Contacts of the strand formed by residues 298 - 305 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296B LEU 4.0 0.2 + - - -
297B GLU* 1.3 76.0 - - - +
299B CYS* 1.4 60.2 + - - +
300B SER* 3.9 0.5 + - - -
331B LYS* 3.3 25.1 - - + +
332B LEU 3.8 8.7 - - - +
333B GLU* 3.6 42.0 - - + +
365B HIS* 3.4 18.2 + - - -
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Residues in contact with CYS 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297B GLU* 3.7 22.2 - - - -
298B THR* 1.4 73.9 - - - +
300B SER* 1.3 59.9 + - - +
330B HIS* 4.2 6.7 - - - -
331B LYS 2.9 13.7 + - - +
332B LEU* 3.4 10.7 - - + +
333B GLU 2.8 20.7 + - - -
365B HIS* 3.7 17.0 - - + -
544B LEU* 4.1 18.8 - - + -
547B SER* 5.1 2.9 - - - -
548B VAL* 3.5 35.9 - - - -
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Residues in contact with SER 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298B THR 5.1 0.7 - - - -
299B CYS* 1.3 76.9 - - - +
301B ILE* 1.3 60.8 + - - +
332B LEU* 5.3 0.4 - - - -
333B GLU* 3.3 32.3 - - - -
335B LYS* 3.6 15.9 - - - -
363B SER 3.6 2.6 + - - -
364B ALA* 3.3 16.6 - - - -
365B HIS* 2.8 51.2 + - - +
366B GLY 3.3 2.8 + - - -
547B SER* 5.1 0.9 + - - -
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Residues in contact with ILE 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300B SER* 1.3 76.7 - - - +
302B ALA* 1.3 63.4 + - - +
303B LEU* 3.4 4.0 + - + +
321B LEU* 4.1 25.4 - - + -
332B LEU* 4.5 6.7 - - + -
333B GLU 3.0 3.3 + - - +
334B ILE* 3.5 34.1 - - + -
335B LYS* 2.9 28.1 + - - +
364B ALA* 4.1 3.1 - - - -
366B GLY* 3.3 15.9 - - - +
367B VAL 4.2 4.9 - - - -
368B LEU* 3.8 18.8 - - + +
543B LEU* 3.6 31.4 - - + -
547B SER* 5.7 2.2 - - - +
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Residues in contact with ALA 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301B ILE* 1.3 73.4 - - - +
303B LEU* 1.3 59.7 + - - +
304B VAL* 3.3 6.1 + - + +
335B LYS* 4.2 6.5 - - + -
337B ILE* 3.9 16.2 - - + -
361B LEU* 3.6 31.4 - - + -
364B ALA* 3.7 15.6 - - + +
366B GLY 2.9 10.1 + - - -
367B VAL* 3.5 5.3 - - + -
368B LEU 2.8 27.4 + - - -
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Residues in contact with LEU 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301B ILE* 3.4 4.2 + - + +
302B ALA* 1.3 70.7 - - - +
304B VAL* 1.3 57.6 + - - +
308B THR* 3.4 13.6 - - + +
314B TYR* 3.6 43.1 - - + -
317B VAL* 5.6 1.1 - - + -
318B ILE* 5.6 0.9 - - + -
334B ILE* 4.5 10.3 - - + -
335B LYS 3.0 18.6 + - - +
336B TYR* 3.9 24.2 - - + -
337B ILE* 2.9 30.0 + - - +
368B LEU* 3.8 20.6 - - + -
370B PRO* 3.8 31.4 - - + -
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Residues in contact with VAL 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302B ALA* 3.7 22.4 - - + +
303B LEU* 1.3 77.0 - - - +
305B GLY* 1.3 60.8 + - - +
308B THR* 3.5 1.8 - - - -
337B ILE* 3.4 8.5 - - + +
339B SER* 3.5 23.3 - - - -
342B LEU* 3.9 18.6 - - + -
361B LEU* 4.2 13.9 - - + -
367B VAL* 5.1 3.1 - - + -
368B LEU 3.0 12.1 + - - +
369B VAL* 4.0 16.1 - - + +
370B PRO* 3.4 21.7 - - - +
381B LYS* 4.5 8.9 - - + -
384B ALA* 4.2 16.4 - - + -
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Residues in contact with GLY 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304B VAL* 1.3 79.2 - - - +
306B LYS* 1.3 58.5 + - - -
308B THR* 2.9 18.3 + - - -
314B TYR* 4.7 2.2 - - - -
337B ILE 3.2 5.7 + - - -
338B ASP* 3.3 10.7 - - - +
339B SER* 2.8 28.7 + - - -
370B PRO* 5.4 1.1 - - - -
381B LYS* 3.8 14.6 - - - -
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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