Contacts of the strand formed by residues 275 - 279 (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 GLY 275 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209B ILE* 4.3 4.7 - - - -
210B MET* 3.1 24.1 + - - +
273B HIS* 3.4 6.4 + - - +
274B CYS* 1.3 81.7 - - - +
276B ILE* 1.3 67.4 + - - +
300B LEU* 3.8 7.3 - - - +
301B PRO 3.3 13.2 - - - -
345B ILE* 4.0 11.9 - - - -
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Residues in contact with ILE 276 (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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210B MET* 3.3 8.5 - - + +
212B LEU* 4.5 12.6 - - + -
266B ILE* 4.3 9.4 - - + -
269B ALA* 4.0 20.9 - - + -
275B GLY* 1.3 79.5 - - - +
277B VAL* 1.3 73.5 + - - +
278B ILE* 3.8 19.1 - - + -
294B LEU* 3.8 23.8 - - + -
297B CYS* 4.2 9.0 - - - -
300B LEU* 3.9 22.0 - - + -
301B PRO 2.9 9.2 + - - +
302B VAL* 3.2 10.5 - - + -
303B VAL 2.8 31.5 + - - -
345B ILE* 3.8 3.3 - - - +
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Residues in contact with VAL 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B ILE* 4.0 11.9 - - + -
210B MET 2.8 7.4 + - - +
211B ILE* 3.2 15.7 - - + +
212B LEU 2.8 26.0 + - - +
276B ILE* 1.3 77.0 - - - +
278B ILE* 1.3 61.3 + - - +
303B VAL* 3.3 5.2 - - + +
305B VAL* 3.8 27.1 - - + -
338B TYR* 4.4 21.3 - - + +
341B GLY* 3.7 35.0 - - - +
342B VAL* 3.9 6.7 - - + +
345B ILE* 3.9 11.7 - - + -
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Residues in contact with ILE 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B LEU* 3.3 29.6 - - + +
213B ASN 6.0 0.2 - - - -
262B LEU* 5.6 5.6 - - + -
266B ILE* 4.6 5.8 - - + -
276B ILE* 3.8 14.4 - - + -
277B VAL* 1.3 76.0 - - - +
279B ASN* 1.3 63.7 + - - +
280B PRO* 3.2 24.6 - - + +
290B ILE* 4.1 28.5 - - + -
294B LEU* 4.4 4.0 - - + -
302B VAL* 4.3 9.9 - - + -
303B VAL 2.8 18.1 + - - +
304B GLU* 3.3 7.7 - - - -
305B VAL* 2.8 25.4 + - - -
322B VAL* 4.2 17.3 - - + -
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Residues in contact with ASN 279 (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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212B LEU 2.8 8.5 + - - -
213B ASN* 3.6 3.7 - - - +
214B GLY 2.8 24.3 + - - -
217B LEU* 3.5 18.1 - - + +
277B VAL 4.3 0.4 - - - -
278B ILE* 1.3 74.1 - - - +
280B PRO* 1.3 61.6 - - - +
281B ALA* 3.1 5.7 + - - -
305B VAL 3.0 18.7 + - - +
306B HIS* 3.9 0.2 + - - -
307B ILE* 4.0 7.5 - - - +
338B TYR* 3.1 37.9 + - + +
360B CA2 2.9 41.8 + - - -
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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