Contacts of the helix formed by residues 291 - 303 (chain D) in PDB entry 2BP1
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 SER 291 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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281D LEU* 4.3 0.2 - - - -
289D ALA 4.0 0.2 + - - -
290D PRO* 1.3 78.3 - - - +
292D VAL* 1.3 59.8 + - - +
293D THR* 3.5 11.0 + - - -
294D SER* 2.8 26.7 + - - -
295D ALA* 3.0 26.2 + - - +
326D GLN* 4.2 10.3 + - - -
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Residues in contact with VAL 292 (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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234D LEU* 3.6 13.0 - - + +
235D THR 3.0 34.5 - - - +
236D GLY* 3.7 7.6 - - - +
274D ILE* 4.4 18.6 - - + -
277D VAL* 4.4 21.5 - - + -
278D GLU* 4.3 16.6 - - + +
281D LEU* 3.9 16.2 - - + +
290D PRO 3.8 0.8 + - - -
291D SER* 1.3 69.5 - - - +
293D THR* 1.3 55.1 + - - +
295D ALA* 3.6 0.6 - - + +
296D ALA* 2.8 36.6 + - + +
344D PHE* 5.4 2.5 - - + -
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Residues in contact with THR 293 (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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229D LEU* 3.8 21.3 - - + -
234D LEU 3.5 8.7 + - - -
235D THR* 3.1 28.3 + - + +
291D SER* 3.6 8.8 + - - -
292D VAL* 1.3 80.7 - - - +
294D SER* 1.3 63.5 + - - +
296D ALA* 3.2 3.5 + - - +
297D LEU* 3.1 26.5 + - + +
326D GLN* 3.9 15.1 + - + +
327D ASN* 3.6 24.0 - - - +
330D ALA* 6.0 0.4 - - + -
1361D NDP 3.9 9.7 + - - +
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Residues in contact with SER 294 (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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290D PRO* 3.7 7.6 - - - +
291D SER* 2.8 26.8 + - - -
293D THR* 1.3 74.5 - - - +
295D ALA* 1.3 59.1 + - - +
297D LEU* 3.4 1.9 + - - +
298D ARG* 2.9 42.7 + - - +
330D ALA* 3.8 15.7 - - - +
333D GLU* 2.6 30.1 + - - -
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Residues in contact with ALA 295 (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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281D LEU* 3.9 31.6 - - + -
290D PRO* 4.9 2.2 - - + +
291D SER 3.0 13.2 + - - +
292D VAL* 3.6 7.6 - - - +
294D SER* 1.3 77.6 + - - +
296D ALA* 1.3 57.2 - - - +
298D ARG 3.2 0.9 + - - -
299D TRP* 2.9 26.9 + - - +
336D LEU* 3.5 24.2 - - + +
344D PHE* 4.0 16.2 - - + -
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Residues in contact with ALA 296 (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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203D ALA* 4.8 3.2 + - + +
228D PRO 4.6 2.5 - - - +
229D LEU* 3.7 22.9 - - + -
234D LEU* 3.9 26.0 - - + +
292D VAL* 2.8 21.8 + - + +
293D THR 3.2 0.4 + - - -
295D ALA* 1.3 72.5 - - - +
297D LEU* 1.3 62.2 + - - +
299D TRP* 3.5 6.6 - - - +
300D MET* 3.5 23.8 + - - +
344D PHE* 4.0 17.4 - - + -
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Residues in contact with LEU 297 (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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228D PRO* 4.2 20.2 - - + +
229D LEU* 3.8 23.3 - - + -
293D THR* 3.1 19.4 + - + +
294D SER 3.8 2.9 - - - +
296D ALA* 1.3 76.9 - - - +
298D ARG* 1.3 64.3 + - - +
300D MET* 3.1 11.8 + - + +
301D TYR* 3.1 29.3 - - + -
314D VAL* 4.9 4.3 - - + -
316D LEU* 4.3 18.4 - - + -
327D ASN* 3.7 49.8 - - + +
330D ALA* 3.9 14.8 - - + -
331D THR* 5.0 0.7 - - + -
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Residues in contact with ARG 298 (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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285D TYR* 4.1 10.3 + - - -
290D PRO* 3.6 23.2 - - - +
294D SER* 2.9 37.3 + - - +
295D ALA 3.7 3.8 - - - +
297D LEU* 1.3 71.3 - - - +
299D TRP* 1.3 60.4 + - - +
301D TYR* 4.8 1.6 - - - -
302D HIS* 2.8 41.9 + - + +
303D HIS* 4.4 2.0 - - - -
330D ALA 3.5 18.8 - - - +
333D GLU* 3.3 32.4 + - + +
334D GLY* 2.8 26.9 + - - +
335D PRO 3.1 23.4 + - - -
336D LEU* 3.6 22.8 - - + +
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Residues in contact with TRP 299 (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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201D TYR* 3.8 17.0 - + - -
202D ASN 3.7 4.0 - - - -
203D ALA* 3.6 30.7 - - + -
206D ARG* 3.3 49.5 - - - +
209D GLU* 4.7 2.0 - - - -
295D ALA 2.9 13.1 + - - +
296D ALA 3.5 10.1 - - - +
297D LEU 3.2 0.2 - - - -
298D ARG* 1.3 75.4 - - - +
300D MET* 1.3 78.5 + - + +
303D HIS* 2.7 66.1 + + + +
304D SER* 3.0 31.6 + - - -
336D LEU* 4.0 4.4 - - + +
341D VAL* 4.7 7.1 - - + +
344D PHE* 3.9 26.0 - + + +
345D ASN* 4.2 5.5 + - - -
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Residues in contact with MET 300 (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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39D VAL* 4.6 0.2 - - - +
201D TYR* 3.3 26.2 - - + +
202D ASN* 3.6 25.4 - - - -
225D ALA* 3.4 24.9 - - + -
228D PRO* 4.3 20.4 - - + +
296D ALA 3.5 14.3 + - - +
297D LEU* 3.1 12.7 + - + +
299D TRP* 1.3 95.9 - - - +
301D TYR* 1.3 63.0 + - + +
304D SER* 2.6 22.7 + - - -
306D LEU* 3.8 24.3 - - + +
314D VAL* 3.8 16.2 - - + -
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Residues in contact with TYR 301 (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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39D VAL* 3.4 53.2 + - + +
40D ALA 3.6 7.6 - - - -
41D SER* 2.5 34.9 + - - -
297D LEU* 3.1 33.2 + - + +
298D ARG* 4.8 0.9 - - - -
300D MET* 1.3 81.4 - - + +
302D HIS* 1.3 81.6 + - + +
306D LEU 5.3 0.6 - - - +
314D VAL* 3.4 28.8 - - + +
316D LEU* 3.8 7.6 - - + +
331D THR* 3.4 43.3 - - + +
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Residues in contact with HIS 302 (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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298D ARG* 2.8 27.8 + - + +
301D TYR* 1.3 96.3 + - + +
303D HIS* 1.3 80.3 + - + +
304D SER 3.9 1.8 - - - -
331D THR 4.7 4.3 + - - -
333D GLU 2.8 24.7 + - - -
334D GLY* 3.5 25.5 - - - -
335D PRO* 4.0 15.8 - - + +
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Residues in contact with HIS 303 (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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298D ARG 3.9 7.9 - - - -
299D TRP* 2.7 42.9 + + + +
302D HIS* 1.3 86.9 + - + +
304D SER* 1.3 62.0 + - - +
335D PRO* 3.7 20.9 - - + +
336D LEU* 3.0 42.1 + - + -
341D VAL* 3.6 37.2 - - + +
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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
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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