Contacts of the strand formed by residues 291 - 298 (chain A) in PDB entry 2F24
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 GLN 291 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168A ASN* 5.9 3.8 - - - +
223A GLU* 4.4 3.5 - - - +
224A VAL* 3.6 32.0 - - + +
278A SER* 4.2 18.4 - - - +
279A PHE* 3.3 19.1 - - - +
280A PRO* 4.5 4.7 - - + +
281A SER 3.9 0.4 - - - +
290A ALA* 1.3 104.7 + - - +
292A TRP* 1.3 78.0 + - - +
315A PRO* 3.2 22.0 - - - +
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Residues in contact with TRP 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A SER* 3.2 5.4 - - - -
279A PHE* 2.9 49.9 + + + -
281A SER* 3.0 25.3 + - - -
282A PRO* 3.5 32.1 - - + -
283A ARG* 3.7 31.2 - - - -
291A GLN* 1.3 83.5 - - - +
293A LEU* 1.3 64.9 + - - +
311A LEU* 3.7 37.2 - - + -
312A ASN 3.4 7.4 - - - +
313A PRO* 3.3 41.8 + - + -
315A PRO* 4.2 0.4 - - - -
369A LEU* 4.5 2.2 - - + -
376A GLU* 3.6 26.7 - - + -
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Residues in contact with LEU 293 (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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222A ALA* 3.8 15.5 - - + -
224A VAL* 3.7 20.2 - - + -
233A THR* 4.2 17.7 - - + +
245A GLN* 5.5 1.3 - - - +
276A VAL* 4.2 6.3 - - + -
277A ILE 3.3 14.1 - - - +
278A SER* 3.8 11.4 - - - -
279A PHE* 3.9 2.5 - - - -
292A TRP* 1.3 73.3 - - - +
294A LEU* 1.3 60.2 + - - +
310A TYR 4.4 0.2 - - - -
311A LEU* 3.3 10.7 - - - +
312A ASN* 3.0 34.4 + - + -
315A PRO* 3.6 27.6 - - + -
316A PRO* 4.6 7.2 - - + -
321A TRP* 3.7 33.0 - - + -
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Residues in contact with LEU 294 (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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276A VAL* 3.3 2.6 - - - +
277A ILE* 2.9 40.8 + - + +
279A PHE* 4.0 11.4 - - + -
293A LEU* 1.3 73.9 - - - +
295A TYR* 1.3 61.6 + - - +
296A THR* 5.4 0.2 - - + -
309A ALA* 4.4 10.8 - - + -
310A TYR 3.4 14.6 - - - +
311A LEU* 4.4 7.4 - - + -
337A LEU* 3.6 26.2 - - + +
350A PHE* 3.6 45.5 - - + -
367A PHE* 4.3 9.4 - - + -
369A LEU* 5.1 0.7 - - + -
373A PHE* 4.1 23.6 - - + -
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Residues in contact with TYR 295 (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 ASN* 3.7 31.9 - - - -
243A ARG* 3.1 30.3 - - - +
264A LEU* 3.8 21.4 - - + +
265A VAL 4.4 1.4 + - - -
274A GLY* 4.4 0.4 - - - -
275A SER 3.0 26.9 - - - +
276A VAL* 4.3 3.4 - - + -
294A LEU* 1.3 75.3 - - - +
296A THR* 1.3 68.9 + - - +
297A HIS* 3.1 37.7 + - + +
309A ALA* 3.3 3.8 - - - -
310A TYR* 2.8 68.9 + + + -
321A TRP* 3.6 22.4 - + + -
337A LEU* 3.9 0.4 - - - -
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Residues in contact with THR 296 (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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274A GLY* 3.3 2.4 - - - -
275A SER* 2.9 33.3 + - - -
294A LEU* 5.4 1.1 - - + -
295A TYR* 1.3 81.1 - - - +
297A HIS* 1.3 66.5 + - - +
307A LEU* 4.4 6.7 - - - -
308A GLY 3.2 7.2 - - - +
309A ALA* 4.1 5.4 - - + -
327A LEU* 3.7 27.6 - - + -
335A SER* 2.8 27.0 + - - -
337A LEU* 3.5 36.3 - - + +
352A CYS* 4.1 2.8 - - - -
367A PHE* 5.4 0.4 - - + -
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Residues in contact with HIS 297 (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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243A ARG* 3.5 8.9 - - - -
265A VAL 3.2 22.5 + - - -
266A GLU* 2.7 27.6 + - - -
267A PRO* 3.6 15.0 - - + -
272A CYS* 3.1 19.7 + - + +
273A GLN 3.7 9.4 - - - -
274A GLY* 3.9 3.6 - - - -
295A TYR* 3.1 32.8 + - + +
296A THR* 1.3 78.9 - - - +
298A PRO* 1.3 102.5 + - + +
299A THR* 3.8 1.9 - - - +
307A LEU* 3.6 10.1 - - - +
308A GLY* 2.9 22.8 + - - +
310A TYR* 4.1 2.8 + - + -
335A SER* 4.7 1.1 - - - -
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Residues in contact with PRO 298 (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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265A VAL* 4.0 4.0 - - - +
267A PRO* 5.6 1.1 - - + -
272A CYS* 4.0 15.0 - - + -
273A GLN 4.4 0.9 - - - +
297A HIS* 1.3 129.8 + - + +
299A THR* 1.3 60.6 + - - +
300A HIS 4.9 1.1 - - - +
303A GLN 4.3 4.7 - - - +
304A ARG* 4.2 6.1 - - - -
305A ALA 3.4 25.1 - - - +
306A ASP 3.8 4.0 - - - +
307A LEU* 4.0 6.5 - - + -
310A TYR* 3.9 5.7 + - - -
332A CYS* 3.5 23.8 - - + +
333A ALA 3.9 17.0 - - - +
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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