Contacts of the strand formed by residues 296 - 299 (chain B) in PDB entry 2E4Y
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 296 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210B TRP* 4.9 3.1 - - + -
270B ARG* 2.8 21.3 + - - +
271B VAL* 3.6 18.8 - - + +
272B VAL 3.1 20.7 + - - -
295B PHE* 1.3 70.7 - - - +
297B TRP* 1.3 65.4 + - - +
298B VAL* 3.4 4.2 + - + +
319B GLY 3.7 21.8 - - - +
320B ALA* 5.0 1.6 - - - -
321B ILE* 5.5 3.1 - - + +
499B TRP* 4.1 15.0 - - + -
500B SER* 5.5 4.9 - - - +
505B PRO* 3.6 37.7 - - + +
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Residues in contact with TRP 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B LEU* 4.1 10.1 - - + -
272B VAL* 3.3 39.3 - - + -
274B LEU* 3.8 15.3 - - + -
284B LEU* 3.6 22.9 - - + -
285B ILE* 3.2 28.8 - - + +
288B ALA* 4.0 13.9 - - + -
295B PHE* 3.6 42.0 + + + +
296B THR* 1.3 70.6 - - - +
298B VAL* 1.3 55.9 + - - +
299B ALA* 3.8 0.7 - - + -
303B TRP* 4.0 15.0 - + + -
316B VAL* 3.0 26.8 + - + -
317B ALA* 3.7 19.5 - - - -
320B ALA* 3.2 14.1 - - + +
321B ILE* 2.5 37.1 + - - +
322B THR* 4.8 0.4 - - + +
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Residues in contact with VAL 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B MET* 3.6 24.7 - - + +
204B ILE* 4.6 6.3 - - + -
205B LEU* 3.9 24.7 - - + -
210B TRP* 4.8 5.2 - - + -
271B VAL* 4.4 9.2 - - + -
272B VAL 2.9 13.0 + - - +
273B VAL* 3.7 22.0 - - + -
274B LEU* 2.5 33.4 + - - +
296B THR* 3.4 3.8 + - + +
297B TRP* 1.3 72.8 - - - +
299B ALA* 1.3 53.1 + - - +
321B ILE* 2.9 26.7 - - + +
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Residues in contact with ALA 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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201B MET* 3.2 9.4 - - - +
274B LEU* 3.2 20.4 - - + -
281B SER* 5.7 0.4 - - - +
297B TRP 3.8 0.2 - - - -
298B VAL* 1.3 73.9 - - - +
300B SER* 1.3 60.8 + - - +
303B TRP* 3.6 27.4 - - + -
321B ILE 2.8 10.5 + - - -
322B THR* 3.2 21.8 - - + -
323B LEU* 2.9 28.2 + - - +
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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
------------------------------------------------------------
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