Contacts of the strand formed by residues 302 - 306 (chain B) in PDB entry 2BT4
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 VAL 302 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276B ILE* 3.2 21.3 - - + +
278B ILE* 4.3 12.6 - - + -
294B LEU* 4.2 34.8 - - + -
297B CYS* 5.1 1.8 - - + -
300B LEU* 3.7 13.5 - - + +
301B PRO* 1.3 80.7 - - - +
303B VAL* 1.3 65.4 + - - +
325B ARG* 3.8 21.1 - - - +
326B ALA* 3.6 15.0 - - + -
327B ASP* 2.7 40.6 + - - +
328B GLY 3.3 4.3 + - - -
348B LEU* 5.6 0.2 - - - +
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Residues in contact with VAL 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B ILE 2.8 11.7 + - - +
277B VAL* 3.3 5.8 - - + +
278B ILE* 2.8 32.1 + - - +
302B VAL* 1.3 81.8 - - - +
304B GLU* 1.3 67.8 + - - +
305B VAL* 4.3 5.6 - - + -
327B ASP* 5.6 1.3 - - + -
328B GLY* 3.4 17.7 - - - +
330B VAL* 4.5 10.5 - - + -
341B GLY* 3.9 24.0 - - - +
344B ARG* 4.0 28.7 - - + -
345B ILE* 3.9 17.0 - - + -
348B LEU* 5.9 1.3 - - + -
1333G CYS* 5.1 2.5 - - - -
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Residues in contact with GLU 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B ILE* 3.3 11.7 - - - +
280B PRO* 4.1 5.1 - - + +
303B VAL* 1.3 74.7 - - - +
305B VAL* 1.3 59.5 + - - +
306B HIS* 2.7 33.4 + - + +
320B SER* 2.7 22.0 + - - -
322B VAL* 3.5 19.0 - - + +
323B SER* 2.4 39.4 + - - -
326B ALA* 3.8 14.9 - - + +
328B GLY 2.9 8.0 + - - +
329B VAL* 3.4 8.0 - - + +
330B VAL 2.8 31.6 + - - +
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Residues in contact with VAL 305 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B VAL* 3.8 26.0 - - + -
278B ILE 2.8 10.0 + - - +
279B ASN* 3.0 33.1 - - + +
280B PRO* 4.1 0.5 - - - +
303B VAL* 4.3 8.7 - - + -
304B GLU* 1.3 79.5 - - - +
306B HIS* 1.3 76.6 + - - +
307B ILE 4.4 1.1 - - - +
330B VAL* 3.4 8.1 - - + +
334B GLY 4.9 1.6 - - - +
337B GLY* 3.5 41.7 - - - +
338B TYR* 3.9 23.3 - - + +
341B GLY* 4.7 0.2 - - - -
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Residues in contact with HIS 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B PRO* 4.0 9.2 - - + -
284B SER* 3.1 32.5 - - - -
285B HIS* 5.1 0.7 - + - -
304B GLU* 2.7 30.5 + - + -
305B VAL* 1.3 79.5 + - - +
307B ILE* 1.3 65.6 + - - +
308B SER 3.5 14.4 - - - +
310B ILE* 4.0 33.0 - - + +
320B SER* 4.6 0.8 + - - -
323B SER* 5.3 0.2 + - - -
329B VAL* 4.8 5.2 - - + -
330B VAL* 2.9 16.0 + - - +
331B ALA* 3.4 9.0 - - + -
332B GLY 3.0 17.0 + - - -
333B CYS 4.3 1.9 + - - -
334B GLY 4.7 0.5 - - - +
337B GLY* 6.0 0.2 - - - -
360B CA2 3.1 33.9 + - + +
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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
------------------------------------------------------------
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