Contacts of the strand formed by residues 242 - 247 (chain A) in PDB entry 1YXJ
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 THR 242 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A SER* 3.2 5.2 - - - -
208A ARG* 2.9 44.1 + - - +
209A ARG 4.7 4.0 + - - -
210A ASN* 5.0 3.6 - - - -
211A PRO* 5.5 0.3 - - - +
215A TRP* 3.5 27.2 - - + -
233A ALA 3.8 10.9 + - - +
234A VAL* 5.5 0.7 - - - -
236A GLN 4.0 10.7 + - - -
238A TYR* 3.6 15.3 + - + -
241A GLY* 1.3 73.3 - - - -
243A CYS* 1.3 63.1 + - - +
253A ALA* 3.7 15.7 - - + -
254A GLU 3.7 15.3 - - - +
256A CYS* 3.1 3.8 - - - -
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Residues in contact with CYS 243 (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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165A TRP* 3.2 36.3 - - + +
203A TRP* 3.4 26.4 - - + -
206A LEU 3.6 4.3 - - - -
207A SER* 3.8 9.4 - - - -
215A TRP* 4.4 2.0 - - - -
242A THR* 1.3 75.5 - - - +
244A ALA* 1.3 61.9 + - - +
252A TYR 3.8 0.3 - - - +
253A ALA* 3.4 3.4 - - - -
254A GLU 2.9 32.5 + - - +
256A CYS* 2.0 45.2 - - - -
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Residues in contact with ALA 244 (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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203A TRP* 3.4 8.0 - - - -
204A MSE 3.1 32.0 + - + +
206A LEU* 3.0 42.6 + - + +
215A TRP* 4.6 7.6 - - + -
230A VAL* 5.1 2.5 - - + -
243A CYS* 1.3 73.6 - - - +
245A TYR* 1.3 61.5 + - - +
251A VAL* 4.2 10.8 - - + -
252A TYR 3.2 11.0 - - - +
253A ALA* 4.5 0.2 - - - +
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Residues in contact with TYR 245 (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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201A PRO* 3.5 22.9 - - + -
202A PHE 3.2 22.7 - - - +
203A TRP* 3.8 12.1 - + + +
204A MSE 4.2 6.5 - - - +
243A CYS 4.5 0.2 - - - -
244A ALA* 1.3 75.3 - - - +
246A ILE* 1.3 63.0 + - - +
247A GLN* 3.5 30.5 + - + -
251A VAL* 3.4 3.5 - - - +
252A TYR* 2.8 69.0 + + + +
253A ALA 5.0 0.5 + - - -
254A GLU* 3.4 53.7 + - + +
260A ALA* 5.1 0.9 - - + -
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Residues in contact with ILE 246 (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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180A LEU* 5.4 0.7 - - + -
182A ILE* 5.6 0.2 - - + -
188A LEU* 4.3 13.2 - - + -
191A ILE* 4.1 24.5 - - + -
192A GLN* 4.1 15.7 - - + -
195A ILE* 3.7 26.2 - - + -
200A PHE 3.8 1.9 - - - +
201A PRO* 3.4 0.7 - - - +
202A PHE* 2.8 47.0 + - + +
204A MSE 3.8 17.0 - - + +
245A TYR* 1.3 74.1 - - - +
247A GLN* 1.3 64.1 + - - +
249A GLY* 3.9 26.2 - - - +
250A ALA 3.3 13.0 - - - +
251A VAL* 4.5 3.6 - - + -
263A ILE* 4.6 2.7 - - + -
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Residues in contact with GLN 247 (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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195A ILE* 6.2 0.4 - - - -
199A SER 2.8 29.0 + - - +
200A PHE 3.8 9.0 - - - +
201A PRO* 3.8 19.8 - - + +
202A PHE* 5.7 0.2 - - - -
245A TYR* 3.5 28.5 + - + -
246A ILE* 1.3 77.1 - - - +
248A ARG* 1.3 105.3 + - + +
249A GLY 3.2 0.9 - - - +
250A ALA* 2.9 18.9 + - - +
252A TYR* 3.5 16.9 + - + -
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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