Contacts of the helix formed by residues 253 - 270 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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241D MET* 3.2 10.5 - - - +
252D CYS* 1.3 80.2 - - - +
254D VAL* 1.3 64.6 + - - -
255D SER* 3.2 14.7 + - - -
256D SER* 3.1 8.5 + - - -
257D GLY 3.3 6.4 + - - -
281D ASP* 3.5 10.7 + - - -
282D ARG 4.1 1.2 + - - -
286D TYR* 3.5 28.5 - - - -
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Residues in contact with VAL 254 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205D SER 5.5 1.3 - - - +
206D ILE* 3.3 20.5 - - + +
207D PRO* 3.8 29.2 - - + -
234D GLN* 4.7 2.9 - - + +
237D ALA* 4.0 7.8 - - + +
238D GLU* 4.0 35.7 - - + +
241D MET* 3.3 19.4 - - - -
253D GLY* 1.3 68.1 - - - -
255D SER* 1.3 66.2 + - - +
256D SER 3.1 0.3 + - - -
257D GLY* 3.2 1.4 + - - -
258D GLY 3.1 19.4 + - - -
286D TYR* 4.0 13.0 - - + -
291D VAL* 4.2 16.2 - - + -
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Residues in contact with SER 255 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172D SER* 3.5 23.2 + - - -
206D ILE* 3.9 13.1 - - - +
207D PRO 4.1 8.9 + - - -
209D ILE* 5.7 0.7 - - - -
253D GLY* 3.3 14.4 - - - -
254D VAL* 1.3 75.0 - - - +
256D SER* 1.3 79.2 + - - -
258D GLY 3.7 4.3 + - - -
259D ALA* 4.2 0.5 - - - +
280D CYS* 3.9 6.1 - - - +
281D ASP* 3.3 7.6 + - - -
286D TYR* 3.9 4.2 + - - -
320D PLP 3.4 40.4 - - - -
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Residues in contact with SER 256 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252D CYS* 3.6 13.9 - - - -
253D GLY 3.1 4.3 + - - -
254D VAL 3.1 0.8 - - - -
255D SER* 1.3 89.6 + - - +
257D GLY* 1.3 60.9 + - - +
259D ALA* 3.3 9.1 + - - +
260D VAL* 3.1 31.8 + - - +
278D ILE 4.7 0.7 - - - -
279D ILE* 3.3 31.8 - - - +
280D CYS* 2.8 24.9 + - - +
281D ASP 3.8 2.8 + - - -
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Residues in contact with GLY 257 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237D ALA* 3.8 8.6 - - - -
240D THR* 3.4 18.3 - - - +
241D MET* 3.7 27.4 - - - -
244D LEU* 4.4 3.8 - - - -
252D CYS* 4.6 0.6 - - - -
253D GLY 3.3 6.7 + - - -
254D VAL 3.2 5.4 + - - -
256D SER* 1.3 76.6 - - - +
258D GLY* 1.3 62.9 + - - +
261D ALA* 3.0 18.9 + - - +
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Residues in contact with GLY 258 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172D SER* 4.2 1.6 - - - -
198D LEU* 3.6 9.3 - - - +
206D ILE* 4.5 5.2 - - - -
232D ILE* 3.8 17.8 - - - +
237D ALA* 3.7 19.1 - - - +
254D VAL 3.1 12.7 + - - -
255D SER 3.7 2.9 + - - -
257D GLY* 1.3 76.2 - - - +
259D ALA* 1.3 56.3 + - - +
261D ALA* 3.1 5.8 + - - +
262D GLY 2.9 23.4 + - - -
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Residues in contact with ALA 259 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170D VAL* 4.4 2.7 - - - +
171D SER* 5.0 5.2 - - - +
172D SER* 3.1 28.0 + - - +
198D LEU* 3.3 15.6 - - + +
255D SER 3.7 3.9 + - - +
256D SER* 3.3 9.5 + - - +
257D GLY 3.3 0.4 - - - -
258D GLY* 1.3 75.1 - - - +
260D VAL* 1.3 59.3 + - - +
262D GLY* 3.9 1.3 - - - -
263D ALA* 3.2 24.9 + - - +
277D ALA* 4.0 8.6 - - + +
278D ILE* 3.9 19.3 - - + +
280D CYS* 5.6 1.8 - - - -
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Residues in contact with VAL 260 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D LEU* 4.2 15.5 - - + -
19D MET* 4.5 3.6 - - + -
27D VAL* 5.9 0.7 - - + -
29D LEU* 4.6 8.7 - - + -
240D THR* 3.7 22.7 - - + -
244D LEU* 3.5 24.2 - - + -
256D SER 3.1 16.3 + - - +
258D GLY 3.1 0.2 - - - -
259D ALA* 1.3 78.1 - - - +
261D ALA* 1.3 66.4 + - - +
262D GLY 3.2 0.9 - - - -
263D ALA* 4.4 4.0 - - + +
264D LEU* 3.0 41.5 + - + +
277D ALA* 5.1 1.3 - - + -
279D ILE* 4.1 17.9 - - + -
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Residues in contact with ALA 261 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232D ILE* 4.5 6.3 - - + -
236D ASP* 4.4 13.0 - - + +
240D THR* 4.0 14.9 - - - +
257D GLY 3.0 14.1 + - - +
258D GLY* 3.1 11.4 + - - +
260D VAL* 1.3 78.6 - - - +
262D GLY* 1.3 62.7 + - - +
264D LEU* 3.2 5.3 + - - +
265D ARG* 3.0 43.5 + - - +
268D LYS* 5.4 0.2 + - - -
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Residues in contact with GLY 262 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170D VAL* 4.4 3.1 - - - -
198D LEU* 4.0 21.1 - - - -
230D LEU* 4.7 3.2 - - - +
232D ILE* 4.1 10.9 - - - +
258D GLY 2.9 13.6 + - - -
260D VAL 3.2 0.2 - - - -
261D ALA* 1.3 76.2 - - - +
263D ALA* 1.3 61.2 - - - +
265D ARG* 2.9 22.2 + - - +
266D VAL* 3.1 16.7 + - - +
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Residues in contact with ALA 263 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D VAL* 4.3 9.6 - - + +
170D VAL* 3.6 27.7 - - + +
259D ALA 3.2 20.6 + - - +
260D VAL* 4.2 4.0 - - - +
262D GLY* 1.3 74.2 - - - +
264D LEU* 1.3 59.4 + - + +
266D VAL* 3.2 6.3 - - - +
267D ALA* 2.9 26.5 + - - +
275D VAL* 3.8 16.2 - - + +
277D ALA* 4.1 13.7 - - + -
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Residues in contact with LEU 264 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D LEU* 3.9 14.8 - - + -
19D MET* 4.3 15.9 - - + -
20D GLY* 3.7 35.0 - - - +
21D PRO* 4.2 1.2 - - + +
27D VAL* 3.7 28.7 - - + -
240D THR* 5.6 1.6 - - + -
260D VAL* 3.0 34.4 + - + +
261D ALA* 3.6 5.2 - - - +
263D ALA* 1.3 77.3 - - - +
265D ARG* 1.3 62.2 + - - +
267D ALA* 3.8 4.4 - - + +
268D LYS* 2.8 36.0 + - - +
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Residues in contact with ARG 265 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230D LEU* 4.0 21.0 - - + +
231D ASP 2.5 29.9 + - - +
232D ILE* 3.1 28.3 - - - +
233D HIS 5.2 0.8 - - - +
236D ASP* 4.3 14.5 + - - +
261D ALA* 3.0 29.4 + - - +
262D GLY* 2.9 10.8 + - - +
264D LEU* 1.3 74.9 - - - +
266D VAL* 1.3 64.8 + - + +
268D LYS* 3.4 28.0 + - - +
269D ALA* 3.5 14.7 + - - +
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Residues in contact with VAL 266 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168D HIS* 3.3 37.7 - - + +
170D VAL* 4.1 5.2 - - + -
196D VAL* 3.9 28.0 - - + -
228D GLU* 5.8 1.1 - - - +
230D LEU* 5.0 4.7 - - + -
262D GLY 3.1 14.9 + - - +
263D ALA* 3.2 15.0 + - - +
265D ARG* 1.3 77.0 - - - +
267D ALA* 1.3 61.9 + - - +
269D ALA* 3.3 2.5 + - - -
270D ASN* 2.9 37.6 + - + +
275D VAL* 4.0 13.7 - - + -
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Residues in contact with ALA 267 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D PRO* 3.7 12.3 - - + -
23D ASN* 2.5 29.1 + - - -
25D SER* 3.1 22.4 + - - +
27D VAL* 3.8 22.9 - - + -
263D ALA 2.9 15.4 + - - +
264D LEU* 3.9 6.7 - - - +
265D ARG 3.3 0.4 - - - -
266D VAL* 1.3 74.1 - - - +
268D LYS* 1.3 57.0 + - - +
270D ASN 3.3 11.1 - - - +
275D VAL* 4.5 7.2 - - + -
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Residues in contact with LYS 268 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D PRO* 3.7 24.8 - - + +
23D ASN* 3.0 19.2 + - - +
264D LEU* 2.8 37.5 + - - +
265D ARG* 3.5 29.7 - - - +
266D VAL 3.2 0.6 - - - -
267D ALA* 1.3 78.8 - - - +
269D ALA* 1.3 58.8 + - + +
270D ASN 3.1 3.5 + - - -
271D PRO* 3.9 4.5 - - - +
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Residues in contact with ALA 269 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265D ARG 3.5 10.5 + - - +
266D VAL* 3.3 2.3 + - - +
268D LYS* 1.3 78.3 - - - +
270D ASN* 1.3 75.9 + - - +
271D PRO* 3.7 6.7 - - - +
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Residues in contact with ASN 270 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D SER* 3.0 11.3 - - - -
168D HIS* 4.1 19.9 + - + -
266D VAL* 2.9 34.3 + - - +
267D ALA 3.3 5.0 - - - +
268D LYS 3.1 2.2 - - - -
269D ALA* 1.3 94.6 - - - +
271D PRO* 1.3 68.7 - - - +
272D ASP* 3.1 4.0 - - + +
273D ALA* 3.0 29.5 + - + +
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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