Contacts of the strand formed by residues 277 - 284 (chain A) in PDB entry 4BGG
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 THR 277 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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237A PHE 5.5 1.6 - - - +
239A SER* 4.7 22.2 + - - -
242A GLU* 4.1 16.6 + - - +
270A MET* 4.5 2.0 - - + -
271A THR 3.2 10.8 - - - +
272A SER* 2.8 26.5 + - - +
273A ARG 4.2 2.3 + - - -
276A SER* 1.3 77.6 - - - +
278A GLN* 1.3 66.3 + - - +
279A LEU* 3.9 30.2 + - + +
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Residues in contact with GLN 278 (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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236A ILE* 5.9 2.9 - - + -
237A PHE 5.8 0.4 - - - -
269A ASP 4.1 0.4 - - - +
270A MET* 3.3 7.6 - - - +
271A THR* 2.8 62.8 + - - +
276A SER* 2.8 34.4 + - - +
277A THR* 1.3 76.7 - - - +
279A LEU* 1.3 61.9 + - - +
280A TRP* 4.2 18.4 - - + +
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Residues in contact with LEU 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A ILE* 3.5 1.5 - - - +
237A PHE* 3.0 40.8 + - + +
238A SER 4.1 19.3 - - - +
239A SER* 4.4 6.5 - - - -
242A GLU* 4.1 25.8 - - + +
245A TRP* 3.6 39.9 - - + +
269A ASP 3.7 2.7 - - - -
270A MET* 3.4 36.6 - - + -
277A THR* 3.9 17.0 + - + +
278A GLN* 1.3 76.0 - - - +
280A TRP* 1.3 66.9 + - - +
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Residues in contact with TRP 280 (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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205A ALA* 3.7 42.0 - - + -
208A ILE* 4.4 17.0 - - + -
210A LEU* 4.2 30.5 - - + -
234A VAL* 3.7 20.4 - - + -
235A LYS 3.3 3.8 - - - +
236A ILE* 3.6 29.5 - - + +
245A TRP* 3.1 12.6 + - - +
268A SER* 3.3 1.0 + - - -
269A ASP* 2.8 39.9 + - + +
278A GLN* 4.4 15.0 - - + +
279A LEU* 1.3 89.5 - - - +
281A LEU* 1.3 59.5 + - - +
282A ILE* 3.9 14.4 - - + -
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Residues in contact with LEU 281 (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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233A ALA 3.7 1.0 - - - +
234A VAL* 3.5 2.6 - - - +
235A LYS* 2.7 37.8 + - + +
237A PHE* 3.8 17.9 - - + -
245A TRP* 4.7 2.7 - - + -
248A GLU* 3.7 34.8 - - + +
249A THR* 4.6 6.5 - - - +
252A TYR* 4.3 10.8 - - + -
265A PHE* 3.7 36.3 - - + -
267A ALA 3.9 1.6 - - - +
268A SER* 4.5 6.7 - - - +
280A TRP* 1.3 73.7 - - - +
282A ILE* 1.3 61.4 + - - +
283A THR* 4.1 13.5 - - + -
1000A 844 3.7 26.0 - - - +
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Residues in contact with ILE 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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204A VAL* 4.7 4.3 - - + -
205A ALA* 4.8 0.9 - - + -
208A ILE* 3.8 22.2 - - + -
232A VAL* 4.0 26.2 - - + -
233A ALA 3.3 7.9 - - - +
234A VAL* 4.4 6.7 - - + -
265A PHE* 4.2 1.7 - - - -
266A ILE* 3.0 35.7 + - + -
267A ALA* 2.8 36.6 + - + +
268A SER* 4.7 0.2 - - - -
269A ASP* 4.7 12.3 - - - +
280A TRP* 3.9 32.8 - - + +
281A LEU* 1.3 77.8 - - - +
283A THR* 1.3 68.7 + - - +
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Residues in contact with THR 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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232A VAL* 3.6 9.4 - - - +
233A ALA* 2.9 33.1 + - - +
252A TYR* 5.3 3.1 - - + -
263A LEU* 3.7 25.9 - - + +
264A GLY 3.2 17.7 - - - +
265A PHE* 4.5 4.0 - - - -
266A ILE* 3.7 9.0 - - - +
281A LEU* 4.1 15.9 - - + -
282A ILE* 1.3 80.2 - - - +
284A HIS* 1.3 72.2 + - - +
1000A 844 3.4 27.9 - - - +
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Residues in contact with HIS 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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231A ASN 5.8 2.7 - - - -
232A VAL* 5.1 0.9 - - - +
233A ALA* 3.6 3.6 - - - +
263A LEU* 3.7 5.4 - - + +
264A GLY* 3.0 31.2 + - - +
265A PHE 4.9 3.6 - - - -
266A ILE* 3.8 23.9 - - + +
283A THR* 1.3 91.1 + - - +
285A TYR* 1.3 61.2 - - - +
286A HIS* 4.2 9.0 - - + +
1000A 844 3.7 7.1 - - - -
1001A FLC 5.7 3.4 - - - +
1004A EDO 4.0 22.7 + - - +
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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