Contacts of the strand formed by residues 248 - 252 (chain A) in PDB entry 1Y5I
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 TYR 248 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A SER* 3.2 2.6 + - - -
247A SER* 1.3 79.9 - - - +
249A ILE* 1.3 59.4 + - - +
250A ILE* 4.3 7.0 - - + -
275A THR* 3.8 0.2 - - - +
276A LYS* 3.6 35.3 - - + -
278A VAL* 4.0 15.7 - - + +
521A ILE* 3.4 21.3 - - + +
524A GLU* 2.7 46.9 + - + +
525A PHE* 3.7 32.9 - + + -
528A ASN* 3.4 29.4 - - + +
535A ARG 3.5 2.0 + - - -
536A SER* 3.3 6.8 - - - +
537A MET 2.7 33.1 + - - +
376B ILE* 4.1 9.6 - - + -
417B ARG* 4.5 0.4 - - - -
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Residues in contact with ILE 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A TRP* 3.8 34.8 - - + +
246A SER* 3.4 20.2 - - - +
248A TYR* 1.3 73.8 - - - +
250A ILE* 1.3 73.4 + - - +
251A ALA 4.1 0.2 + - - -
267A PHE* 3.8 23.6 - - + -
270A VAL* 4.0 21.8 - - + -
275A THR* 4.1 6.7 - - + -
276A LYS 3.1 9.7 + - - +
277A THR* 3.2 8.0 - - + -
278A VAL* 3.0 24.3 + - - +
537A MET* 3.3 12.8 - - + +
539A ILE* 3.6 27.6 - - + -
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Residues in contact with ILE 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248A TYR* 4.3 5.6 - - + -
249A ILE* 1.3 78.9 - - - +
251A ALA* 1.3 61.2 + - - +
252A TRP* 3.9 23.8 - - + -
278A VAL* 3.3 21.1 - - + +
280A VAL* 3.7 26.0 - - + -
305A MET* 6.4 0.9 - - + -
309A MET* 4.3 12.8 - - + -
521A ILE* 4.2 19.5 - - + -
525A PHE* 3.7 31.9 - - + -
537A MET 3.0 8.0 + - - +
538A ILE* 3.3 8.9 - - + +
539A ILE 2.9 26.3 + - - +
560A MET* 4.6 2.5 - - + -
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Residues in contact with ALA 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A ILE* 4.1 1.4 + - - +
250A ILE* 1.3 70.8 - - - +
252A TRP* 1.3 59.1 + - - +
253A GLY 4.0 1.3 + - - -
254A SER* 4.2 9.3 - - - +
256A VAL* 4.5 6.1 - - + -
267A PHE* 4.2 15.5 - - + -
278A VAL 2.7 11.6 + - - +
279A ALA* 3.5 1.6 - - - -
280A VAL 3.0 24.4 + - - +
281A THR* 5.0 1.0 - - - +
287A ILE* 3.7 35.8 - - + +
539A ILE* 3.5 10.1 - - + +
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Residues in contact with TRP 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A ILE* 3.6 21.3 + - + -
251A ALA* 1.3 72.1 - - - +
253A GLY* 1.3 65.6 + - - +
254A SER 3.3 0.7 + - - +
280A VAL* 3.5 17.9 - - + +
302A ASP* 2.7 50.3 + - + +
305A MET* 4.2 18.4 - - + -
306A ALA* 4.0 11.4 - - + -
309A MET* 3.9 22.0 - - - -
538A ILE* 4.1 15.7 - - + -
539A ILE 2.8 12.1 + - - +
540A VAL* 3.4 23.2 - - - +
544A LEU* 3.5 13.6 - - + +
557A LEU* 3.7 36.6 - - + -
560A MET* 3.9 20.4 - - + -
2800A MD1 3.5 9.0 - - - -
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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