Contacts of the helix formed by residues 296 - 309 (chain A) in PDB entry 2ADU
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 ARG 296 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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294A ASP 3.4 2.6 + - - +
295A VAL* 1.3 75.1 - - - +
297A LEU* 1.3 65.5 + - - +
298A CYS* 4.3 15.0 - - - -
299A ASP* 3.0 54.6 + - - +
300A VAL* 3.5 8.0 + - - +
352A ALA* 3.7 13.4 - - + +
353A THR 3.8 4.5 - - - -
354A ARG* 3.6 43.4 - - + +
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Residues in contact with LEU 297 (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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295A VAL 3.5 0.8 + - - -
296A ARG* 1.3 71.9 - - - +
298A CYS* 1.3 62.2 + - - +
300A VAL* 3.1 16.9 + - + +
301A GLY 3.3 8.3 + - - -
342A LYS* 4.4 13.0 - - + -
343A THR 3.3 23.8 - - - +
344A VAL* 4.0 18.6 - - + -
345A PRO* 3.7 11.8 - - + +
351A GLU* 4.0 10.1 - - + +
353A THR* 2.8 38.2 + - - +
354A ARG 4.6 0.7 - - - +
355A MET* 3.6 42.6 - - + -
361A TYR* 4.1 14.6 - - + +
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Residues in contact with CYS 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A ARG* 4.3 13.9 - - - -
297A LEU* 1.3 76.1 - - - +
299A ASP* 1.3 69.8 + - - +
300A VAL 3.2 0.2 - - - -
301A GLY* 3.5 1.1 + - - -
302A GLU* 3.1 28.5 + - - +
345A PRO* 4.3 9.4 - - - -
347A ILE 4.8 1.9 - - - +
348A LYS* 5.0 2.1 - - - -
349A GLY 5.3 1.2 + - - +
350A GLY* 3.3 26.9 - - - +
351A GLU 3.0 23.1 + - - +
352A ALA* 3.8 18.6 - - - -
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Residues in contact with ASP 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 CYS* 5.0 2.6 - - - +
295A VAL* 5.0 6.9 - - + +
296A ARG* 3.0 64.8 + - - +
298A CYS* 1.3 82.1 - - - +
300A VAL* 1.3 64.7 + - - +
302A GLU* 3.9 14.9 - - - +
303A ALA* 3.3 22.5 + - - +
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Residues in contact with VAL 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A GLY* 3.8 21.1 - - - +
290A CYS* 4.0 25.4 - - + +
291A ALA* 4.4 7.9 - - + -
295A VAL* 4.0 7.2 - - + -
296A ARG 3.8 12.8 - - - +
297A LEU* 3.1 12.0 + - - +
299A ASP* 1.3 77.1 - - - +
301A GLY* 1.3 59.9 + - - +
303A ALA* 3.4 4.6 + - - +
304A ILE* 3.0 51.6 + - + +
344A VAL* 3.7 18.6 - - + -
355A MET* 4.8 11.0 - - + -
363A ILE* 5.5 1.3 - - + -
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Residues in contact with GLY 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A LEU 3.3 7.3 + - - -
298A CYS 3.5 0.4 + - - -
299A ASP 3.4 0.2 - - - -
300A VAL* 1.3 78.3 - - - +
302A GLU* 1.3 62.6 + - - +
304A ILE 3.5 0.2 + - - -
305A GLN* 3.1 18.9 + - - +
345A PRO* 3.0 29.7 + - - -
346A ILE* 3.6 1.6 - - - -
347A ILE 3.4 30.1 + - - -
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Residues in contact with GLU 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A CYS* 3.1 18.0 + - - +
299A ASP* 4.0 17.9 - - - +
301A GLY* 1.3 77.0 - - - +
303A ALA* 1.3 63.8 + - - +
305A GLN* 4.0 2.5 - - - +
306A GLU* 3.1 26.1 + - + +
347A ILE 4.0 1.0 + - - -
348A LYS* 4.2 25.9 - - + +
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Residues in contact with ALA 303 (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 THR* 4.3 9.0 - - + -
290A CYS* 3.7 28.7 - - - -
299A ASP 3.3 16.3 + - - +
300A VAL 3.6 4.0 - - - +
302A GLU* 1.3 78.6 - - - +
304A ILE* 1.3 67.3 + - + +
306A GLU* 3.2 19.0 + - - +
307A VAL* 3.2 18.4 + - - +
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Residues in contact with ILE 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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283A ALA* 3.8 19.4 - - + +
286A THR* 4.7 3.1 - - - -
287A GLY* 3.5 24.7 - - - -
300A VAL* 3.0 40.9 + - + +
301A GLY 3.8 4.0 - - - +
303A ALA* 1.3 75.8 - - + +
305A GLN* 1.3 56.2 + - - +
307A VAL* 3.5 1.1 + - - +
308A MET* 3.0 29.2 + - + +
344A VAL* 4.6 4.5 - - + -
345A PRO 3.8 14.6 - - - +
346A ILE* 4.1 15.9 - - + +
363A ILE* 5.0 3.6 - - + -
365A THR* 3.4 39.5 - - + -
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Residues in contact with GLN 305 (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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301A GLY 3.1 15.7 + - - +
302A GLU 4.0 3.1 - - - +
304A ILE* 1.3 75.2 - - - +
306A GLU* 1.3 61.5 + - - +
308A MET 3.1 0.5 + - - -
309A GLU* 2.8 73.2 + - + +
324A PRO* 3.9 13.4 - - + +
346A ILE 3.6 11.0 + - - +
347A ILE* 3.8 16.1 - - - +
348A LYS* 2.9 50.7 + - - +
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Residues in contact with GLU 306 (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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302A GLU* 3.1 21.8 + - + +
303A ALA* 3.2 10.1 + - - +
305A GLN* 1.3 79.6 - - - +
307A VAL* 1.3 64.2 + - + +
309A GLU* 4.1 3.7 - - - +
310A SER* 3.4 19.8 + - - -
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Residues in contact with VAL 307 (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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282A ASP* 3.4 35.4 - - - +
283A ALA* 4.1 9.9 - - - +
286A THR* 3.5 36.3 - - + +
303A ALA 3.2 6.3 + - - +
304A ILE 3.9 6.1 - - - +
305A GLN 3.1 0.6 - - - -
306A GLU* 1.3 77.5 - - + +
308A MET* 1.3 67.9 + - - +
310A SER* 2.5 27.9 + - - +
311A TYR* 3.1 11.9 - - + -
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Residues in contact with MET 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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279A ALA 4.4 2.7 - - - +
280A VAL* 4.2 11.4 - - + -
283A ALA* 3.9 24.4 - - + +
304A ILE* 3.0 22.9 + - + +
305A GLN 3.5 4.3 - - - +
307A VAL* 1.3 77.8 - - - +
309A GLU* 1.3 58.2 + - - +
310A SER 3.2 3.8 + - - -
311A TYR* 3.3 21.5 + - - +
322A VAL* 3.6 36.4 - - + +
323A LYS 4.1 0.4 - - - -
324A PRO* 3.6 33.4 - - + -
365A THR* 3.9 15.9 - - - +
366A PHE 3.4 28.7 - - - +
367A GLY* 3.9 7.4 - - - +
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Residues in contact with GLU 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A GLN* 2.8 58.2 + - + +
306A GLU* 4.1 5.0 - - - +
308A MET* 1.3 68.7 - - - +
310A SER* 1.3 57.9 + - - +
311A TYR 3.0 7.3 + - - -
321A GLN* 3.0 40.6 + - - +
322A VAL 3.6 17.3 - - - +
323A LYS* 4.6 5.8 - - + +
324A PRO* 3.7 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