Contacts of the strand formed by residues 290 - 296 (chain D) in PDB entry 5DO7
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 290 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89D GLN* 3.1 40.8 - - + +
286D MET* 2.8 30.4 - - - +
287D THR 3.1 14.8 + - - -
289D GLY* 1.3 78.6 - - - +
291D PRO* 1.4 61.6 - - - +
292D ILE* 3.7 10.4 + - - +
336D LEU* 4.6 6.6 + - - +
337D ALA* 4.5 9.6 - - + +
340D GLU* 4.2 21.1 - - + -
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Residues in contact with PRO 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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89D GLN 3.4 17.5 - - - +
90D ASN 4.0 14.8 - - - +
91D LEU* 4.2 16.6 - - + -
284D LEU* 4.1 20.2 - - + -
285D LEU 3.6 6.1 - - - +
286D MET* 3.8 4.4 - - + -
289D GLY 3.9 2.2 - - - +
290D THR* 1.4 84.0 - - - +
292D ILE* 1.3 67.1 + - - +
293D TYR* 4.8 2.9 - - - +
294D LEU* 5.5 1.3 - - + +
340D GLU* 3.6 29.5 - - + +
343D GLN* 5.7 2.4 - - - +
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Residues in contact with ILE 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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285D LEU* 2.8 25.8 + - + +
287D THR* 3.8 30.5 - - - +
290D THR* 3.7 13.2 + - - +
291D PRO* 1.3 77.7 - - - +
293D TYR* 1.3 64.9 + - - +
303D TYR* 4.8 1.7 + - - -
304D PHE* 3.5 25.0 - - + -
321D TYR* 3.5 52.9 - - + +
336D LEU* 4.9 11.0 - - + +
339D ARG* 4.3 12.5 - - + +
340D GLU* 4.7 2.9 - - - +
343D GLN* 4.1 13.7 - - - +
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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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284D LEU* 4.2 2.2 - - - -
285D LEU* 3.4 22.3 + - - +
291D PRO* 4.5 2.0 - - - -
292D ILE* 1.3 85.1 - - - +
294D LEU* 1.3 83.1 + - + +
295D GLY* 3.7 2.9 + - - -
299D HIS* 5.3 0.2 - - + -
300D MET* 2.8 41.3 - - + +
303D TYR* 3.8 26.5 - + + -
304D PHE* 4.1 9.6 - - + -
343D GLN* 2.7 51.1 - - + -
346D ALA 6.1 0.4 - - - -
347D ALA* 5.5 1.8 - - + -
354D ARG 1.7 39.2 + - - -
355D ASP 2.1 34.6 - - - -
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Residues in contact with LEU 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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92D SER 4.0 13.7 - - - +
93D PHE* 5.0 8.7 - - + -
94D LYS 5.0 1.1 - - - +
101D LEU* 4.1 15.9 - - + -
282D LEU* 5.1 4.0 - - + -
283D VAL 3.6 7.9 - - - +
284D LEU* 3.6 39.6 - - + +
291D PRO* 5.5 1.6 - - + +
293D TYR* 1.3 120.2 - - + +
295D GLY* 1.3 52.2 + - - +
300D MET* 3.4 0.4 - - - -
343D GLN* 4.0 11.7 - - - +
352D LYS 2.9 27.1 - - - +
353D VAL* 3.8 25.1 - - + -
354D ARG 4.7 0.7 - - - -
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Residues in contact with GLY 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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282D LEU* 3.6 12.1 - - - +
283D VAL* 2.8 36.4 + - - +
293D TYR* 3.7 9.6 - - - -
294D LEU* 1.3 77.9 - - - +
296D ALA* 1.3 66.1 + - - -
299D HIS* 5.1 0.4 - - - -
300D MET* 3.3 10.2 - - - +
354D ARG* 4.2 7.9 - - - -
355D ASP 4.9 0.2 - - - -
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Residues in contact with ALA 296 (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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281D ASP 3.4 17.5 - - - +
282D LEU* 3.8 9.3 - - + +
283D VAL* 4.0 1.3 - - - -
295D GLY* 1.3 76.1 - - - -
297D ALA* 1.3 58.8 - - + +
298D GLN* 3.4 6.3 - - + +
299D HIS* 3.1 28.5 + - + +
300D MET* 2.8 34.0 + - - +
354D ARG* 4.7 2.9 - - - +
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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