Contacts of the strand formed by residues 290 - 295 (chain D) in PDB entry 2W8B
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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261D ALA* 3.9 0.9 - - - +
268D LEU* 2.7 27.3 + - - +
269D ASN* 3.2 28.6 + - - +
270D LEU* 3.7 6.2 - - + +
284D THR* 3.8 17.2 - - - +
286D GLY* 4.5 4.2 - - - +
288D SER* 3.2 30.1 + - - -
289D ASN* 1.3 71.6 - - - +
291D THR* 1.3 62.8 + - - +
304D PHE* 3.5 20.9 - - + -
305D THR 3.2 4.7 - - - -
306D SER* 2.7 32.2 + - - -
308D GLN* 5.8 0.3 + - - -
324D PRO* 5.9 0.4 - - - +
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Residues in contact with THR 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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248D ALA* 3.4 10.4 - - - +
261D ALA* 3.3 24.6 - - - +
268D LEU* 4.0 20.0 - - + +
270D LEU* 3.9 5.6 - - - +
290D ASN* 1.3 75.8 - - - +
292D GLU* 1.4 75.2 + - + +
293D PRO* 3.3 3.3 - - - -
304D PHE* 3.5 3.3 - - - +
305D THR* 2.8 37.4 + - - +
116E GLU* 3.9 8.9 + - - +
117E TYR* 3.9 37.5 - - + -
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Residues in contact with GLU 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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248D ALA* 3.7 5.3 - - - +
291D THR* 1.4 86.2 + - + +
293D PRO* 1.3 72.3 - - - +
294D THR* 3.7 1.0 + - - +
303D ALA 3.9 0.3 - - - +
304D PHE* 3.7 10.4 - - - -
305D THR* 2.6 36.7 + - - +
335D GLN* 4.0 0.3 - - - +
336D ASP* 3.2 33.0 + - - +
337D ALA 4.5 10.8 + - - +
114E THR* 2.7 32.7 + - - -
115E PRO* 4.9 0.3 - - - +
116E GLU* 3.4 23.5 + - + +
117E TYR* 3.0 18.7 + - - +
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Residues in contact with PRO 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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248D ALA* 3.3 29.4 - - + +
249D PRO 4.9 0.9 - - - +
250D ALA* 3.4 19.2 - - + +
259D ALA* 4.1 16.6 - - + +
260D PHE* 4.1 19.3 - - - +
270D LEU* 4.0 22.2 - - + -
291D THR* 3.3 4.9 - - - -
292D GLU* 1.3 94.0 - - - +
294D THR* 1.3 61.3 + - - +
302D LEU* 4.3 11.0 - - + -
303D ALA 3.4 9.2 - - - +
304D PHE* 4.0 2.9 - - + -
337D ALA 5.1 0.3 - - - +
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Residues in contact with THR 294 (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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250D ALA* 4.5 5.6 - - - -
292D GLU 4.6 0.9 - - - +
293D PRO* 1.3 76.4 - - - +
295D TRP* 1.3 62.3 + - - +
302D LEU* 3.4 7.3 - - - -
303D ALA* 2.9 55.6 + - + +
337D ALA* 3.4 34.3 - - + +
338D ASP* 3.4 11.2 + - - -
339D VAL* 3.0 27.9 + - + +
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Residues in contact with TRP 295 (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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250D ALA* 2.9 33.3 + - + +
251D PHE 3.1 20.2 - - - +
252D SER* 3.3 19.9 - - - +
253D PRO* 3.5 18.8 - - + +
257D LYS* 3.9 29.8 - - + -
259D ALA* 3.8 21.7 - - + +
272D VAL* 4.4 5.6 - - + -
294D THR* 1.3 75.8 + - - +
296D PHE* 1.3 63.0 + - - +
297D PRO* 4.6 0.3 - - - +
299D SER* 3.4 37.9 - - - -
300D GLN* 3.8 2.9 - - - -
301D ASN 3.8 9.9 - - - -
302D LEU* 3.3 18.2 - - + -
319D ILE* 4.0 25.8 - - + -
339D VAL* 3.5 21.4 - - - +
340D SER 5.0 0.9 - - - +
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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