Contacts of the strand formed by residues 260 - 266 (chain A) in PDB entry 2Q41
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 VAL 260 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249A VAL* 4.4 16.4 - - + +
252A CYS* 3.6 26.5 - - + +
253A ARG* 3.7 32.3 - - + +
256A PHE* 3.9 18.2 - - + +
258A GLY 4.0 0.8 + - - +
259A SER* 1.3 72.0 - - - +
261A ASN* 1.3 67.3 + - - +
278A MSE 4.6 5.8 - - + -
279A LEU 3.1 5.4 - - - -
280A CYS* 3.6 21.5 - - - -
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Residues in contact with ASN 261 (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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259A SER* 2.9 34.2 + - - -
260A VAL* 1.3 78.4 - - - +
262A TYR* 1.3 60.4 + - - +
263A ALA 4.1 0.4 - - - -
278A MSE 3.4 9.3 - - - +
279A LEU* 2.6 37.9 + - + +
289A PHE* 3.0 28.2 - - + +
290A LYS* 4.5 17.4 - - - +
319A PHE* 3.5 22.7 - - + -
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Residues in contact with TYR 262 (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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235A ALA* 3.0 33.4 + - + -
236A GLU 3.1 12.3 + - - -
238A LEU* 3.4 26.8 + - + +
245A ILE* 3.2 33.1 - - + +
249A VAL* 6.2 0.2 - - + -
261A ASN* 1.3 75.5 - - - +
263A ALA* 1.3 60.0 + - - +
264A TRP* 4.1 8.3 - - + -
274A VAL 5.1 0.2 + - - -
276A GLY* 3.1 17.0 - - - -
277A PHE 3.2 17.0 - - - -
278A MSE 3.6 20.9 - - - -
319A PHE* 3.7 11.4 - - - +
321A LEU* 3.6 23.0 - - + +
329A ILE* 3.7 36.6 - - + +
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Residues in contact with ALA 263 (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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113A LEU* 4.2 19.1 - - + -
261A ASN 4.1 0.2 - - - -
262A TYR* 1.3 75.4 - - - +
264A TRP* 1.3 61.4 + - - +
276A GLY* 3.6 0.3 - - - -
277A PHE* 2.8 34.3 + - - +
279A LEU* 4.2 4.9 - - + +
318A ALA* 3.9 7.0 - - + -
319A PHE* 3.5 45.2 - - + +
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Residues in contact with TRP 264 (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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109A MSE 5.8 0.2 - - - -
113A LEU* 6.3 0.2 - - - -
238A LEU* 3.5 21.1 - - + -
239A TRP* 4.0 5.8 - + - -
262A TYR* 4.1 6.3 - - + -
263A ALA* 1.3 74.4 - - - +
265A THR* 1.3 64.0 + - - +
274A VAL* 3.5 44.4 - - + +
275A ILE 4.0 6.5 - - - +
276A GLY* 4.1 11.0 - - - -
277A PHE* 5.5 1.1 - - - -
317A ALA 5.0 0.4 + - - -
318A ALA* 2.8 60.5 + - - +
320A CYS 2.9 21.9 + - - -
321A LEU* 3.3 18.7 - - + +
322A PRO* 3.6 18.8 - - + -
266D SER* 3.8 11.9 - - - -
309D PHE* 3.7 34.8 - + - -
314D ILE* 4.5 4.0 - - + -
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Residues in contact with THR 265 (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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105A ALA 4.4 0.7 - - - +
106A TYR* 5.3 0.2 - - - -
109A MSE 3.4 50.6 - - + +
264A TRP* 1.3 79.3 - - - +
266A SER* 1.3 64.8 + - - +
267A VAL* 3.8 21.8 - - + -
274A VAL* 3.5 25.9 - - - +
275A ILE* 3.3 17.5 + - + +
277A PHE* 4.1 8.3 - - + -
309A PHE* 3.5 9.4 - - - -
314A ILE* 5.2 2.1 - - - +
318A ALA* 5.6 1.0 - - - +
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Residues in contact with SER 266 (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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105A ALA* 3.3 15.6 - - - +
265A THR* 1.3 74.1 + - - +
267A VAL* 1.3 73.3 + - - +
268A PRO* 4.3 1.6 - - - +
273A GLY 3.7 7.0 + - - -
274A VAL* 5.0 2.7 - - - +
309A PHE* 3.5 8.6 - - - -
239D TRP* 3.2 20.4 + - - -
264D TRP* 3.7 27.7 - - - -
266D SER* 6.5 0.2 - - - -
272D SER 4.8 0.5 + - - -
274D VAL* 3.6 21.2 - - - +
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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