Contacts of the helix formed by residues 250 - 260 (chain B) in PDB entry 2BTU
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 250 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249B GLY* 1.3 69.0 - - - -
251B GLY* 1.3 55.4 - - - +
254B GLU* 2.8 46.0 + - - +
295B ASN* 2.7 39.2 - - - +
296B ILE* 4.4 0.9 - - - -
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Residues in contact with GLY 251 (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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247B ILE* 4.1 10.3 - - - -
248B THR 3.7 1.9 + - - -
249B GLY 3.3 7.5 + - - -
250B GLY* 1.3 72.6 - - - +
252B PHE* 1.3 67.2 + - - -
253B ILE 3.3 0.2 - - - -
255B ASN* 2.8 30.0 + - - +
294B PHE 3.3 9.6 - - - -
295B ASN 3.5 6.5 - - - -
296B ILE 3.7 4.5 + - - +
297B PHE 4.0 15.7 - - - -
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Residues in contact with PHE 252 (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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247B ILE* 4.1 14.1 - - + -
251B GLY* 1.3 71.2 - - - -
253B ILE* 1.3 61.5 + - + +
256B ILE* 2.6 61.2 + - + +
257B PRO* 3.1 3.3 - - - +
268B ILE* 4.0 14.8 - - + -
273B TRP* 4.2 11.2 - + - -
294B PHE* 3.0 43.2 + + + +
297B PHE 4.8 0.9 - - - -
298B ASN 2.8 30.5 - - - -
301B ILE* 3.5 36.1 - - + -
329B ILE* 3.8 19.7 - - + -
338B VAL* 4.6 8.1 - - + -
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Residues in contact with ILE 253 (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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252B PHE* 1.3 74.4 - - + +
254B GLU* 1.3 68.0 + - - +
257B PRO* 2.8 34.5 - - + +
291B LYS 4.9 2.2 - - - +
294B PHE* 3.0 28.0 - - + +
295B ASN* 3.0 42.2 - - + +
337B GLY* 6.2 2.0 - - - -
338B VAL* 4.0 15.7 - - + +
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Residues in contact with GLU 254 (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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249B GLY* 4.9 0.7 - - - -
250B GLY* 2.8 54.5 + - - +
253B ILE* 1.3 87.8 - - - +
255B ASN* 1.3 58.8 + - - +
257B PRO* 4.3 1.0 - - - +
258B ARG* 2.8 34.5 + - + +
295B ASN* 3.5 9.8 + - - +
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Residues in contact with ASN 255 (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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245B ALA* 3.9 12.1 - - + +
246B HIS 3.6 21.9 - - - +
247B ILE* 4.0 11.4 - - + +
248B THR* 3.2 37.4 + - - +
249B GLY* 3.3 17.4 + - - +
251B GLY 2.8 23.8 + - - +
254B GLU* 1.3 79.0 - - - +
256B ILE* 1.3 62.8 + - - +
258B ARG* 2.8 29.5 - - - +
259B MET 3.6 2.3 + - - -
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Residues in contact with ILE 256 (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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178B LEU* 4.8 3.4 - - + -
245B ALA* 4.6 6.5 - - + -
247B ILE* 3.9 12.6 - - + -
252B PHE* 2.6 64.3 + - + +
255B ASN* 1.3 71.5 - - - +
257B PRO* 1.3 65.8 - - + +
259B MET* 3.0 30.5 + - + +
260B LEU* 3.3 12.3 - - + +
266B ALA* 3.7 28.5 - - + -
268B ILE* 4.5 14.1 - - + -
304B VAL* 4.4 17.3 - - + -
338B VAL* 4.6 6.3 - - + -
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Residues in contact with PRO 257 (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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252B PHE 3.1 5.6 - - - +
253B ILE* 2.8 36.1 - - + +
254B GLU 4.3 1.1 - - - +
255B ASN 3.7 0.2 - - - -
256B ILE* 1.3 89.8 - - + +
258B ARG* 1.3 54.6 - - - +
260B LEU* 2.7 47.7 + - + +
337B GLY* 4.6 15.0 - - - +
338B VAL* 3.9 16.4 - - + -
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Residues in contact with ARG 258 (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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254B GLU* 2.8 28.2 + - - +
255B ASN* 2.8 21.8 - - - +
257B PRO* 1.3 79.3 - - - +
259B MET* 1.3 57.4 + - - +
260B LEU 4.3 2.1 - - - +
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Residues in contact with MET 259 (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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169B GLY* 4.1 19.5 + - - +
172B ILE* 5.0 0.5 - - - +
178B LEU* 3.4 33.0 - - + -
243B GLY* 4.3 8.3 - - - -
244B MET 3.7 43.1 - - - +
245B ALA* 3.7 13.0 - - + -
255B ASN 3.6 0.2 + - - -
256B ILE* 3.0 18.4 + - + +
258B ARG* 1.3 79.4 - - - +
260B LEU* 1.3 83.1 - - + +
261B PRO* 3.6 4.7 - - - +
304B VAL* 3.9 15.7 - - + +
306B ALA* 4.7 7.6 - - + -
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Residues in contact with LEU 260 (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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172B ILE* 5.3 0.2 - - - -
178B LEU* 5.6 0.7 - - + -
256B ILE* 3.4 12.6 - - + +
257B PRO* 2.7 37.5 + - + +
258B ARG 4.3 2.4 - - - +
259B MET* 1.3 98.6 - - + +
261B PRO* 1.3 74.3 - - + +
264B ILE* 4.1 7.4 - - + +
265B GLY* 3.3 44.2 - - - +
266B ALA* 3.5 12.1 - - + +
332B THR* 5.2 5.8 - - - +
337B GLY 4.3 7.4 - - - +
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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