Contacts of the strand formed by residues 263 - 269 (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 PHE 263 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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427A ILE* 5.0 8.3 - - + -
430A SER* 3.1 27.1 - - - +
432A CYS* 4.3 15.3 - - - -
447A HIS* 4.4 1.6 - + - -
448A CYS* 3.3 38.8 - - + -
451A HIS* 3.8 21.8 - + + -
261I GLY* 4.1 4.5 - - - -
262I SER* 1.3 80.6 - - - +
264I PRO* 1.3 68.9 - - - +
265I ARG* 3.2 22.6 + - - +
279I VAL* 4.0 1.9 - - - +
280I TYR* 2.8 51.7 + - + +
282I GLY* 3.7 23.3 - - - -
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Residues in contact with PRO 264 (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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429A ASP* 3.2 40.2 - - + +
430A SER* 3.7 5.5 + - - +
550A TYR* 4.7 2.9 - - - +
262I SER* 3.4 12.8 - - - +
263I PHE* 1.3 80.2 - - - +
265I ARG* 1.3 70.9 + - - +
266I TRP* 5.4 2.0 - - - -
277I SER* 5.1 7.6 - - - +
278I PHE 3.6 7.9 - - - +
279I VAL* 4.6 6.7 - - + -
291I LEU 4.6 5.4 - - - +
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Residues in contact with ARG 265 (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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451A HIS* 3.9 20.4 + - - -
263I PHE* 3.4 33.4 - - - +
264I PRO* 1.3 81.1 + - - +
266I TRP* 1.3 69.6 + - - +
277I SER* 3.4 9.0 + - - -
278I PHE* 2.9 45.3 + - + -
280I TYR* 3.6 19.7 - - + -
289I ASN* 2.7 42.8 + - - +
290I TYR 3.3 11.4 - - - +
291I LEU* 3.3 33.6 - - - +
304I PO4 2.7 28.9 + - - -
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Residues in contact with TRP 266 (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* 5.4 1.6 + - - +
265I ARG* 1.3 83.3 + - - +
267I TYR* 1.3 60.5 + - - +
275I CYS 4.1 6.5 - - - -
276I LYS* 3.3 26.5 - - - -
277I SER* 3.6 24.4 + - - -
278I PHE* 3.6 2.7 - - - -
289I ASN* 3.3 7.6 - - - -
290I TYR* 2.7 43.6 + - + +
291I LEU 3.7 10.4 + - - -
292I ARG* 3.6 6.3 - - - +
293I GLU* 3.4 64.9 - - + +
296I CYS* 4.1 17.7 - - + -
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Residues in contact with TYR 267 (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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252I ALA 5.4 0.4 - - - -
253I SER* 5.8 0.4 - - - -
254I ASN* 3.6 40.2 + - + -
266I TRP* 1.3 73.3 - - - +
268I TYR* 1.3 69.0 + - - +
269I ASP* 3.8 20.7 + - + +
275I CYS* 3.2 1.7 - - - -
276I LYS* 2.7 89.9 + - + +
277I SER 3.8 11.0 - - - -
278I PHE* 3.6 23.6 - + + -
288I ASN* 3.2 27.8 - - - +
290I TYR* 4.6 0.2 - - - -
296I CYS* 3.6 7.9 - - - -
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Residues in contact with TYR 268 (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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250I CYS* 3.1 23.2 - - + +
252I ALA 4.7 0.5 - - - +
267I TYR* 1.3 79.2 - - - +
269I ASP* 1.3 58.9 + - - +
270I PRO* 3.2 28.2 - - + +
273I GLN* 3.4 43.0 - - - +
274I ILE* 3.6 16.4 - - - -
275I CYS* 3.9 7.0 - - - -
288I ASN* 2.8 26.8 + - - +
296I CYS* 3.7 6.6 - - - -
300I CYS* 3.5 43.7 - - + -
302I GLY 4.0 2.4 + - - -
303I VAL* 2.6 50.7 + - + -
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Residues in contact with ASP 269 (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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267I TYR* 3.8 14.6 + - + -
268I TYR* 1.3 73.6 - - - +
270I PRO* 1.3 64.1 - - - +
271I THR* 3.2 15.6 + - - +
272I GLU* 3.1 40.7 + - + +
273I GLN* 2.8 27.9 + - - -
274I ILE 2.9 13.1 + - - +
276I LYS* 3.6 28.4 + - + -
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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