Contacts of the helix formed by residues 295 - 312 (chain A) in PDB entry 2B9S
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 295 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293A SER* 2.9 13.0 + - - +
294A ASN* 1.3 82.8 + - - +
296A LEU* 1.3 65.9 + - - +
297A HIS* 2.9 22.0 + - - +
298A VAL* 3.3 22.9 + - + +
299A ALA* 3.1 22.9 + - - +
373A ARG* 5.2 0.2 - - - -
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Residues in contact with LEU 296 (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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294A ASN 3.5 4.9 + - - +
295A ASP* 1.3 72.4 + - - +
297A HIS* 1.3 63.8 + - - +
299A ALA* 3.5 0.9 + - - +
300A GLN* 3.1 42.9 + - - +
373A ARG* 3.6 31.0 - - + +
374A PHE* 4.1 18.2 - - + -
386A ASP* 4.9 3.1 - - - +
387A GLN* 3.8 24.2 - - + -
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Residues in contact with HIS 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A ASP* 2.9 11.2 + - - +
296A LEU* 1.3 78.0 - - - +
298A VAL* 1.3 58.1 + - + +
300A GLN* 3.4 2.1 + - - +
301A ARG* 2.8 63.8 + - - +
387A GLN* 2.8 36.3 + - + +
388A LEU* 3.7 15.4 - - + -
392A GLN* 3.3 47.9 + - + +
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Residues in contact with VAL 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A ASP* 3.6 33.7 - - + +
293A SER* 3.6 21.5 - - - +
295A ASP* 3.3 25.8 + - + +
297A HIS* 1.3 81.0 - - + +
299A ALA* 1.3 57.7 + - - +
301A ARG* 3.4 29.3 + - - +
302A ALA* 2.9 27.5 + - - +
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Residues in contact with ALA 299 (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 ASP 3.6 17.4 + - - +
291A PHE* 4.6 0.9 - - - +
293A SER* 4.3 7.8 - - - +
295A ASP 3.1 16.1 + - - +
296A LEU 4.0 3.6 - - - +
298A VAL* 1.3 76.2 - - - +
300A GLN* 1.3 61.8 + - - +
302A ALA* 3.4 4.7 + - - +
303A VAL* 3.2 26.9 + - - +
370A LEU* 4.3 12.8 - - + +
373A ARG* 4.1 19.7 - - - +
374A PHE* 3.9 10.1 - - + -
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Residues in contact with GLN 300 (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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296A LEU* 3.1 35.6 + - - +
297A HIS 3.7 3.6 - - - +
299A ALA* 1.3 74.2 - - - +
301A ARG* 1.3 64.7 + - - +
303A VAL* 3.2 2.6 + - - -
304A ALA* 3.0 24.9 + - - +
374A PHE* 3.6 32.2 - - + +
378A LYS* 5.1 1.6 - - - +
384A ILE 3.5 9.7 + - - -
385A PHE* 3.4 25.4 - - + -
386A ASP* 3.4 21.8 + - - -
387A GLN* 2.9 37.0 + - - +
388A LEU* 3.6 7.8 + - + -
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Residues in contact with ARG 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A ASP* 4.2 7.5 + - - -
297A HIS* 2.8 46.9 + - - +
298A VAL* 3.4 36.0 + - - +
300A GLN* 1.3 71.7 - - - +
302A ALA* 1.3 57.2 + - - +
304A ALA* 3.5 2.1 + - - +
305A MET* 3.0 40.8 + - - +
388A LEU* 3.9 24.5 - - + +
392A GLN 4.5 7.0 + - - -
393A LEU* 4.1 8.8 - - + +
396A HIS* 3.4 56.9 + - - +
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Residues in contact with ALA 302 (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 TYR* 3.5 29.6 - - + +
290A ASP* 3.6 14.3 + - + -
291A PHE* 3.5 15.4 - - + -
298A VAL 2.9 13.2 + - - +
299A ALA 3.4 10.3 - - - +
300A GLN 3.2 0.4 - - - -
301A ARG* 1.3 73.7 - - - +
303A VAL* 1.3 60.2 + - - +
305A MET* 3.5 11.2 + - - +
306A TYR* 2.9 28.4 + - - +
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Residues in contact with VAL 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A PHE* 4.1 7.0 - - + -
299A ALA 3.2 14.0 + - - +
300A GLN 3.2 5.4 + - - +
302A ALA* 1.3 73.2 - - - +
304A ALA* 1.3 59.9 + - - +
306A TYR* 3.3 7.7 + - + +
307A PHE* 2.9 47.5 + - + -
367A VAL* 4.1 14.1 - - + -
370A LEU* 3.5 30.1 - - + -
371A LEU* 4.0 11.7 - - + -
374A PHE* 3.8 9.6 - - + -
385A PHE* 3.9 22.9 - - + -
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Residues in contact with ALA 304 (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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300A GLN 3.0 7.6 + - - +
301A ARG 3.7 0.7 - - - +
303A VAL* 1.3 77.2 - - - +
305A MET* 1.3 58.3 + - - +
307A PHE 3.2 1.2 + - - -
308A ILE* 2.9 34.2 + - - +
329A CYS* 3.6 24.5 - - - -
330A CYS* 4.9 0.4 - - - -
385A PHE* 4.2 8.0 - - + -
388A LEU* 3.2 35.7 - - + -
393A LEU* 3.7 10.3 - - + -
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Residues in contact with MET 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A ILE* 3.8 30.5 - - + +
287A TYR* 3.8 29.0 - - + -
290A ASP* 5.4 1.8 - - - +
301A ARG* 3.0 29.9 + - - +
302A ALA* 3.7 9.0 - - - +
304A ALA* 1.3 73.0 - - - +
306A TYR* 1.3 59.1 + - - +
308A ILE* 4.0 6.9 - - + +
309A ASP* 2.9 32.4 + - - +
393A LEU* 4.2 13.6 - - + +
396A HIS* 3.9 21.5 - - + +
397A LEU* 4.2 15.0 - - + -
400A PHE* 4.0 22.2 - - + -
409A PHE* 5.5 5.3 - - + -
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Residues in contact with TYR 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A TYR* 3.8 30.4 - + + -
288A MET* 6.1 0.4 - - + -
291A PHE* 3.9 10.3 - + + -
302A ALA 2.9 20.0 + - - +
303A VAL 3.3 5.4 - - - +
305A MET* 1.3 75.5 - - - +
307A PHE* 1.3 80.9 + + - +
310A ARG* 2.9 56.0 + - + +
311A LEU* 6.2 1.3 - - + -
361A VAL* 5.6 1.7 - - + +
362A ALA 4.4 2.8 + - - -
363A VAL* 3.5 15.3 - - + +
364A LEU* 3.4 45.3 + - + +
367A VAL* 3.8 26.9 - - + -
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Residues in contact with PHE 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A VAL* 2.9 26.3 + - + -
304A ALA 3.6 6.5 - - - +
306A TYR* 1.3 99.9 - + - +
308A ILE* 1.3 61.0 + - - +
311A LEU* 2.9 46.3 + - + +
312A ALA 3.4 1.0 + - - -
313A LEU* 3.9 13.0 + - + -
329A CYS* 4.0 14.6 - - - -
332A LEU* 4.4 9.2 - - + -
337A ILE* 5.6 2.5 - - + -
347A PHE* 3.6 34.1 - + - -
363A VAL* 4.6 7.6 - - + -
367A VAL* 4.3 4.9 - - + -
371A LEU* 3.9 22.2 - - + -
384A ILE* 6.3 0.9 - - + -
385A PHE* 4.0 26.5 - + - -
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Residues in contact with ILE 308 (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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304A ALA 2.9 19.7 + - - +
305A MET* 4.0 5.8 - - + +
307A PHE* 1.3 74.8 - - - +
309A ASP* 1.3 59.4 - - - +
312A ALA* 3.1 24.3 - - - -
313A LEU 3.8 23.3 - - - +
315A VAL* 4.2 8.1 - - + -
329A CYS* 4.0 23.1 - - + -
330A CYS* 5.3 0.2 - - - -
393A LEU* 3.8 33.4 - - + -
397A LEU* 6.2 0.4 - - + -
406A ALA* 3.7 35.7 - - + +
409A PHE* 3.9 18.7 - - + +
413A ASN* 3.7 4.2 + - - -
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Residues in contact with ASP 309 (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 ILE* 5.7 0.2 - - - +
284A ARG* 2.7 47.2 + - - +
287A TYR* 2.8 22.4 + - + +
305A MET 2.9 19.8 + - - +
306A TYR 3.9 2.5 - - - +
308A ILE* 1.3 76.9 - - - +
310A ARG* 1.3 68.6 + - - +
409A PHE* 3.8 29.7 - - + -
412A TYR* 4.8 1.9 - - - -
413A ASN* 2.8 28.9 + - - +
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Residues in contact with ARG 310 (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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284A ARG* 3.4 42.2 - - - +
287A TYR* 3.7 4.8 + - - -
288A MET* 5.5 5.1 - - - +
306A TYR* 2.9 51.6 + - + +
309A ASP* 1.3 93.7 + - - +
311A LEU* 1.3 70.2 + - + +
312A ALA 3.6 0.2 - - - -
413A ASN* 5.1 2.1 - - - +
450A LEU* 4.6 10.0 - - - +
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Residues in contact with LEU 311 (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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306A TYR* 6.2 1.1 - - + -
307A PHE* 2.9 28.3 + - + +
310A ARG* 1.3 85.9 - - + +
312A ALA* 1.3 69.3 + - - +
313A LEU* 3.3 19.4 + - + +
347A PHE* 3.8 37.5 - - + -
357A TYR* 4.0 21.5 + - - +
359A ASN* 4.3 4.7 - - - +
361A VAL* 3.8 32.1 - - + -
363A VAL* 6.2 0.2 - - + -
450A LEU* 4.0 18.4 - - - +
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Residues in contact with ALA 312 (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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308A ILE 3.1 19.6 + - - -
309A ASP 4.0 0.8 + - - -
310A ARG 3.6 1.6 - - - -
311A LEU* 1.3 79.4 - - - +
313A LEU* 1.3 59.1 + - - +
409A PHE* 5.8 0.2 - - - -
410A ARG* 2.6 52.6 + - + +
413A ASN* 3.6 30.1 - - + +
450A LEU* 4.5 15.6 - - + +
451A CYS* 5.8 1.8 - - - -
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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