Contacts of the strand formed by residues 281 - 290 (chain A) in PDB entry 2ASL
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 PRO 281 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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273A TYR* 4.3 7.4 - - + +
276A LEU* 3.9 17.5 - - + -
279A ARG 3.7 8.7 - - - +
280A ILE* 1.3 85.3 - - + +
282A LYS* 1.3 61.8 + - - +
283A ALA 4.1 3.6 - - - +
305A GLY* 3.6 1.7 - - - -
306A ILE* 2.8 43.3 + - + +
337A PHE* 3.8 35.2 - - + -
338A SER 3.5 16.6 - - - +
339A LYS 3.8 1.3 - - - +
340A PHE* 3.9 10.3 - - + -
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Residues in contact with LYS 282 (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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281A PRO* 1.3 74.8 - - - +
283A ALA* 1.3 58.6 + - - +
301A THR* 3.6 4.2 - - + -
302A PHE* 2.8 41.2 + - - +
303A PRO* 2.8 31.7 + - - +
304A HIS* 3.9 18.6 - - - +
305A GLY* 4.5 0.4 - - - +
306A ILE* 3.4 10.1 - - - +
338A SER 3.3 0.2 + - - -
339A LYS* 3.0 30.7 + - + +
340A PHE 5.7 0.4 - - - +
341A ILE* 4.3 27.8 - - + +
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Residues in contact with ALA 283 (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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281A PRO* 4.1 0.5 - - - +
282A LYS* 1.3 80.6 - - - +
284A ILE* 1.3 61.5 + - - +
285A HIS* 5.1 7.0 - - - +
300A ARG 3.4 6.3 - - - +
301A THR* 3.5 22.4 - - - +
306A ILE* 3.4 4.6 - - - +
337A PHE* 3.4 11.5 - - - +
338A SER* 3.1 47.3 + - - +
339A LYS* 4.0 11.0 - - + -
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Residues in contact with ILE 284 (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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269A ILE* 4.7 0.2 - - + -
283A ALA* 1.3 74.5 - - - +
285A HIS* 1.3 69.9 + - - +
286A VAL* 4.2 1.1 - - + +
299A GLY* 3.2 2.3 - - - -
300A ARG* 3.0 36.0 + - + +
302A PHE* 4.1 13.9 - - + -
306A ILE* 4.0 13.0 - - + -
311A ALA* 3.9 26.0 - - + +
314A GLU* 4.1 8.1 - - + -
315A SER* 4.2 13.2 - - - +
318A LEU* 3.9 16.3 - - + +
335A VAL* 3.6 21.8 - - + -
336A ARG 3.6 3.8 - - - -
337A PHE* 3.6 28.9 - - + -
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Residues in contact with HIS 285 (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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283A ALA* 5.1 5.6 - - + +
284A ILE* 1.3 78.6 + - - +
286A VAL* 1.3 63.0 + - - +
287A VAL* 4.8 3.1 - - + -
297A SER* 3.5 23.4 + - - +
298A ARG 3.4 2.5 - - - -
299A GLY* 3.2 28.1 + - - -
300A ARG 4.6 1.3 + - - -
301A THR* 5.7 0.2 + - - -
335A VAL* 3.3 4.0 - - - +
336A ARG* 2.8 54.7 + - + +
338A SER* 4.6 14.6 + - - -
339A LYS* 6.2 1.2 - - - -
806D G 4.5 29.5 + + + -
807D A 4.6 4.7 + + - -
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Residues in contact with VAL 286 (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 LEU* 4.3 6.5 - - + -
284A ILE* 4.2 4.0 - - + -
285A HIS* 1.3 74.2 - - - +
287A VAL* 1.3 61.0 + - - +
296A VAL 3.8 1.9 - - - +
297A SER* 3.4 4.5 + - - -
298A ARG 2.9 35.1 + - - +
315A SER* 3.7 41.5 - - - +
318A LEU* 3.8 14.8 - - + +
319A LEU* 4.6 8.5 - - + -
322A ILE* 3.7 16.3 - - + +
333A ILE* 3.7 22.0 - - + -
334A GLY 3.4 14.6 - - - +
335A VAL* 5.1 0.9 - - + -
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Residues in contact with VAL 287 (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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248A ILE* 4.4 24.1 - - + +
285A HIS* 4.3 13.0 - - + +
286A VAL* 1.3 75.2 - - - +
288A ALA* 1.3 64.1 + - - +
289A VAL* 4.1 3.2 + - + -
295A ILE* 3.7 31.2 - - + -
296A VAL 4.0 1.6 - - - -
297A SER* 4.6 7.2 - - - +
333A ILE* 3.5 5.5 - - - -
334A GLY 3.0 33.8 + - - +
335A VAL 5.0 2.2 - - - +
336A ARG* 4.4 18.8 - - + -
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Residues in contact with ALA 288 (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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286A VAL 4.0 0.8 - - - -
287A VAL* 1.3 73.6 - - - +
289A VAL* 1.3 61.5 + - - +
290A THR* 3.9 1.6 + - + +
295A ILE* 3.6 1.9 - - - +
296A VAL* 2.9 43.1 + - + +
322A ILE* 4.0 17.9 - - + -
330A ILE* 4.0 26.2 - - + -
332A ARG 3.5 5.2 - - - -
333A ILE* 3.8 15.0 - - + -
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Residues in contact with VAL 289 (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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248A ILE* 3.4 30.1 - - + -
287A VAL* 4.0 2.7 - - + -
288A ALA* 1.3 72.7 - - - +
290A THR* 1.3 64.3 + - - +
293A LEU* 3.7 29.4 - - + +
294A ASP 3.4 13.0 - - - +
295A ILE* 4.0 19.1 - - + -
330A ILE* 3.8 2.1 - - - +
331A ARG 2.8 23.6 + - - -
332A ARG* 2.8 41.5 + - + +
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Residues in contact with THR 290 (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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288A ALA* 4.5 3.8 - - + +
289A VAL* 1.3 77.5 - - - +
291A GLU* 1.3 60.3 - - - +
292A ASP* 2.6 26.8 + - - -
293A LEU* 2.9 20.8 + - - +
294A ASP* 2.9 19.3 + - - +
296A VAL* 3.6 31.6 - - + -
322A ILE* 6.4 0.2 - - + -
326A ASP* 4.8 0.9 - - - +
328A ARG* 3.7 26.0 + - + +
329A LYS 3.4 12.8 - - - +
330A ILE* 4.3 4.3 - - + +
331A ARG* 3.8 9.6 - - - +
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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