Contacts of the strand formed by residues 274 - 280 (chain I) in PDB entry 1YC0
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 ILE 274 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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268I TYR* 3.6 9.6 - - - -
269I ASP* 2.9 27.3 + - - +
272I GLU* 3.2 34.7 - - + +
273I GLN* 1.3 85.0 - - - +
275I CYS* 1.3 64.2 + - - +
276I LYS* 3.9 22.9 - - + -
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Residues in contact with CYS 275 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266I TRP* 4.1 11.8 - - + -
267I TYR 3.2 3.8 - - - +
268I TYR* 3.9 13.0 - - - -
274I ILE* 1.3 81.0 - - - +
276I LYS* 1.3 63.4 + - - +
293I GLU* 4.3 22.4 + - + +
296I CYS* 2.0 64.4 - - + -
297I ILE* 3.5 12.8 - - + +
300I CYS 4.9 0.7 - - - -
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Residues in contact with LYS 276 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266I TRP* 3.3 10.5 - - - -
267I TYR* 2.7 60.7 + - + +
269I ASP* 3.6 28.7 + - + -
272I GLU* 3.0 36.3 + - - +
274I ILE* 3.9 15.9 - - + +
275I CYS* 1.3 78.6 - - - +
277I SER* 1.3 62.8 + - - +
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Residues in contact with SER 277 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264I PRO* 5.1 6.6 - - - +
265I ARG 3.4 12.7 + - - -
266I TRP* 3.6 24.6 + - - -
267I TYR* 3.8 6.5 - - - -
276I LYS* 1.3 78.2 - - - +
278I PHE* 1.3 68.2 + - - +
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Residues in contact with PHE 278 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254I ASN* 4.1 17.7 - - + +
255I LYS 3.7 29.8 - - - -
256I VAL* 4.5 5.6 - - + -
264I PRO* 3.6 2.5 - - - +
265I ARG* 2.9 57.1 + - + +
266I TRP 3.6 17.3 - - - -
267I TYR* 3.6 29.8 - + + -
277I SER* 1.3 78.3 + - - +
279I VAL* 1.3 72.5 + - - +
280I TYR* 3.5 11.3 + - + -
288I ASN 4.3 7.2 - - - -
289I ASN* 3.7 24.5 - - + -
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Residues in contact with VAL 279 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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542A HIS* 3.9 27.3 - - + +
548A SER* 3.3 29.2 - - - +
549A GLY 5.1 0.2 - - - +
550A TYR* 6.6 0.2 - - + -
595A GLN* 4.4 3.3 - - + +
256I VAL* 3.5 28.1 - - - +
261I GLY 4.3 3.1 - - - +
262I SER* 3.3 38.8 - - - +
263I PHE 4.0 4.7 - - - +
264I PRO* 4.6 7.0 - - + -
278I PHE* 1.3 75.4 - - - +
280I TYR* 1.3 64.3 + - - +
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Residues in contact with TYR 280 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255I LYS 3.5 14.6 - - - -
256I VAL* 3.6 3.6 - - - -
261I GLY 3.3 4.4 - - - +
263I PHE* 2.8 44.8 + - + +
265I ARG* 3.6 34.3 - - + -
278I PHE* 3.5 10.1 + - + -
279I VAL* 1.3 73.8 - - - +
281I GLY* 1.3 66.3 + - - +
282I GLY* 3.3 23.0 + - - -
283I CYS* 2.9 35.9 - - - -
285I GLY* 3.0 31.0 + - - -
289I ASN* 3.4 14.4 - - - +
304I PO4 2.8 37.7 + - - -
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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