Contacts of the strand formed by residues 274 - 281 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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266B SER* 3.4 27.6 - - - +
273B GLY 5.1 1.6 - - - +
274B VAL* 5.4 1.1 - - + -
237C SER* 3.6 16.9 - - - +
238C LEU 4.9 0.7 - - - +
239C TRP* 3.8 9.4 - - + -
264C TRP* 3.6 35.4 - - + -
265C THR 3.5 12.6 - - - +
266C SER* 4.4 8.1 - - - +
267C VAL* 4.1 3.8 - - - +
270C TYR* 4.3 3.1 - - - +
271C PRO 3.7 5.7 - - - +
272C SER* 3.5 20.8 + - - +
273C GLY* 1.3 83.1 - - - +
275C ILE* 1.3 72.3 + - - +
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Residues in contact with ILE 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C TYR* 4.0 4.0 - - + -
234C GLN* 4.5 18.8 - - + +
236C GLU* 3.5 20.2 - - - +
237C SER* 4.8 2.9 - - - +
262C TYR* 4.7 0.2 - - - -
264C TRP* 3.2 6.2 - - - +
265C THR* 3.0 44.4 + - + +
267C VAL* 3.9 10.8 - - + -
270C TYR* 3.4 38.8 - - + -
271C PRO* 5.4 3.8 - - + +
274C VAL* 1.3 81.5 - - - +
276C GLY* 1.3 65.4 + - - +
277C PHE* 3.7 28.9 - - + -
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Residues in contact with GLY 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234C GLN* 3.6 1.7 - - - +
235C ALA* 2.6 28.9 + - - -
236C GLU 2.5 21.9 + - - -
262C TYR* 3.1 15.7 - - - -
263C ALA 3.4 6.5 - - - -
275C ILE* 1.3 76.5 - - - +
277C PHE* 1.3 70.2 + - - -
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Residues in contact with PHE 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C TYR* 3.5 36.6 - + - -
109C MSE 3.9 12.6 - - + -
110C ILE* 3.4 41.3 - - + -
113C LEU* 4.0 16.4 - - + -
232C CYS* 4.1 7.6 - - - -
233C THR 3.1 16.4 - - - +
234C GLN* 3.9 3.6 - - - -
235C ALA* 3.8 6.1 - - - +
261C ASN 3.6 0.3 - - - +
262C TYR* 3.3 10.5 - - - -
263C ALA 2.8 37.5 + - - +
264C TRP* 5.1 0.2 - - - -
265C THR* 3.8 26.5 - - + -
275C ILE* 3.7 7.2 - - + -
276C GLY* 1.3 86.6 - - - -
278C MSE 1.3 60.7 + - - +
279C LEU* 3.9 15.5 - - + -
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Residues in contact with MSE 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231C VAL 2.8 14.4 - - - +
232C CYS* 2.9 15.4 - - - -
233C THR* 3.0 28.0 + - + +
235C ALA* 4.1 8.7 - - + -
248C ILE* 3.7 18.6 - - + +
249C VAL* 3.3 45.8 - - + -
252C CYS* 3.4 35.0 - - + -
260C VAL* 3.4 16.2 - - + -
261C ASN 3.6 18.8 - - - +
262C TYR* 4.2 7.6 - - + -
277C PHE* 1.3 74.4 - - - +
279C LEU* 1.3 62.2 + - - +
280C CYS* 3.9 6.9 - - - -
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Residues in contact with LEU 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C LEU* 4.3 6.3 - - + -
114C PRO* 3.9 16.2 - - + -
231C VAL 3.2 1.3 - - - +
232C CYS* 3.7 30.1 - - + -
260C VAL* 3.5 0.7 - - - -
261C ASN* 2.7 44.5 + - + +
263C ALA* 3.9 28.3 - - + -
277C PHE* 3.9 15.5 - - + +
278C MSE 1.3 77.5 - - - +
280C CYS* 1.3 60.4 + - - +
289C PHE* 3.3 48.1 - - + -
319C PHE* 3.9 10.8 - - + -
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Residues in contact with CYS 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229C GLY 3.5 0.5 - - - +
230C VAL* 3.0 6.2 - - - -
231C VAL* 2.8 42.7 + - + +
252C CYS* 3.3 41.5 - - - -
256C PHE* 3.7 27.1 - - + -
259C SER 3.3 5.8 - - - +
260C VAL* 4.1 6.1 - - + -
278C MSE 3.9 14.8 - - - -
279C LEU* 1.3 83.4 - - - +
281C SER* 1.3 60.4 + - - +
289C PHE* 3.3 5.1 - - - -
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Residues in contact with SER 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228C GLY 4.4 0.4 - - - -
229C GLY 3.1 8.5 - - - -
230C VAL* 4.4 0.9 - - - -
256C PHE* 3.5 10.4 - - - +
258C GLY* 2.7 30.7 + - - -
259C SER* 2.5 42.3 + - - -
280C CYS* 1.3 74.2 - - - +
282C THR* 1.3 60.3 + - - +
285C PRO 5.3 0.7 + - - -
286C ASP* 5.7 0.5 - - - -
287C VAL* 3.7 36.0 + - - +
289C PHE* 4.3 3.8 - - - -
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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