Contacts of the helix formed by residues 253 - 270 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A MET* 3.4 2.6 - - - +
252A CYS* 1.3 95.4 - - - +
254A VAL* 1.3 65.6 + - - -
255A SER 3.2 3.1 - - - -
256A SER* 3.1 14.9 + - - -
257A GLY 3.2 0.9 + - - -
281A ASP* 4.0 3.9 + - - -
282A ARG* 2.9 19.4 + - - +
286A TYR* 3.5 20.4 - - - -
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Residues in contact with VAL 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A ILE* 3.3 28.7 - - + -
207A PRO* 4.2 12.1 - - + -
237A ALA* 3.4 25.1 - - + +
238A GLU* 4.5 8.1 - - + +
241A MET* 3.2 26.6 - - + -
253A GLY* 1.3 67.4 - - - -
255A SER* 1.3 59.8 + - - +
256A SER 3.0 2.0 - - - -
258A GLY* 2.8 32.6 + - - -
286A TYR* 4.1 22.9 - - + -
291A VAL* 4.5 12.6 - - + -
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Residues in contact with SER 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A SER* 3.1 25.8 + - - -
206A ILE* 4.2 7.1 - - - +
207A PRO 3.6 15.2 + - - -
209A ILE* 3.6 15.6 - - - +
253A GLY 4.9 0.9 - - - -
254A VAL* 1.3 85.2 - - - +
256A SER* 1.3 58.2 + - - +
258A GLY* 3.6 1.3 + - - -
259A ALA* 3.2 13.5 + - - +
278A ILE 4.9 0.2 - - - +
280A CYS* 4.0 4.6 - - - -
281A ASP* 5.4 0.4 - - - -
286A TYR* 5.2 2.4 + - - -
320A PLP 3.0 41.2 + - - -
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Residues in contact with SER 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A LEU* 5.5 0.4 - - - -
252A CYS* 3.6 6.7 - - - -
253A GLY* 3.4 16.5 + - - -
254A VAL 3.0 1.0 - - - -
255A SER* 1.3 74.8 - - - +
257A GLY* 1.3 58.3 + - - +
258A GLY 3.0 4.7 - - - -
259A ALA* 3.2 2.8 + - - +
260A VAL* 3.0 33.0 + - - +
278A ILE 4.3 9.5 - - - +
279A ILE* 3.0 45.7 - - - +
280A CYS* 3.3 11.5 + - - +
281A ASP* 4.2 3.5 + - - -
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Residues in contact with GLY 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A ASP 4.0 0.5 - - - +
237A ALA 3.7 6.1 - - - -
240A THR* 2.7 33.1 - - - +
241A MET* 3.4 28.9 - - - -
244A LEU* 3.9 11.4 - - - -
252A CYS* 3.5 1.6 - - - -
253A GLY 3.2 8.3 + - - -
254A VAL 3.3 1.5 + - - -
256A SER* 1.3 77.4 - - - +
258A GLY* 1.3 59.8 + - - +
260A VAL 4.0 0.4 - - - -
261A ALA* 3.6 1.6 + - - +
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Residues in contact with GLY 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A SER* 4.9 0.9 - - - -
198A LEU* 4.4 3.4 - - - -
232A ILE* 4.1 12.4 - - - +
237A ALA* 3.8 17.2 + - - -
254A VAL 2.8 15.8 + - - -
255A SER* 3.8 2.7 - - - -
257A GLY* 1.3 74.5 - - - +
259A ALA* 1.3 56.6 + - - +
260A VAL 3.0 1.6 - - - -
261A ALA* 2.5 37.0 + - - +
262A GLY 3.3 3.1 + - - -
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Residues in contact with ALA 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A VAL* 3.7 14.7 - - - +
172A SER* 3.6 25.1 + - - +
198A LEU* 3.3 16.8 - - + -
255A SER 3.2 10.5 + - - +
256A SER 3.2 2.2 + - - +
258A GLY* 1.3 74.0 - - - +
260A VAL* 1.3 57.2 + - - +
262A GLY 3.7 0.4 + - - -
263A ALA* 2.9 28.8 + - - +
277A ALA* 3.9 2.5 - - + +
278A ILE 3.6 25.1 - - - +
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Residues in contact with VAL 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LEU* 4.4 10.8 - - + -
19A MET* 5.1 0.9 - - + -
27A VAL* 5.7 1.1 - - + -
29A LEU* 4.2 23.6 - - + -
240A THR* 3.9 17.3 - - + -
244A LEU* 3.6 25.1 - - + -
256A SER 3.0 19.4 + - - +
258A GLY 3.0 1.0 - - - -
259A ALA* 1.3 75.8 - - - +
261A ALA* 1.3 57.0 + - - +
263A ALA* 3.9 4.9 - - + -
264A LEU* 2.7 60.6 + - + +
277A ALA* 4.6 9.2 - - + -
279A ILE* 6.0 0.4 - - + -
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Residues in contact with ALA 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A ILE* 4.6 10.3 - - + -
236A ASP* 4.2 13.9 - - + +
240A THR* 4.1 15.0 - - - +
257A GLY 3.6 9.1 + - - +
258A GLY* 2.5 24.3 + - - +
260A VAL* 1.3 72.2 - - - +
262A GLY* 1.3 49.2 + - - +
264A LEU* 3.0 9.3 + - - +
265A ARG* 2.8 40.0 + - - +
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Residues in contact with GLY 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A VAL* 4.2 2.9 - - - -
198A LEU* 4.2 17.5 - - - -
230A LEU* 4.6 4.3 - - - -
232A ILE* 4.1 8.3 - - - +
258A GLY 3.3 5.9 + - - -
259A ALA 4.1 1.6 - - - -
261A ALA* 1.3 77.6 - - - +
263A ALA* 1.3 53.2 + - - +
265A ARG* 2.9 17.2 + - - +
266A VAL* 2.7 41.2 + - - +
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Residues in contact with ALA 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A VAL* 4.4 10.1 - - + +
170A VAL* 3.5 16.9 - - + +
259A ALA 2.9 22.2 + - - +
260A VAL* 3.5 6.3 - - - +
262A GLY* 1.3 73.9 - - - +
264A LEU* 1.3 59.5 + - - +
266A VAL* 3.4 3.0 + - - +
267A ALA* 3.0 26.9 + - - +
275A VAL* 3.7 18.4 - - + +
277A ALA* 3.6 22.4 - - + -
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Residues in contact with LEU 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A LEU* 3.7 19.1 - - + -
19A MET* 4.8 10.8 - - + -
20A GLY* 4.0 25.6 - - - +
21A PRO* 4.3 2.5 - - + -
27A VAL* 4.6 11.0 - - + -
240A THR* 5.2 4.3 - - + +
243A GLU* 6.0 0.7 - - - +
260A VAL* 2.7 51.2 + - + +
261A ALA* 3.4 7.6 - - - +
263A ALA* 1.3 76.4 - - + +
265A ARG* 1.3 58.1 + - - +
267A ALA* 3.1 3.3 + - - +
268A LYS* 2.5 61.0 + - - +
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Residues in contact with ARG 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A LEU* 2.9 43.9 - - + +
231A ASP 3.1 29.3 + - - +
232A ILE* 4.8 5.4 - - - +
261A ALA* 2.8 18.7 + - - +
262A GLY* 3.1 13.7 - - - +
264A LEU* 1.3 74.5 - - - +
266A VAL* 1.3 52.7 + - + +
268A LYS* 3.6 8.2 - - - +
269A ALA* 2.6 36.7 + - - +
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Residues in contact with VAL 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A HIS* 3.3 31.2 - - + -
170A VAL* 4.1 15.5 - - + -
196A VAL* 4.5 13.7 - - + -
230A LEU* 4.5 13.0 - - + -
262A GLY 2.7 24.9 + - - +
263A ALA* 3.6 6.3 - - - +
265A ARG* 1.3 71.7 - - - +
267A ALA* 1.3 53.4 + - - +
269A ALA* 2.8 9.1 - - - +
270A ASN* 2.5 48.2 + - + +
275A VAL* 3.7 16.4 - - + -
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Residues in contact with ALA 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A PRO* 3.8 12.3 - - + -
23A ASN* 3.6 7.3 - - - +
25A SER* 3.3 20.6 + - - +
27A VAL* 3.9 20.9 - - + -
263A ALA 3.0 17.8 + - - +
264A LEU* 3.6 3.8 - - - +
266A VAL* 1.3 74.2 - - - +
268A LYS* 1.3 65.6 + - - +
269A ALA 3.0 3.1 + - - +
270A ASN 2.6 26.4 - - - +
273A ALA* 4.4 5.2 - - + -
275A VAL* 4.6 2.2 - - + +
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Residues in contact with LYS 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A GLY* 3.3 14.8 - - - -
21A PRO* 3.0 39.5 - - + +
23A ASN* 4.1 5.6 - - - +
264A LEU* 2.5 44.7 + - - +
265A ARG* 3.6 8.3 - - + +
267A ALA* 1.3 70.9 - - - +
269A ALA* 1.3 63.0 + - - +
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Residues in contact with ALA 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ASN* 4.1 1.0 - - - +
265A ARG 2.6 18.9 + - - +
266A VAL* 2.8 11.4 - - - +
267A ALA 3.1 1.0 - - - +
268A LYS* 1.3 77.7 - - - +
270A ASN* 1.3 77.6 + - - +
271A PRO* 3.0 11.5 - - - +
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Residues in contact with ASN 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A SER* 3.3 1.2 - - - -
168A HIS* 3.7 29.9 + - + -
266A VAL* 2.5 27.0 + - + +
267A ALA 2.6 18.0 - - - +
269A ALA* 1.3 77.6 - - - +
271A PRO* 1.3 71.3 - - + +
273A ALA* 2.9 27.2 - - + +
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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