Contacts of the strand formed by residues 298 - 305 (chain D) in PDB entry 5U03
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 298 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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296D LEU 4.0 0.2 + - - -
297D GLU* 1.3 75.2 - - - +
299D CYS* 1.4 61.1 + - - +
300D SER* 3.9 0.3 + - - -
331D LYS* 3.3 26.4 - - + +
332D LEU 3.8 7.4 - - - +
333D GLU* 3.6 41.7 - - + +
365D HIS* 3.4 17.7 + - - -
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Residues in contact with CYS 299 (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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297D GLU* 3.7 23.1 - - - -
298D THR* 1.4 72.2 - - - +
300D SER* 1.3 60.4 + - - +
330D HIS* 4.2 5.8 - - - -
331D LYS 2.9 13.9 + - - +
332D LEU* 3.4 10.7 - - + +
333D GLU 2.8 20.9 + - - -
365D HIS* 3.7 18.6 - - + -
544D LEU* 4.1 19.5 - - + -
547D SER* 5.1 2.0 - - - -
548D VAL* 3.5 35.4 - - + -
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Residues in contact with SER 300 (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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298D THR 5.1 0.4 - - - -
299D CYS* 1.3 75.4 - - - +
301D ILE* 1.3 61.9 + - - +
332D LEU* 5.3 0.2 - - - -
333D GLU* 3.3 32.8 - - - -
335D LYS* 3.6 16.5 - - - -
363D SER 3.6 2.9 + - - -
364D ALA* 3.3 16.1 - - - -
365D HIS* 2.8 51.4 + - - +
366D GLY 3.3 2.8 + - - -
547D SER* 5.1 1.0 + - - -
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Residues in contact with ILE 301 (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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300D SER* 1.3 74.5 - - - +
302D ALA* 1.3 64.5 + - - +
303D LEU* 3.4 3.7 + - + +
321D LEU* 4.1 23.8 - - + -
332D LEU* 4.5 6.7 - - + -
333D GLU 3.0 4.1 + - - +
334D ILE* 3.5 35.4 - - + -
335D LYS* 2.9 27.2 + - - +
364D ALA* 4.1 2.5 - - - -
366D GLY* 3.3 15.9 - - - +
367D VAL 4.2 5.2 - - - -
368D LEU* 3.8 19.3 - - + +
543D LEU* 3.6 31.4 - - + -
547D SER* 5.7 1.8 - - - +
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Residues in contact with ALA 302 (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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301D ILE* 1.3 73.2 - - - +
303D LEU* 1.3 60.9 + - - +
304D VAL* 3.3 5.5 + - + +
335D LYS* 4.2 7.0 - - + -
337D ILE* 3.9 15.3 - - + -
361D LEU* 3.6 31.6 - - + -
364D ALA* 3.7 14.1 - - + +
366D GLY 2.9 9.5 + - - -
367D VAL* 3.5 6.2 - - + -
368D LEU 2.8 27.1 + - - +
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Residues in contact with LEU 303 (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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301D ILE* 3.4 4.9 + - + +
302D ALA* 1.3 70.5 - - - +
304D VAL* 1.3 58.0 + - - +
308D THR* 3.4 13.4 - - + +
314D TYR* 3.6 44.0 - - + -
317D VAL* 5.6 1.1 - - + -
318D ILE* 5.6 1.1 - - + -
334D ILE* 4.5 9.6 - - + -
335D LYS 3.0 19.4 + - - +
336D TYR* 3.9 24.5 - - + -
337D ILE* 2.9 29.8 + - - +
368D LEU* 3.8 20.6 - - + -
370D PRO* 3.8 32.3 - - + -
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Residues in contact with VAL 304 (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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302D ALA* 3.7 22.7 - - + +
303D LEU* 1.3 76.9 - - - +
305D GLY* 1.3 62.7 + - - +
308D THR* 3.5 1.8 - - - -
337D ILE* 3.4 7.6 - - + +
339D SER* 3.5 22.7 - - - -
342D LEU* 3.9 19.5 - - + -
361D LEU* 4.2 13.7 - - + -
367D VAL* 5.1 2.9 - - + -
368D LEU 3.0 11.0 + - - +
369D VAL* 4.0 16.5 - - + +
370D PRO* 3.4 22.1 - - - +
381D LYS* 4.5 8.7 - - + -
384D ALA* 4.2 15.7 - - + -
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Residues in contact with GLY 305 (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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304D VAL* 1.3 78.3 - - - +
306D LYS* 1.3 57.6 + - - -
308D THR* 2.9 18.5 + - - -
314D TYR* 4.7 2.0 - - - -
337D ILE 3.2 5.9 + - - -
338D ASP* 3.3 10.9 - - - +
339D SER* 2.8 28.2 + - - -
370D PRO* 5.4 1.6 - - - -
381D LYS* 3.8 15.7 - - - -
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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