Contacts of the strand formed by residues 290 - 300 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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772A THR* 4.8 0.2 + - - -
284B GLY 3.8 1.0 - - - +
285B ALA* 3.3 4.9 - - - -
286B GLY* 2.7 42.5 + - - +
287B SER 3.4 17.6 + - - +
288B TRP 3.8 0.9 - - - +
289B ASP* 1.3 70.9 - - - +
291B TYR* 1.3 61.1 + - - +
316B GLN* 2.6 30.5 + - - +
317B ASP 3.8 2.0 - - - -
318B LYS* 3.6 25.1 - - + +
808B MET* 3.3 22.2 - - - +
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Residues in contact with TYR 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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772A THR* 2.7 37.9 - - + +
774A LYS* 4.4 12.2 + - - +
775A LEU* 4.4 25.2 - - + +
284B GLY 3.5 8.3 - - - +
285B ALA* 4.5 9.0 - - + -
286B GLY 6.0 0.2 - - - -
289B ASP* 3.7 26.5 + - + -
290B ASN* 1.3 75.2 + - - +
292B ARG* 1.3 61.9 + - - +
315B TYR* 4.1 1.6 - - - +
316B GLN* 3.4 4.7 - - - +
317B ASP* 2.9 49.7 + - + +
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Residues in contact with ARG 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B ASN* 3.5 40.6 + - - +
239B ASP* 2.5 45.9 + - - -
241B ALA* 4.4 1.4 - - - +
282B GLU* 3.8 3.8 - - + +
283B LEU* 3.5 3.5 - - - +
284B GLY* 2.7 44.3 + - - +
290B ASN* 4.3 0.6 + - - +
291B TYR* 1.3 74.7 - - - +
293B SER* 1.3 67.9 + - - +
294B GLU* 2.8 33.5 + - + +
314B ALA* 4.3 11.7 - - - +
315B TYR 3.4 7.2 + - - +
316B GLN* 3.0 35.3 + - + +
808B MET* 5.6 4.9 - - + -
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Residues in contact with SER 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282B GLU 3.4 5.6 - - - -
283B LEU* 3.6 20.9 - - - -
292B ARG* 1.3 76.6 - - - +
294B GLU* 1.3 62.2 + - - +
314B ALA* 3.3 3.7 - - - +
315B TYR* 2.8 51.8 + - - +
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Residues in contact with GLU 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B ASN* 5.2 0.3 + - - -
241B ALA* 3.3 29.5 - - + +
271B LYS* 4.9 3.8 + - - -
280B HIS* 2.9 31.1 + - - +
281B VAL* 3.3 7.1 - - - +
282B GLU* 2.9 49.3 + - + +
283B LEU* 5.1 0.2 - - - +
292B ARG* 2.8 31.7 + - + +
293B SER* 1.3 76.8 + - - +
295B LEU* 1.3 65.6 + - - +
296B ASP* 5.5 0.7 - - + -
312B VAL* 4.5 5.4 - - + -
313B ALA 3.3 11.4 - - - +
314B ALA* 4.2 3.8 - - + -
1818B PO4 5.5 0.5 + - - -
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Residues in contact with LEU 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280B HIS 3.5 4.9 - - - +
281B VAL* 3.6 25.8 - - + -
294B GLU* 1.3 74.5 - - - +
296B ASP* 1.3 64.2 + - - +
297B VAL* 3.9 17.3 - - + -
311B ALA 3.9 0.2 - - - +
312B VAL* 3.1 7.5 - - - +
313B ALA* 2.8 45.2 + - + +
815B PHE* 3.9 13.7 - - + -
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Residues in contact with ASP 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271B LYS* 3.2 17.1 + - - +
279B GLY* 3.2 7.7 - - - -
280B HIS* 3.0 56.4 + - + +
294B GLU* 4.4 1.3 - - - +
295B LEU* 1.3 74.0 - - - +
297B VAL* 1.3 68.6 + - - +
298B SER* 4.7 0.5 + - - -
310B ARG* 2.7 48.9 + - - +
311B ALA 3.5 3.6 - - - -
312B VAL* 3.8 15.7 - - + +
815B PHE* 4.2 0.9 - - - -
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Residues in contact with VAL 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B PHE* 4.0 28.9 - - + -
278B LYS 3.9 2.5 - - - +
295B LEU* 3.9 24.7 - - + -
296B ASP* 1.3 79.7 + - - +
298B SER* 1.3 64.7 + - - +
309B GLY 4.0 0.3 - - - +
310B ARG* 3.2 6.0 - - - +
311B ALA* 2.9 43.9 + - + +
815B PHE* 4.8 8.3 - - + -
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Residues in contact with SER 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272B LYS 4.0 0.2 + - - -
273B PRO* 3.4 11.6 - - - +
274B THR* 2.8 36.1 + - - -
276B GLU 4.1 1.1 - - - -
277B PHE* 3.2 9.8 - - - -
278B LYS* 2.9 41.9 + - - +
296B ASP* 4.8 0.4 - - - -
297B VAL* 1.3 78.6 - - - +
299B GLY* 1.3 58.0 + - - +
309B GLY 3.4 5.6 + - - -
310B ARG* 3.6 20.1 - - - +
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Residues in contact with GLY 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274B THR 3.4 13.9 + - - +
276B GLU 3.7 3.6 - - - -
277B PHE* 4.0 7.0 - - - -
298B SER* 1.3 77.6 + - - +
300B PRO* 1.3 75.5 - - - +
301B LEU* 4.6 2.2 - - - +
308B ARG* 3.6 1.9 - - - -
309B GLY* 3.0 31.9 + - - +
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Residues in contact with PRO 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B GLN* 3.6 32.1 - - - +
71B LEU* 4.2 2.7 - - + -
274B THR 3.7 1.3 - - - +
275B HIS 3.1 27.6 - - - +
277B PHE* 4.0 3.1 - - + +
299B GLY* 1.3 84.9 - - - +
301B LEU* 1.3 66.3 + - - +
302B THR 3.4 17.9 - - - +
303B GLU* 6.0 0.4 - - - -
305B GLY* 4.0 16.6 - - - -
307B VAL 3.6 5.8 - - - +
308B ARG* 4.3 5.2 - - + -
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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