Contacts of the strand formed by residues 278 - 286 (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 LYS 278 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142B GLU* 3.3 29.7 + - - +
143B ASP* 3.0 40.0 + - - +
274B THR* 4.2 22.9 - - - +
276B GLU* 3.2 25.1 + - + +
277B PHE* 1.3 83.3 - - - +
279B GLY* 1.3 61.7 + - - +
296B ASP* 5.5 0.2 - - - +
297B VAL* 3.9 2.4 - - - +
298B SER* 2.9 35.7 + - - +
310B ARG* 4.7 5.6 - - - +
812B ARG* 5.6 1.8 - - - +
815B PHE 5.4 3.6 - - - -
1818B PO4 4.3 7.5 + - - -
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Residues in contact with GLY 279 (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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278B LYS* 1.3 81.3 - - - +
280B HIS* 1.3 69.6 + - - +
296B ASP* 3.2 16.6 - - - -
812B ARG* 5.4 0.2 - - - -
814B ASP* 3.3 8.2 - - - +
815B PHE* 3.0 40.1 + - - -
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Residues in contact with HIS 280 (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* 4.5 1.3 - - - -
279B GLY* 1.3 78.6 - - - +
281B VAL* 1.3 68.8 + - - +
282B GLU* 4.2 10.5 + - + -
294B GLU* 2.9 27.9 + - - -
295B LEU* 3.5 7.4 - - - +
296B ASP* 3.0 61.5 + - + +
812B ARG* 3.1 32.0 + - + +
813B TRP 3.2 13.9 - - - +
814B ASP* 3.8 13.0 - - - +
815B PHE* 3.7 5.5 - - - -
1818B PO4 3.1 26.7 + - - -
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Residues in contact with VAL 281 (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* 1.3 74.8 - - - +
282B GLU* 1.3 70.6 + - - +
283B LEU* 4.6 15.5 - - + -
294B GLU 3.3 7.0 - - - +
295B LEU* 3.6 28.7 - - + -
811B THR 3.9 0.3 - - - +
812B ARG* 3.6 2.1 - - - +
813B TRP* 2.9 53.8 + - + +
815B PHE* 3.8 14.8 - - + -
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Residues in contact with GLU 282 (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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178B ASP* 6.0 0.5 - - - -
280B HIS* 4.2 7.8 - - + -
281B VAL* 1.3 78.3 - - - +
283B LEU* 1.3 67.6 + - - +
284B GLY* 5.0 0.9 - - - +
292B ARG* 3.8 4.9 - - + +
293B SER* 3.4 5.4 - - - -
294B GLU* 2.9 51.9 + - + +
778B SER* 5.6 1.0 + - - -
810B SER* 2.9 27.8 + - - +
811B THR 3.3 9.6 - - - +
812B ARG* 3.8 32.6 + - - +
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Residues in contact with LEU 283 (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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283A LEU* 5.9 7.4 - - + -
1817A N8E 3.6 12.7 + - - +
281B VAL* 4.6 15.7 - - + -
282B GLU* 1.3 84.5 - - - +
284B GLY* 1.3 57.8 + - - +
292B ARG 3.5 2.5 - - - +
293B SER* 3.6 22.9 - - - -
810B SER* 3.7 0.2 - - - -
811B THR* 3.1 36.9 + - - +
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Residues in contact with GLY 284 (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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1817A N8E 4.7 1.1 - - - -
282B GLU* 4.2 1.6 - - - +
283B LEU* 1.3 74.4 - - - +
285B ALA* 1.3 60.8 + - - +
290B ASN 4.2 0.2 - - - -
291B TYR* 3.5 5.5 - - - +
292B ARG* 2.7 43.2 + - - +
808B MET* 4.2 10.8 - - - -
809B PHE 3.1 10.8 - - - -
810B SER* 4.3 5.6 - - - -
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Residues in contact with ALA 285 (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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771A ILE* 3.8 13.6 - - + +
772A THR* 5.7 0.9 - - - +
775A LEU* 3.7 32.3 - - + -
1817A N8E 4.5 4.2 + - - +
284B GLY* 1.3 74.9 - - - +
286B GLY* 1.3 55.0 + - - +
290B ASN 3.3 6.3 - - - -
291B TYR* 4.5 14.4 - - + -
808B MET* 3.5 4.1 - - - +
809B PHE* 2.7 38.4 + - - +
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Residues in contact with GLY 286 (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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771A ILE* 3.5 15.5 - - - +
772A THR* 4.2 3.7 + - - -
285B ALA* 1.3 75.3 - - - +
287B SER* 1.3 61.2 + - - -
288B TRP 3.6 0.7 + - - -
289B ASP* 3.7 2.8 + - - -
290B ASN* 2.7 43.1 + - - -
291B TYR* 6.0 0.2 - - - -
807B LEU 3.1 15.5 - - - -
808B MET* 3.8 7.8 - - - -
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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