Contacts of the strand formed by residues 286 - 293 (chain D) in PDB entry 3BFO
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 GLY 286 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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262D LYS* 4.6 1.1 - - - -
263D ASN* 3.6 13.2 - - - -
284D HIS 3.5 1.8 + - - -
285D GLN* 1.3 78.1 - - - +
287D THR* 1.3 63.4 + - - -
288D TYR* 3.5 12.0 - - - -
305D GLU* 3.5 7.1 - - - +
306D ILE 2.9 33.9 + - - -
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Residues in contact with THR 287 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261D PHE 3.9 0.2 - - - +
262D LYS* 3.3 1.9 - - - -
263D ASN* 2.7 46.1 + - - -
264D GLU 4.7 0.2 + - - -
286D GLY* 1.3 73.7 - - - -
288D TYR* 1.3 64.4 + - - +
289D TRP* 4.8 2.1 - - - -
303D LYS* 3.6 40.8 - - + +
304D VAL 3.3 12.7 + - - +
305D GLU* 4.5 10.0 + - + +
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Residues in contact with TYR 288 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244D LEU* 3.9 9.3 - - + +
246D LEU* 3.6 24.7 - - + -
260D TRP* 4.7 6.1 - + + -
261D PHE 3.1 13.7 - - - +
262D LYS* 3.3 32.0 - - + +
267D LEU* 4.0 9.6 - - + -
275D TYR* 3.6 26.8 + + - -
284D HIS* 2.7 40.9 + - - +
286D GLY 3.5 16.4 - - - -
287D THR* 1.3 75.1 - - - +
289D TRP* 1.3 67.4 + - - +
302D LYS 3.9 0.3 - - - +
303D LYS* 3.3 1.6 - - - -
304D VAL* 2.9 40.6 + - + +
306D ILE* 3.6 22.9 - - + -
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Residues in contact with TRP 289 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296A ARG* 3.7 16.2 - - + -
269C HIS* 3.6 23.8 - + - -
233D PRO* 5.3 0.2 - - - -
260D TRP* 3.5 10.5 - - - -
261D PHE* 2.8 77.5 + + + +
264D GLU* 3.2 33.3 + - - +
287D THR 4.8 3.1 - - - -
288D TYR* 1.3 83.1 - - - +
290D CYS* 1.3 74.8 + - - +
291D HIS* 3.9 8.3 - - + -
300D ASP* 3.0 36.8 - - + -
301D SER* 3.4 15.7 - - - +
302D LYS 3.7 6.7 - - - +
303D LYS* 3.8 31.1 - - + +
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Residues in contact with CYS 290 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248D CYS* 3.9 11.9 - - + -
258D TYR* 3.8 39.0 - - - -
259D GLN 3.4 10.5 - - - -
260D TRP* 3.8 37.7 - - + -
289D TRP* 1.3 80.0 - - - +
291D HIS* 1.3 65.2 + - - +
292D VAL* 3.8 3.8 + - - +
300D ASP* 3.6 1.2 - - - -
301D SER* 2.8 40.6 + - - +
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Residues in contact with HIS 291 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294A ASN 4.0 3.0 + - - -
295A ASP 3.2 36.1 - - - +
296A ARG* 2.8 25.9 + - - -
297A ASP* 3.7 6.4 + - - -
298A SER 5.0 0.2 - - - -
257D HIS 3.7 0.5 - - - +
258D TYR* 3.3 6.6 - - - -
259D GLN 2.9 31.4 + - - +
261D PHE* 3.8 12.1 - - + -
289D TRP* 3.9 4.0 - - + -
290D CYS* 1.3 72.2 - - - +
292D VAL* 1.3 59.4 + - - +
293D TYR* 3.6 25.1 - + + +
298D SER* 3.5 36.1 + - - -
299D GLN 3.8 5.6 + - - -
300D ASP* 2.7 28.0 + - - +
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Residues in contact with VAL 292 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227D LEU* 4.1 9.5 - - + +
229D ILE* 3.7 16.4 - - + -
248D CYS* 3.7 31.6 - - - -
250D ALA* 3.5 29.2 - - + -
256D PRO* 3.7 10.5 - - + -
257D HIS 3.2 9.2 - - - +
258D TYR* 3.9 11.9 - - + -
290D CYS* 4.0 5.6 - - - +
291D HIS* 1.3 77.6 - - - +
293D TYR* 1.3 63.9 + - - +
298D SER* 3.2 4.3 - - - -
299D GLN 2.9 37.7 + - - +
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Residues in contact with TYR 293 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293A TYR* 3.9 31.6 - + + -
294A ASN 4.0 9.9 - - - +
295A ASP* 3.7 29.6 - - + +
227D LEU* 3.6 7.0 - - - -
257D HIS* 2.8 76.0 + + + +
258D TYR 4.1 11.8 + - - -
291D HIS* 3.6 24.9 - + - +
292D VAL* 1.3 79.5 - - - +
294D ASN* 1.3 65.6 + - - +
297D ASP 3.4 6.5 - - - +
298D SER* 3.6 16.8 - - - -
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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