Contacts of the strand formed by residues 274 - 281 (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 274 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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266A SER* 3.6 25.1 - - - +
273A GLY 5.7 1.3 - - - +
274A VAL* 6.0 0.2 - - + -
237D SER* 3.5 18.8 - - - +
238D LEU 4.9 1.6 - - - +
239D TRP* 3.9 14.4 - - + -
264D TRP* 3.8 31.2 - - + -
265D THR 3.2 14.4 - - - +
266D SER* 4.2 7.6 - - - -
267D VAL 4.3 1.6 - - - +
270D TYR* 4.2 5.9 + - - +
271D PRO 3.6 6.9 - - - +
272D SER* 3.3 23.5 + - - +
273D GLY* 1.3 87.0 - - - +
275D ILE* 1.3 68.1 + - - +
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Residues in contact with ILE 275 (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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106D TYR* 3.8 11.4 - - + -
204D ASP* 4.9 5.8 - - - +
234D GLN* 3.9 35.2 - - + +
236D GLU* 3.9 12.6 - - - +
237D SER* 5.0 1.6 - - - +
264D TRP* 3.4 3.7 - - - -
265D THR* 3.0 49.1 + - + +
267D VAL* 3.9 7.2 - - + -
270D TYR* 3.7 29.4 - - + -
271D PRO* 6.0 2.2 - - + +
274D VAL* 1.3 79.3 - - - +
276D GLY* 1.3 62.7 + - - +
277D PHE* 3.8 14.9 - - + -
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Residues in contact with GLY 276 (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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234D GLN* 3.4 3.5 - - - +
235D ALA* 2.6 30.0 + - - -
236D GLU 2.7 22.5 + - - -
237D SER* 4.7 0.6 - - - +
238D LEU 5.6 0.2 - - - +
262D TYR* 3.4 15.9 - - - -
263D ALA 3.3 7.6 - - - -
264D TRP* 4.1 3.1 - - - -
275D ILE* 1.3 73.8 - - - +
277D PHE* 1.3 68.4 + - - -
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Residues in contact with PHE 277 (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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106D TYR* 3.4 42.0 - + - -
109D MSE 3.8 11.4 - - + -
110D ILE* 3.6 32.5 - - + -
113D LEU* 4.1 14.8 - - + -
232D CYS* 4.3 7.4 - - - -
233D THR 3.2 14.6 - - - +
234D GLN* 3.8 5.2 - - - -
235D ALA* 4.1 1.9 - - - +
262D TYR* 3.2 7.8 - - - -
263D ALA* 2.5 47.5 + - + +
265D THR* 3.4 28.5 - - + -
275D ILE* 3.8 7.2 - - + -
276D GLY* 1.3 79.8 - - - -
278D MSE 1.3 63.3 + - - +
279D LEU* 4.0 15.7 - - + -
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Residues in contact with MSE 278 (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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218D PHE* 5.9 0.4 - - + -
231D VAL* 3.2 2.2 - - - +
232D CYS* 3.1 25.6 - - - -
233D THR* 2.9 20.3 + - - +
235D ALA* 3.6 12.6 - - + -
248D ILE* 3.5 25.4 - - + -
249D VAL* 3.6 34.8 - - + -
252D CYS* 4.0 14.6 - - + -
260D VAL* 3.5 26.7 - - + -
261D ASN 3.2 19.1 - - - +
262D TYR* 3.6 14.8 - - - -
277D PHE* 1.3 73.2 - - - +
279D LEU* 1.3 61.7 + - - +
280D CYS* 3.7 15.0 - - - -
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Residues in contact with LEU 279 (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* 4.5 6.1 - - + -
114D PRO* 3.8 19.7 - - + -
231D VAL 3.2 3.8 - - - +
232D CYS* 3.6 23.8 - - - -
260D VAL* 3.3 1.4 - - - -
261D ASN* 2.6 46.3 + - + -
263D ALA* 4.2 3.4 - - + -
277D PHE* 4.0 25.1 - - + +
278D MSE 1.3 77.1 - - - +
280D CYS* 1.3 59.7 + - - +
289D PHE* 3.4 42.8 - - + -
319D PHE* 3.5 27.8 - - + -
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Residues in contact with CYS 280 (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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218D PHE* 6.2 0.2 - - - -
230D VAL* 3.0 5.4 - - - +
231D VAL* 2.7 41.3 + - + +
252D CYS* 3.7 22.4 - - - -
256D PHE* 3.5 33.7 - - + -
259D SER 2.9 7.4 - - - +
260D VAL* 3.8 7.4 - - + -
278D MSE 3.7 28.9 - - - -
279D LEU* 1.3 80.9 - - - +
281D SER* 1.3 61.0 + - - +
289D PHE* 3.6 3.7 - - - -
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Residues in contact with SER 281 (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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228D GLY* 4.3 2.5 - - - -
229D GLY 3.0 9.0 - - - -
230D VAL* 3.9 12.8 - - - -
256D PHE* 3.6 12.2 - - - +
258D GLY* 3.3 16.6 + - - -
259D SER* 2.6 48.5 + - - -
280D CYS* 1.3 75.9 - - - +
282D THR* 1.3 67.1 + - - +
285D PRO 5.2 1.8 + - - -
287D VAL* 4.0 22.0 + - - +
289D PHE* 4.3 1.1 - - - -
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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