Contacts of the helix formed by residues 283 - 295 (chain A) in PDB entry 3BMW
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 ASP 283 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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281A LEU 3.4 0.4 + - - -
282A LEU* 1.3 69.2 - - - +
284A PHE* 1.3 57.3 + - - +
285A ARG* 3.5 9.5 + - - +
286A PHE* 3.0 27.0 + - + +
287A SER* 3.0 26.3 + - - -
311A THR* 4.4 2.4 - - - +
315A TYR* 4.6 2.3 + - - -
321A MET* 3.4 28.5 - - + +
322A VAL 2.7 20.4 + - - +
323A THR* 4.0 8.1 - - + -
324A PHE* 3.8 6.3 - - - -
353A ARG* 2.8 40.2 + - - -
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Residues in contact with PHE 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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258A GLU* 4.0 20.2 - - + -
259A TRP 3.4 20.2 - - - +
260A PHE* 3.6 37.9 - + - -
261A LEU* 3.6 45.9 - - + +
282A LEU* 3.2 28.9 + - + -
283A ASP* 1.3 71.0 - - - +
285A ARG* 1.3 61.3 + - - +
287A SER* 4.2 4.0 - - - -
288A GLN* 2.9 36.7 + - - +
315A TYR* 5.9 0.2 + - - -
324A PHE* 3.8 24.7 - + - -
327A ASN* 4.1 13.0 - - - -
330A MET* 4.2 16.2 - - + -
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Residues in contact with ARG 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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261A LEU* 3.8 21.9 - - + +
265A GLU 4.7 10.8 - - - +
270A ASN* 4.9 0.6 + - - -
271A THR* 4.1 8.5 + - - -
283A ASP* 3.3 6.8 + - - +
284A PHE* 1.3 77.7 - - - +
286A PHE* 1.3 61.2 + - - +
288A GLN* 4.3 2.4 - - - +
289A LYS* 3.2 26.0 + - - +
307A MET* 3.7 5.2 - - - +
310A SER* 2.9 38.6 + - - -
311A THR* 3.5 16.0 - - + +
314A ASP* 2.8 32.1 + - - +
315A TYR* 3.6 28.0 + - - -
700A CL 3.2 24.0 - - + +
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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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283A ASP* 3.0 29.6 + - + +
285A ARG* 1.3 74.8 - - - +
287A SER* 1.3 67.3 + - - +
289A LYS* 3.3 3.1 + - - +
290A VAL* 2.9 37.8 + - + +
307A MET* 3.6 22.5 - - + +
308A ILE* 4.1 5.8 - - + -
323A THR* 3.7 25.1 - - + -
324A PHE 4.4 4.9 - - - -
348A PHE* 3.4 33.7 - + - -
349A THR* 3.6 24.7 - - + -
352A SER* 4.0 22.2 - - - -
353A ARG* 3.6 24.5 - - - -
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Residues in contact with SER 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 ASP 3.0 15.5 + - - -
284A PHE* 4.0 2.7 - - - -
285A ARG 3.4 0.2 - - - -
286A PHE* 1.3 78.0 - - - +
288A GLN* 1.3 64.0 + - - +
290A VAL* 3.3 4.8 + - - +
291A ARG* 3.0 24.7 + - - +
324A PHE* 3.0 60.6 + - - -
325A ILE* 3.9 7.8 + - - +
330A MET* 3.8 11.9 - - - +
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Residues in contact with GLN 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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260A PHE* 4.3 8.7 - - - -
261A LEU 3.0 28.1 + - - +
262A GLY* 3.8 15.3 - - - +
263A THR* 3.7 30.4 + - + +
264A ASN 5.1 1.3 - - - +
284A PHE* 2.9 26.2 + - + +
285A ARG* 4.4 2.0 - - - +
287A SER* 1.3 71.8 - - - +
289A LYS* 1.3 58.1 + - - +
291A ARG* 3.3 15.1 + - - +
292A GLN* 3.0 33.5 + - - +
330A MET* 3.4 30.9 - - + +
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Residues in contact with LYS 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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264A ASN* 3.7 14.3 + - - +
285A ARG 3.2 20.5 + - - +
286A PHE 3.8 2.7 - - - +
288A GLN* 1.3 75.4 - - - +
290A VAL* 1.3 65.6 + - - +
292A GLN* 2.9 27.9 + - - +
293A VAL* 2.9 34.3 + - + +
299A ASP* 2.8 29.9 + - + +
303A GLY* 3.7 26.0 - - - +
304A LEU* 3.9 16.4 - - + -
307A MET* 3.9 17.3 - - + -
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Residues in contact with VAL 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* 2.9 47.0 + - + +
287A SER* 3.6 6.1 - - - +
289A LYS* 1.3 74.7 - - - +
291A ARG* 1.3 57.5 + - - +
294A PHE* 2.9 38.4 + - + +
304A LEU* 4.0 11.4 - - + -
325A ILE* 3.9 15.9 - - + -
333A PHE* 4.2 4.3 - - + -
345A ALA* 3.8 31.2 - - + +
348A PHE* 3.8 21.1 - - + -
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Residues in contact with ARG 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 SER* 3.0 18.5 + - - +
288A GLN* 3.6 23.9 + - - +
289A LYS 3.2 0.2 - - - -
290A VAL* 1.3 73.9 - - - +
292A GLN* 1.3 58.8 + - - +
295A ARG* 2.9 30.9 + - + +
296A ASP* 2.9 40.5 + - - +
325A ILE* 2.9 33.0 + - - +
326A ASP* 3.4 10.3 - - - +
330A MET* 4.1 21.5 - - - +
331A ASP* 2.9 48.3 + - - +
333A PHE* 3.9 22.1 - - + +
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Residues in contact with GLN 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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263A THR* 3.4 32.2 - - + +
264A ASN* 3.6 15.4 + - - +
288A GLN 3.0 16.3 + - - +
289A LYS* 2.9 41.7 + - - +
291A ARG* 1.3 76.0 - - - +
293A VAL* 1.3 58.1 + - - +
296A ASP* 4.7 4.5 + - - +
297A ASN* 3.1 10.6 + - - -
298A THR* 2.9 65.0 + - - +
299A ASP* 3.4 14.8 + - + +
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Residues in contact with VAL 293 (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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289A LYS* 2.9 35.0 + - + +
290A VAL 4.1 2.0 - - - +
292A GLN* 1.3 80.3 - - - +
294A PHE* 1.3 72.3 + - + +
297A ASN* 4.9 3.2 - - - -
299A ASP 3.6 12.6 - - - +
300A THR 3.4 23.3 - - - +
301A MET* 3.7 29.6 - - - -
304A LEU* 4.2 12.3 - - + -
436A ARG* 2.9 39.9 + - - +
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Residues in contact with PHE 294 (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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290A VAL* 2.9 31.5 + - + +
293A VAL* 1.3 85.1 - - + +
295A ARG* 1.3 59.7 + - - +
297A ASN 5.2 0.7 - - - -
301A MET* 3.8 24.0 - - + -
304A LEU* 3.8 23.8 - - + -
333A PHE* 3.8 15.0 - - + -
341A PRO* 3.4 30.9 - - + +
344A GLN* 3.5 38.6 - - + -
345A ALA* 4.4 5.8 - - + -
348A PHE* 4.5 16.4 - + + -
434A ILE* 3.8 27.8 - - + -
436A ARG* 4.2 8.7 - - + +
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Residues in contact with ARG 295 (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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291A ARG* 2.9 42.5 + - - +
294A PHE* 1.3 80.5 - - - +
296A ASP* 1.3 97.8 + - - +
297A ASN* 3.6 2.2 + - - +
331A ASP* 3.7 10.7 + - - +
332A ARG 2.9 22.6 + - - -
333A PHE* 3.0 48.8 + - + +
335A ASN* 3.2 38.6 - - + +
341A PRO* 5.4 0.9 - - - -
369A ASN* 3.3 15.8 + - - +
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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