Contacts of the strand formed by residues 290 - 300 (chain A) in PDB entry 2W77
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 ASN 290 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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284A GLY 4.5 0.2 - - - -
285A ALA* 3.3 4.5 + - - -
286A GLY* 2.7 36.6 + - - +
287A SER 3.4 17.9 + - - +
288A TRP* 4.2 1.7 - - - +
289A ASP* 1.3 73.4 - - - +
291A TYR* 1.3 62.4 + - - +
292A ARG 4.4 0.2 + - - -
316A GLN* 2.6 32.7 + - - +
317A ASP 3.7 3.6 - - - -
318A LYS* 3.7 27.7 - - + +
319A HIS 5.6 0.2 - - - +
808A MET* 4.5 15.0 - - - +
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Residues in contact with TYR 291 (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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284A GLY 3.5 6.3 - - - +
285A ALA* 4.3 20.0 - - + -
289A ASP* 3.6 31.8 + - + -
290A ASN* 1.3 75.6 + - - +
292A ARG* 1.3 61.3 + - - +
315A TYR* 4.1 0.5 - - - +
316A GLN* 3.3 3.8 - - - +
317A ASP* 2.9 41.8 + - + +
772B THR* 2.9 41.2 + - - +
774B LYS* 4.7 5.9 - - - +
775B LEU* 4.6 17.0 - - + -
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Residues in contact with ARG 292 (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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183A ASN* 3.4 43.1 + - - +
239A ASP* 2.2 49.1 + - - -
241A ALA* 4.4 0.8 - - - +
283A LEU* 3.6 2.1 - - - +
284A GLY* 3.0 30.3 + - - +
291A TYR* 1.3 76.8 - - - +
293A SER* 1.3 69.7 + - - +
294A GLU* 3.1 33.3 + - + +
314A ALA* 4.3 9.6 - - - +
315A TYR 3.4 8.0 - - - +
316A GLN* 2.8 35.4 + - - +
808A MET* 4.3 15.7 - - + +
1823A PO4 5.2 0.2 + - - -
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Residues in contact with SER 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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281A VAL* 6.1 0.2 - - - -
282A GLU* 3.3 7.4 - - - -
283A LEU* 3.4 24.0 - - - -
292A ARG* 1.3 77.9 - - - +
294A GLU* 1.3 66.0 + - - +
314A ALA* 3.3 3.6 - - - +
315A TYR* 2.8 48.6 + - - +
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Residues in contact with GLU 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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183A ASN* 5.1 1.4 + - - -
241A ALA* 3.7 12.9 - - + +
271A LYS* 4.4 1.6 + - - -
280A HIS* 3.0 12.2 + - - +
281A VAL* 3.2 9.5 - - - +
282A GLU* 2.9 46.6 + - + +
292A ARG* 3.1 24.9 + - + +
293A SER* 1.3 79.8 - - - +
295A LEU* 1.3 66.0 + - - +
296A ASP* 4.5 1.6 - - + +
312A VAL* 5.1 1.3 - - + -
313A ALA 3.5 12.3 - - - +
314A ALA* 4.2 6.7 - - + -
1823A PO4 2.9 46.1 + - - -
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Residues in contact with LEU 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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280A HIS 3.5 6.3 - - - +
281A VAL* 3.7 27.6 - - + -
294A GLU* 1.3 74.2 - - - +
296A ASP* 1.3 62.2 + - - +
297A VAL* 4.6 16.8 - - + -
311A ALA 4.3 0.4 - - - +
312A VAL* 3.1 7.9 - - - +
313A ALA* 3.0 43.4 + - + +
815A PHE* 4.0 14.4 - - + -
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Residues in contact with ASP 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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271A LYS* 2.8 21.4 + - - +
278A LYS* 5.2 0.3 - - - +
279A GLY* 3.0 8.7 - - - -
280A HIS* 3.0 59.7 + - + +
294A GLU* 4.5 4.0 - - - +
295A LEU* 1.3 75.8 - - - +
297A VAL* 1.3 63.3 + - - +
298A SER* 4.8 0.9 - - - -
310A ARG* 2.8 47.6 + - - +
311A ALA 3.4 4.7 - - - -
312A VAL* 4.0 10.3 - - + +
815A PHE* 4.6 1.0 - - - -
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Residues in contact with VAL 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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277A PHE* 4.0 27.8 - - + -
278A LYS 3.8 2.5 - - - +
295A LEU* 4.6 18.8 - - + -
296A ASP* 1.3 75.7 + - - +
298A SER* 1.3 63.1 + - - +
310A ARG* 3.1 5.2 - - - +
311A ALA* 2.7 59.1 + - + +
815A PHE* 4.6 12.3 - - + -
1816A N8E 3.8 18.2 - - - +
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Residues in contact with SER 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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273A PRO* 3.4 10.7 - - - +
274A THR* 3.1 20.6 + - - +
277A PHE* 3.3 6.8 - - - -
278A LYS* 2.9 45.1 + - - -
296A ASP* 4.8 0.4 - - - -
297A VAL* 1.3 79.0 - - - +
299A GLY* 1.3 59.0 + - - +
309A GLY 3.3 3.8 - - - -
310A ARG* 3.1 33.9 - - - +
1816A N8E 4.1 5.6 + - - -
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Residues in contact with GLY 299 (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 THR 3.1 17.5 + - - -
276A GLU 3.7 4.0 - - - -
277A PHE* 4.1 1.6 - - - -
298A SER* 1.3 78.1 + - - +
300A PRO* 1.4 73.9 - - - +
301A LEU* 3.8 2.6 + - - +
308A ARG* 3.3 0.9 - - - -
309A GLY* 2.8 34.9 + - - +
1816A N8E 4.0 7.9 - - - +
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Residues in contact with PRO 300 (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 THR 3.6 0.2 - - - -
275A HIS* 3.3 30.7 - - - +
276A GLU* 4.7 0.2 - - - -
277A PHE* 3.8 15.7 - - + +
299A GLY* 1.4 84.4 - - - +
301A LEU* 1.3 60.3 + - - +
302A THR 4.1 6.3 - - - +
305A GLY* 4.1 24.5 - - - -
307A VAL 3.7 5.8 - - - +
308A ARG* 4.1 7.2 - - + -
1816A N8E 4.0 20.1 - - - +
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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