Contacts of the strand formed by residues 281 - 290 (chain P) in PDB entry 2IMW
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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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273P TYR* 4.6 5.2 - - + +
276P LEU* 4.1 13.5 - - + -
279P ARG 3.6 8.7 - - - +
280P ILE* 1.3 88.9 - - + +
282P LYS* 1.3 60.0 + - - +
283P ALA 3.8 4.3 - - - +
305P GLY* 3.4 1.6 - - - -
306P ILE* 2.8 44.1 + - + +
337P PHE* 3.6 41.7 - - + -
338P SER 3.3 19.3 - - - +
339P LYS 3.9 0.2 - - - +
340P PHE* 3.8 9.4 - - + -
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Residues in contact with LYS 282 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281P PRO* 1.3 72.8 - - - +
283P ALA* 1.3 56.5 + - - +
301P THR* 3.5 5.0 - - + -
302P PHE* 2.8 49.7 + - - +
303P PRO* 4.7 4.3 - - + +
304P HIS* 3.5 20.4 - - - +
306P ILE* 3.6 11.4 - - - +
339P LYS* 2.8 48.4 + - + +
340P PHE 3.7 12.7 + - - -
341P ILE* 3.6 31.5 - - + +
342P GLU 5.4 0.4 - - - +
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Residues in contact with ALA 283 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281P PRO* 3.8 1.0 - - - +
282P LYS* 1.3 80.5 - - - +
284P ILE* 1.3 61.0 + - - +
285P HIS* 4.7 6.5 - - + -
300P ARG 3.3 5.2 - - - +
301P THR* 3.7 17.5 - - - +
306P ILE* 3.5 6.6 - - - +
337P PHE* 3.4 7.1 - - - -
338P SER* 3.0 46.1 + - - +
339P LYS* 3.7 20.2 - - + -
348P LYS 4.5 0.7 - - - +
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Residues in contact with ILE 284 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269P ILE* 5.4 0.2 - - + -
283P ALA* 1.3 74.9 - - - +
285P HIS* 1.3 69.5 + - - +
286P VAL* 4.8 0.4 - - + +
299P GLY* 3.0 2.3 - - - -
300P ARG 2.8 34.6 + - - +
302P PHE* 4.2 3.6 - - + -
306P ILE* 3.7 15.7 - - + -
311P ALA* 3.7 26.2 - - - +
314P GLU* 4.1 23.6 - - + -
315P SER* 4.2 13.2 - - - +
318P LEU* 3.7 5.3 - - + +
335P VAL* 3.5 26.7 - - + -
336P ARG 3.4 4.0 - - - -
337P PHE* 3.4 29.4 - - + -
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Residues in contact with HIS 285 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283P ALA* 4.7 8.1 - - + -
284P ILE* 1.3 82.2 - - - +
286P VAL* 1.3 62.5 + - - +
287P VAL* 3.9 2.1 + - + +
297P SER* 3.6 20.9 - - - +
298P ARG 3.3 4.9 - - - +
299P GLY* 3.4 17.9 - - - -
300P ARG 5.0 0.9 - - - -
301P THR* 5.6 2.5 - - - -
335P VAL* 3.3 4.3 - - - +
336P ARG* 2.8 37.0 + - + +
338P SER* 4.4 6.0 + - - -
339P LYS* 5.7 1.1 - - - -
348P LYS* 4.1 21.3 - - - -
504P EDO 3.6 32.7 + - - +
1912T T 3.0 36.5 + - + +
1913T T 6.5 0.4 - - + -
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Residues in contact with VAL 286 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265P LEU* 4.2 10.3 - - + -
285P HIS* 1.3 75.2 - - - +
287P VAL* 1.3 64.0 + - - +
297P SER* 3.5 3.6 + - - -
298P ARG 2.8 30.5 + - - -
315P SER* 3.4 41.1 - - - +
318P LEU* 3.7 21.4 - - + +
319P LEU* 4.4 9.2 - - + -
322P ILE* 3.6 16.5 - - + +
333P ILE* 3.7 22.7 - - + -
334P GLY 3.5 11.4 - - - +
335P VAL* 4.5 3.6 - - + -
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Residues in contact with VAL 287 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248P ILE* 3.8 31.3 - - + +
285P HIS* 4.4 8.3 - - + +
286P VAL* 1.3 78.4 - - - +
288P ALA* 1.3 64.5 + - - +
289P VAL* 4.2 1.1 + - + -
295P ILE* 3.7 27.8 - - + -
296P VAL 3.5 2.7 - - - +
297P SER* 4.1 6.3 - - - +
332P ARG 4.2 0.3 - - - +
333P ILE* 3.5 5.8 - - - +
334P GLY* 2.9 35.8 + - - +
335P VAL 5.4 0.4 - - - -
336P ARG* 4.8 10.3 - - + +
504P EDO 3.7 26.7 - - - +
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Residues in contact with ALA 288 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286P VAL 4.2 0.6 - - - -
287P VAL* 1.3 74.2 - - - +
289P VAL* 1.3 63.0 + - - +
290P THR* 3.9 2.3 + - + +
294P ASP 3.8 0.2 - - - +
295P ILE* 3.4 6.2 - - - +
296P VAL* 2.8 42.3 + - + +
322P ILE* 4.1 17.0 - - + +
330P ILE* 4.0 27.4 - - + -
332P ARG 3.5 4.5 - - - -
333P ILE* 3.9 15.0 - - + -
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Residues in contact with VAL 289 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248P ILE* 4.3 20.6 - - + -
287P VAL* 4.2 1.1 + - + -
288P ALA* 1.3 75.6 - - - +
290P THR* 1.3 61.6 + - - +
293P LEU* 3.9 16.6 - - + +
294P ASP 3.2 12.3 - - - +
295P ILE* 4.2 16.6 - - + -
330P ILE* 3.7 1.8 - - - -
331P ARG* 2.7 33.1 + - - +
332P ARG* 2.9 60.6 + - + +
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Residues in contact with THR 290 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288P ALA* 4.9 2.7 - - + +
289P VAL* 1.3 79.6 - - - +
291P GLU* 1.3 56.8 + - - +
292P ASP* 3.2 14.6 + - - -
293P LEU* 2.8 24.3 + - - +
294P ASP* 3.0 35.2 + - + +
296P VAL* 4.0 24.0 - - + -
322P ILE* 6.6 0.2 - - + -
326P ASP* 4.1 6.1 - - - +
328P ARG* 3.8 26.2 + - + +
329P LYS 3.3 11.7 - - - +
330P ILE* 4.3 7.4 - - + +
331P ARG* 3.9 5.3 - - - +
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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