Contacts of the helix formed by residues 282 - 291 (chain A) in PDB entry 1B3U
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 LEU 282 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244A MET* 5.0 1.3 - - + -
247A LEU* 4.4 23.3 - - + -
266A PHE* 3.4 32.2 - - + +
269A LEU* 4.3 6.1 - - + -
270A GLN* 3.7 36.8 - - + +
273A VAL* 3.7 19.1 - - + -
277A ILE* 3.5 2.4 + - + +
278A THR* 3.2 28.4 + - + +
281A ASP* 1.3 80.1 - - + +
283A VAL* 1.3 56.0 + - - +
285A ALA* 4.1 4.5 - - + -
286A PHE* 2.7 36.6 + - - +
308A PHE* 4.2 2.0 - - + -
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Residues in contact with VAL 283 (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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278A THR 2.8 21.7 + - - +
279A LYS* 3.5 19.5 - - + +
282A LEU* 1.3 73.9 - - - +
284A PRO* 1.3 73.9 - - + +
286A PHE* 3.4 2.4 + - - +
287A GLN* 3.4 24.1 + - - +
308A PHE* 4.0 21.7 - - + -
312A LEU* 4.4 11.0 - - + -
320A VAL* 4.9 13.0 - - + -
324A GLN* 4.5 29.2 - - + +
325A ILE* 4.7 8.3 - - + +
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Residues in contact with PRO 284 (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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279A LYS 3.7 4.5 - - - +
280A THR 3.5 17.7 - - - +
281A ASP* 3.0 17.5 - - - +
283A VAL* 1.3 99.4 - - + +
285A ALA* 1.3 61.1 + - - +
287A GLN* 3.2 29.0 + - - +
288A ASN* 3.2 20.5 + - - +
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Residues in contact with ALA 285 (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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251A ALA* 5.0 16.6 - - + -
266A PHE* 4.3 11.0 - - + -
281A ASP 3.1 18.9 + - - +
282A LEU* 3.5 11.4 - - + +
284A PRO* 1.3 77.7 - - - +
286A PHE* 1.3 61.8 + - - +
288A ASN* 3.2 12.7 + - - +
289A LEU* 3.1 28.5 + - + +
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Residues in contact with PHE 286 (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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263A ALA* 6.1 0.9 - - + -
266A PHE* 3.8 35.4 - + + -
282A LEU 2.7 20.7 + - - +
283A VAL 3.8 5.2 - - - +
284A PRO 3.2 0.2 - - - -
285A ALA* 1.3 73.1 - - - +
287A GLN* 1.3 63.2 + - - +
289A LEU* 3.3 8.5 + - + +
290A MET* 3.0 53.5 + - + +
301A ALA* 3.4 39.0 - - + -
304A LYS* 4.2 13.2 - - + -
305A VAL* 4.0 23.1 - - + -
308A PHE* 3.6 32.8 - + + -
309A CYS* 5.9 0.2 - - - -
325A ILE* 4.6 9.6 - - + -
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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 10.8 + - + +
284A PRO* 3.2 29.4 + - - +
286A PHE* 1.3 78.7 - - - +
288A ASN* 1.3 62.2 + - - +
290A MET* 3.4 14.8 + - + +
291A LYS* 3.3 32.3 + - - +
324A GLN* 3.3 47.1 + - + +
325A ILE* 5.2 3.1 - - + -
328A CYS* 4.1 19.2 - - - -
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Residues in contact with ASN 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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252A GLU* 6.1 3.8 - - - +
284A PRO* 3.2 20.5 + - - +
285A ALA* 3.2 12.5 + - - +
287A GLN* 1.3 76.3 - - - +
289A LEU* 1.3 62.6 + - + +
291A LYS* 2.9 22.2 + - - +
292A ASP* 3.0 13.4 + - - +
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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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251A ALA* 4.7 13.0 - - + +
259A ARG* 4.1 23.1 - - + +
262A VAL* 4.3 9.6 - - + -
263A ALA* 4.2 14.1 - - + -
266A PHE* 3.8 31.9 - - + -
285A ALA* 3.1 16.0 + - + +
286A PHE* 3.3 10.7 + - + +
288A ASN* 1.3 76.9 - - + +
290A MET* 1.3 63.3 + - - +
291A LYS 3.0 1.2 + - - -
292A ASP* 3.0 23.7 + - - +
297A VAL* 3.9 22.5 - - + +
298A ARG* 3.9 10.9 - - - -
301A ALA* 4.1 14.1 - - + -
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Residues in contact with MET 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* 3.0 51.0 + - + +
287A GLN* 3.7 14.1 - - + +
288A ASN 3.3 0.4 - - - -
289A LEU* 1.3 75.5 - - - +
291A LYS* 1.3 62.7 + - + +
292A ASP 3.5 0.4 - - - -
298A ARG* 3.5 13.8 - - - +
301A ALA* 4.1 20.0 - - + -
305A VAL* 4.3 10.3 - - - -
325A ILE* 4.6 14.1 - - + -
328A CYS* 3.5 30.3 - - + -
329A ILE* 4.7 5.8 - - - -
332A LEU* 3.5 48.9 - - + +
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Residues in contact with LYS 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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287A GLN* 3.3 17.2 + - - +
288A ASN* 2.9 10.4 + - - +
290A MET* 1.3 84.7 - - + +
292A ASP* 1.3 64.8 + - - +
293A CYS* 3.7 1.2 + - - -
298A ARG* 4.4 2.9 - - - +
328A CYS* 3.2 38.0 + - + +
331A GLU* 2.7 30.8 + - + +
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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