Contacts of the helix formed by residues 253 - 265 (chain C) in PDB entry 2BHT
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 253 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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241C MET* 3.3 14.1 - - - +
252C CYS* 1.3 78.7 - - - +
254C VAL* 1.3 65.0 + - - -
255C SER 3.5 1.8 - - - -
256C SER* 3.3 12.6 + - - -
257C GLY 3.4 4.2 + - - -
281C ASP* 3.5 12.9 + - - -
283C GLY* 3.9 2.6 - - - -
286C TYR* 3.5 30.7 - - - -
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Residues in contact with VAL 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206C ILE* 4.1 17.9 - - + -
207C PRO* 4.0 15.9 - - + -
234C GLN* 5.2 0.2 - - + -
237C ALA* 4.0 16.3 - - + +
238C GLU* 3.8 27.6 - - + +
241C MET* 3.9 20.0 - - + -
253C GLY* 1.3 66.6 - - - -
255C SER* 1.3 58.7 + - - +
256C SER 3.0 4.5 - - - -
257C GLY* 2.9 19.2 + - - -
258C GLY* 3.0 10.4 + - - -
286C TYR* 3.6 29.3 - - + -
291C VAL* 4.4 9.9 - - + -
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Residues in contact with SER 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172C SER* 3.3 11.7 + - - -
206C ILE* 4.0 10.1 - - - +
207C PRO* 3.8 12.7 + - - +
209C ILE* 3.9 18.4 - - - -
237C ALA* 5.9 0.2 - - - -
254C VAL* 1.3 79.4 - - - +
256C SER* 1.3 59.8 + - - +
258C GLY* 3.7 2.9 - - - +
259C ALA* 2.9 24.1 + - - +
280C CYS* 3.4 15.4 - - - +
281C ASP* 5.1 1.0 + - - -
286C TYR* 4.9 1.7 + - - -
320C PLP 3.0 33.6 + - - +
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Residues in contact with SER 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244C LEU* 4.6 2.0 - - - -
252C CYS* 3.4 25.5 - - - +
253C GLY 3.3 11.6 + - - -
254C VAL 3.0 0.6 - - - -
255C SER* 1.3 76.4 + - - +
257C GLY* 1.3 66.7 + - - +
259C ALA* 3.2 9.3 + - - +
260C VAL* 2.9 26.6 + - - +
278C ILE 4.8 0.9 - - - -
279C ILE* 3.7 11.8 - - - +
280C CYS* 2.9 28.7 + - - +
281C ASP* 3.7 10.2 + - - -
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Residues in contact with GLY 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237C ALA 3.5 16.4 - - - -
240C THR* 3.1 16.9 - - - +
241C MET* 3.9 8.1 - - - -
244C LEU* 4.0 8.2 - - - +
253C GLY 3.4 5.5 + - - -
254C VAL 2.9 8.0 + - - -
256C SER* 1.3 77.2 - - - +
258C GLY* 1.3 52.2 + - - +
260C VAL 2.8 1.9 + - - -
261C ALA* 2.5 35.9 + - - +
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Residues in contact with GLY 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172C SER* 4.2 1.1 - - - -
198C LEU* 2.8 15.0 - - - +
232C ILE* 3.8 18.7 - - - +
237C ALA* 3.8 19.9 - - - +
254C VAL 3.0 11.2 + - - -
255C SER* 3.8 4.9 - - - -
257C GLY* 1.3 75.5 - - - +
259C ALA* 1.3 52.7 + - - +
261C ALA* 4.3 0.4 - - - -
262C GLY* 2.6 29.3 + - - -
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Residues in contact with ALA 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170C VAL* 3.6 11.5 - - + +
171C SER 5.4 0.4 - - - +
172C SER* 3.6 12.4 + - - +
198C LEU* 3.3 12.4 - - - +
255C SER 2.9 15.7 + - - +
256C SER 3.3 9.4 - - - +
258C GLY* 1.3 74.7 - - - +
260C VAL* 1.3 59.6 + - + +
262C GLY* 3.6 1.7 - - - -
263C ALA* 3.1 26.7 + - - +
277C ALA* 4.2 10.8 - - + +
278C ILE 3.7 24.0 - - - +
280C CYS* 5.6 0.2 - - - -
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Residues in contact with VAL 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C LEU* 5.0 7.4 - - + -
19C MET* 5.3 4.3 - - - -
27C VAL* 5.3 3.1 - - + -
29C LEU* 3.3 34.5 - - + -
240C THR* 3.3 18.2 - - + -
244C LEU* 4.2 20.0 - - + -
256C SER 2.9 15.4 + - - +
257C GLY 2.8 4.3 + - - +
259C ALA* 1.3 75.8 - - - +
261C ALA* 1.3 56.2 + - - +
262C GLY 3.1 0.9 - - - -
263C ALA* 2.7 23.1 + - - +
264C LEU* 2.8 37.1 + - + +
277C ALA* 4.8 2.5 - - + -
279C ILE* 4.0 9.2 - - + -
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Residues in contact with ALA 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232C ILE* 4.6 4.5 - - + -
236C ASP* 4.1 12.1 - - - +
240C THR* 3.2 28.9 - - - +
257C GLY 2.5 19.6 + - - +
258C GLY* 4.0 5.4 - - - +
260C VAL* 1.3 74.5 - - - +
262C GLY* 1.3 63.8 + - - +
263C ALA 3.1 0.5 + - - -
264C LEU* 3.5 7.8 + - - +
265C ARG* 3.3 35.5 + - - +
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Residues in contact with GLY 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170C VAL* 5.0 1.3 - - - -
198C LEU* 3.7 21.1 - - - -
230C LEU* 4.6 2.4 - - - +
232C ILE* 4.8 0.2 - - - +
258C GLY 2.6 24.9 + - - -
259C ALA 3.6 3.4 - - - -
260C VAL 3.1 0.2 - - - -
261C ALA* 1.3 73.5 - - - +
263C ALA* 1.3 55.9 + - - +
265C ARG* 2.9 24.4 - - - +
266C VAL* 2.8 23.2 - - - +
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Residues in contact with ALA 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C VAL* 3.9 11.6 - - + +
170C VAL* 3.9 22.2 - - + -
259C ALA 3.1 15.1 + - - +
260C VAL* 2.7 14.9 + - - +
262C GLY* 1.3 71.6 - - - +
264C LEU* 1.3 60.9 + - - +
265C ARG 3.2 0.2 - - - -
266C VAL* 3.6 9.3 - - - -
267C ALA* 3.1 25.8 + - - +
275C VAL* 4.0 13.9 - - + +
277C ALA* 4.5 8.3 - - + -
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Residues in contact with LEU 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C LEU* 4.2 9.0 - - + -
19C MET* 5.1 8.5 - - + -
20C GLY* 3.4 39.7 - - - +
21C PRO* 4.6 0.7 - - + -
27C VAL* 4.0 17.9 - - + -
240C THR* 5.0 2.2 - - + +
260C VAL* 2.8 53.9 + - + +
261C ALA* 4.0 7.9 - - - +
263C ALA* 1.3 73.6 - - - +
265C ARG* 1.3 57.6 + - - +
266C VAL 3.0 9.0 + - - -
267C ALA* 3.4 5.4 + - - +
268C LYS* 3.3 40.0 + - - +
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Residues in contact with ARG 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198C LEU* 5.3 0.4 - - - +
201C GLU* 4.9 4.2 + - - -
230C LEU* 4.6 18.3 - - + +
231C ASP 2.7 29.9 + - - -
232C ILE* 3.8 27.5 - - - +
236C ASP* 4.9 7.9 + - - +
261C ALA* 3.3 22.9 + - - +
262C GLY* 2.9 22.7 + - - +
264C LEU* 1.3 78.9 - - - +
266C VAL* 1.3 59.7 + - + +
268C LYS* 4.8 6.4 - - - +
269C ALA* 4.1 12.5 + - - +
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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