Contacts of the helix formed by residues 286 - 292 (chain A) in PDB entry 2BAP
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 PHE 286 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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271A LEU* 3.8 24.2 - - + -
274A MET* 3.8 21.1 - - + -
284A GLU* 3.1 2.9 - - + +
285A ARG* 1.3 92.5 - - + +
287A GLN* 1.3 59.5 + - - +
288A PRO* 3.3 4.0 - - - -
289A LEU* 2.8 47.0 + - + +
290A LEU* 3.3 8.5 + - - +
312A LEU* 4.8 4.7 - - + -
325A ILE* 4.1 13.5 - - + -
328A GLU* 3.4 42.0 - - + -
329A LEU* 3.8 38.5 - - + +
332A LEU* 3.7 17.7 - - + -
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Residues in contact with GLN 287 (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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283A VAL* 3.4 25.6 - - + +
284A GLU* 3.4 10.4 + - + +
286A PHE* 1.3 75.6 - - - +
288A PRO* 1.4 57.5 - - + +
290A LEU* 4.5 9.4 - - + +
291A ASP* 2.7 62.4 + - - +
294A LYS* 5.2 3.0 - - - +
332A LEU* 4.0 29.9 - - + +
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Residues in contact with PRO 288 (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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239A MET* 4.8 6.7 - - + +
240A ASP* 5.1 3.8 - - - +
241A PRO* 5.0 5.8 - - + -
247A MET* 3.5 24.7 - - + +
277A ARG* 3.4 40.8 - - - +
284A GLU 4.1 8.1 - - - +
285A ARG 4.6 4.3 - - - +
286A PHE* 3.4 4.9 - - - +
287A GLN* 1.4 90.3 - - + +
289A LEU* 1.3 64.0 + - + +
290A LEU 3.0 1.6 + - - -
291A ASP* 3.1 18.2 + - + +
292A GLY 3.3 10.2 + - - -
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Residues in contact with LEU 289 (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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239A MET* 5.1 3.4 - - - -
247A MET* 4.3 11.0 - - + -
251A ALA* 5.6 1.6 - - + -
274A MET* 4.3 13.5 - - + -
286A PHE* 2.8 40.5 + - + +
288A PRO* 1.3 77.1 - - + +
290A LEU* 1.3 56.9 + - - +
293A LEU* 3.3 21.7 - - - +
304A GLY 4.8 0.4 - - - +
305A CYS* 3.5 43.9 - - + +
308A LEU* 3.8 29.8 - - + -
309A ILE* 4.1 26.4 - - + +
312A LEU* 5.2 3.8 - - + -
329A LEU* 5.0 5.6 - - + -
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Residues in contact with LEU 290 (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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286A PHE 3.3 9.0 + - - +
287A GLN* 4.0 12.3 - - + +
288A PRO 3.1 0.6 - - - -
289A LEU* 1.3 75.2 - - - +
291A ASP* 1.3 67.9 + - - +
292A GLY 3.2 1.8 - - - -
293A LEU* 3.0 23.4 + - + +
294A LYS* 4.3 12.8 - - + +
329A LEU* 4.0 12.6 - - + +
332A LEU* 3.7 25.4 - - + +
333A GLY* 3.7 16.4 - - - +
334A LEU* 3.5 34.8 - - + +
337A VAL* 4.7 19.1 - - + -
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Residues in contact with ASP 291 (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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241A PRO* 3.5 38.0 - - + +
287A GLN* 2.7 51.3 + - - +
288A PRO* 3.5 6.6 - - + +
290A LEU* 1.3 72.2 - - - +
292A GLY* 1.3 57.4 + - - +
293A LEU 3.0 5.9 + - - -
294A LYS* 2.6 53.6 + - + +
297A THR* 4.1 3.1 - - - +
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Residues in contact with GLY 292 (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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241A PRO* 5.0 3.9 - - - +
247A MET* 5.4 3.1 - - - -
288A PRO 3.3 8.0 + - - -
290A LEU 3.2 0.8 - - - -
291A ASP* 1.3 75.3 - - - +
293A LEU* 1.3 70.1 + - - +
294A LYS 3.8 1.3 - - - -
297A THR* 3.8 7.7 + - - -
301A LEU* 4.0 22.4 - - - -
302A LYS* 3.6 13.2 + - - +
305A CYS* 3.2 21.2 - - - -
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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