Contacts of the strand formed by residues 260 - 266 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249D VAL* 4.6 7.4 - - + +
252D CYS* 4.1 7.0 - - + +
253D ARG* 4.1 35.6 + - + +
256D PHE* 3.8 33.2 - - + +
259D SER* 1.3 79.2 + - - +
261D ASN* 1.3 73.3 + - - +
278D MSE 3.5 26.7 - - + -
279D LEU 3.3 3.1 - - - -
280D CYS* 3.8 7.4 - - - +
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Residues in contact with ASN 261 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259D SER* 3.0 26.7 + - - -
260D VAL* 1.3 77.6 + - - +
262D TYR* 1.3 61.3 + - - +
278D MSE 3.2 14.3 - - - +
279D LEU* 2.6 35.7 + - + +
289D PHE* 3.1 26.4 - - - +
290D LYS* 4.4 23.1 + - - +
319D PHE* 3.4 24.1 - - + -
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Residues in contact with TYR 262 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235D ALA* 3.1 33.0 + - + -
236D GLU 3.6 1.9 + - - -
238D LEU* 3.3 37.4 + - + +
245D ILE* 3.2 36.3 - - + +
249D VAL* 4.4 1.3 - - + -
261D ASN* 1.3 75.9 - - - +
263D ALA* 1.3 72.6 + - - +
264D TRP* 4.2 0.9 - - + -
276D GLY* 3.4 14.3 - - - -
277D PHE 3.2 12.6 - - - -
278D MSE 3.6 20.0 - - - -
318D ALA 3.7 0.2 - - - +
319D PHE* 3.1 14.5 - - - -
321D LEU* 3.4 39.9 - - + +
329D ILE* 4.5 13.5 - - + -
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Residues in contact with ALA 263 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D LEU* 4.3 8.1 - - + -
262D TYR* 1.3 77.8 - - - +
264D TRP* 1.3 58.6 + - - +
276D GLY* 3.3 1.4 - - - -
277D PHE* 2.5 46.3 + - + +
279D LEU* 4.2 7.6 - - + -
318D ALA* 2.8 32.1 - - + +
319D PHE* 3.4 24.0 - - + -
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Residues in contact with TRP 264 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266A SER* 3.7 23.8 - - - -
309A PHE* 3.4 34.3 - + - -
314A ILE* 5.9 2.2 - - + -
238D LEU* 3.5 33.0 - - + -
239D TRP* 4.1 10.1 - + - -
262D TYR* 4.2 4.7 - - + -
263D ALA* 1.3 75.4 - - - +
265D THR* 1.3 60.5 + - - +
274D VAL* 3.8 31.4 - - + -
275D ILE 3.4 10.5 - - - +
276D GLY* 4.3 2.9 - - - -
277D PHE* 5.3 0.9 - - - -
317D ALA 4.8 3.2 + - - -
318D ALA* 3.0 35.5 + - - +
320D CYS 4.2 15.5 + - - -
321D LEU* 4.6 7.0 - - + -
322D PRO* 3.6 19.0 - - + +
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Residues in contact with THR 265 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105D ALA 4.9 0.5 + - - -
106D TYR* 5.1 0.4 - - - -
109D MSE 3.2 34.5 - - + -
264D TRP* 1.3 76.7 - - - +
266D SER* 1.3 64.9 + - - +
267D VAL* 4.0 8.7 - - + -
274D VAL* 3.2 8.0 - - - -
275D ILE* 3.0 50.7 + - + +
277D PHE* 3.4 7.4 - - + -
309D PHE* 3.0 26.9 - - - -
318D ALA* 5.7 1.3 - - - -
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Residues in contact with SER 266 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A TRP* 3.3 18.0 + - - -
264A TRP* 3.8 18.4 - - - -
266A SER* 6.5 0.2 - - - -
274A VAL* 3.2 32.8 - - - +
105D ALA* 3.5 15.4 - - - +
265D THR* 1.3 79.2 + - - +
267D VAL* 1.3 65.1 + - - +
268D PRO* 4.0 2.1 - - - +
273D GLY 3.4 7.5 + - - -
274D VAL* 4.2 5.4 - - - +
309D PHE* 3.9 7.1 - - - -
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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