + - - +
261C THR* 4.7 9.7 + - - -
264C LEU* 6.3 1.0 - - - +
267C GLU* 4.4 8.4 + - - +
286C LEU* 4.3 2.5 + - + +
287C PHE* 1.3 71.1 - - - +
289C LEU* 1.3 62.9 + - - +
290C SER* 3.6 14.8 + - - +
291C VAL* 3.1 31.9 + - + +
292C SER* 2.9 18.0 + - - -
26D GLY* 5.2 6.7 - - - -
27D PRO* 5.2 1.8 - - - +
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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