Contacts of the strand formed by residues 283 - 289 (chain D) in PDB entry 5U0A
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 LEU 283 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7D HIS* 4.9 2.7 - - + +
8D ALA* 3.0 7.6 - - - +
9D ILE* 2.9 45.8 + - + -
281D PRO* 4.2 0.7 - - - +
282D ASP* 1.3 80.4 - - - +
284D VAL* 1.3 83.2 + - - +
285D HIS* 4.2 12.3 - - + +
315D CYS* 3.4 39.7 - - + +
318D LEU* 4.9 8.5 - - + -
337D TYR* 4.6 3.1 - - + -
338D ALA 3.6 2.9 - - - -
339D THR* 3.9 13.9 - - + +
341D GLU* 4.3 2.0 - - - +
346D LEU* 4.0 17.0 - - + -
349D LEU* 4.5 12.1 - - + -
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Residues in contact with VAL 284 (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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6D ILE* 4.8 5.8 - - + -
7D HIS 3.1 7.4 - - - +
8D ALA* 4.3 1.8 - - + -
264D LEU* 3.4 38.4 - - + -
281D PRO* 4.1 7.6 - - + -
283D LEU* 1.3 82.8 - - - +
285D HIS* 1.3 61.2 + - - +
286D ILE* 5.1 3.4 - - + -
337D TYR* 3.2 5.2 - - - +
338D ALA 3.0 31.4 + - - +
356D TYR* 3.5 39.9 - - + -
359D LEU* 3.7 21.5 - - + -
360D ILE* 6.2 0.2 - - + -
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Residues in contact with HIS 285 (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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5D ASP 3.8 0.3 - - - +
6D ILE* 3.4 2.3 - - - +
7D HIS* 2.9 46.0 + - + +
283D LEU* 4.2 10.3 - - + -
284D VAL* 1.3 75.3 - - - +
286D ILE* 1.3 61.2 + - - +
287D ALA* 4.0 13.0 + - + +
296D PHE* 3.9 22.6 - + - -
318D LEU* 5.1 1.5 - - + +
322D ALA* 5.5 0.7 - - + -
335D ARG* 3.6 27.4 - - - +
336D GLY 3.0 28.7 - - - -
337D TYR* 3.9 7.4 - - + -
349D LEU* 2.8 50.1 + - + +
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Residues in contact with ILE 286 (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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4D VAL* 3.7 28.5 - - + -
5D ASP 3.4 7.4 - - - +
6D ILE* 3.9 26.7 - - + -
260D LEU* 3.8 23.8 - - + -
284D VAL* 4.2 2.9 - - + -
285D HIS* 1.3 76.4 - - - +
287D ALA* 1.3 63.1 - - - +
335D ARG* 3.7 2.3 - - - -
336D GLY 3.2 27.2 + - - +
359D LEU* 3.5 28.7 - - + +
360D ILE* 3.9 17.0 - - + -
363D MET* 3.7 21.9 - - + +
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Residues in contact with ALA 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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3D PHE 3.6 3.3 - - - +
5D ASP* 2.6 40.8 + - - +
7D HIS* 5.5 2.9 - - + -
285D HIS* 4.0 15.1 - - + +
286D ILE* 1.3 73.1 - - - +
288D VAL* 1.3 60.8 + - - +
289D ARG* 3.0 22.6 + - + +
296D PHE* 6.3 0.4 - - + -
333D ALA* 5.4 0.7 - - + -
334D ILE 3.4 4.9 - - - -
335D ARG* 3.6 23.3 - - + -
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Residues in contact with VAL 288 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2D THR* 4.0 26.0 - - + -
3D PHE 3.8 5.6 - - - +
4D VAL* 4.0 22.9 - - + +
286D ILE 4.0 0.4 - - - -
287D ALA* 1.3 68.8 - - - +
289D ARG* 1.3 57.2 + - - +
290D PHE* 4.2 16.5 + - + -
333D ALA* 3.5 3.2 - - - -
334D ILE* 2.8 41.2 + - + +
363D MET* 3.8 37.5 - - + +
366D ALA* 4.4 6.3 - - + +
367D ALA* 4.4 12.6 - - + +
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Residues in contact with ARG 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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2D THR* 3.8 1.2 - - - +
3D PHE* 2.8 41.6 + - + +
5D ASP* 4.1 17.3 - - - +
287D ALA* 3.2 24.4 - - + +
288D VAL* 1.3 72.7 - - - +
290D PHE* 1.3 63.8 + - - +
291D ASP* 2.5 36.0 + - - +
292D ARG 2.9 26.7 + - - +
293D PRO* 4.6 0.7 - - + -
294D ILE* 3.4 36.0 - - - +
296D PHE* 6.0 1.2 - - - -
329D TRP* 5.3 6.9 + - - +
331D ASP* 4.2 12.5 - - - +
333D ALA* 4.3 21.4 - - + +
335D ARG* 4.7 7.9 - - - +
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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