Contacts of the helix formed by residues 320 - 336 (chain A) in PDB entry 2O1S
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 SER 320 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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319A PRO* 1.3 77.2 - - - +
321A TYR* 1.3 64.7 + - - +
322A SER* 3.5 13.0 + - - -
323A LYS* 3.2 25.2 + - - +
324A ILE* 3.1 19.1 + - - +
479A GLY 3.1 20.4 - - - -
480A ASN* 3.7 13.5 - - - +
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Residues in contact with TYR 321 (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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320A SER* 1.3 74.2 - - - +
322A SER* 1.3 56.8 + - - +
324A ILE* 3.1 8.1 + - + +
325A PHE* 2.9 30.3 + - - +
451A PRO* 5.1 2.2 - - + -
452A SER 4.0 1.2 + - - -
453A ASP* 3.4 23.1 - - - -
454A GLU* 3.6 25.5 + - + -
457A CYS* 4.0 18.5 - - + -
476A TYR* 3.4 37.7 - - + -
477A PRO* 3.9 28.2 + - + +
479A GLY 3.1 17.8 + - - -
480A ASN 3.5 20.3 + - - -
481A ALA* 3.9 13.2 - - - -
482A VAL* 4.4 5.9 + - - +
513A THR* 3.4 23.8 - - + +
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Residues in contact with SER 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A SER* 3.1 11.1 + - - -
321A TYR* 1.3 80.2 - - - +
323A LYS* 1.3 56.5 + - - +
325A PHE* 3.5 4.2 + - - +
326A GLY 3.0 21.0 + - - -
348A GLU 5.5 0.2 - - - -
349A GLY 3.6 12.8 - - - -
350A SER 3.5 16.5 - - - +
351A GLY* 3.7 8.8 - - - -
419A ASP* 2.4 30.4 + - - -
420A ARG* 2.7 19.3 + - - -
476A TYR* 4.6 0.4 - - - -
477A PRO 5.5 0.2 + - - -
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Residues in contact with LYS 323 (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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319A PRO* 4.0 20.4 - - + -
320A SER* 3.2 21.0 + - - +
322A SER* 1.3 76.9 - - - +
324A ILE* 1.3 60.7 + - - +
326A GLY* 4.3 1.6 - - - +
327A ASP* 2.8 61.7 + - - +
351A GLY* 5.2 3.6 - - - -
354A GLU* 5.2 4.6 + - - -
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Residues in contact with ILE 324 (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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319A PRO* 3.8 23.1 - - + +
320A SER 3.1 16.1 + - - +
321A TYR* 3.3 13.9 - - + +
323A LYS* 1.3 77.3 - - - +
325A PHE* 1.3 63.6 + - - +
327A ASP* 3.3 8.8 + - + +
328A TRP* 2.9 22.7 + - - +
454A GLU* 3.8 38.1 - - + +
457A CYS* 4.3 15.3 - - + -
458A ARG* 3.7 33.3 + - + +
461A LEU* 5.0 1.6 - - + -
486A LEU* 5.3 7.4 - - + -
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Residues in contact with PHE 325 (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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321A TYR 2.9 13.7 + - - +
322A SER* 3.6 3.4 - - - +
324A ILE* 1.3 76.8 - - - +
326A GLY* 1.3 59.6 + - - +
328A TRP* 3.1 10.3 + + - +
329A LEU* 2.8 64.3 + - + +
350A SER* 3.3 24.0 - - - -
352A MSE 4.1 3.8 - - + -
388A ILE* 3.8 19.5 - - + -
390A ALA* 3.8 24.5 - - + -
417A ALA* 3.4 24.9 - - + -
457A CYS* 5.9 0.2 - - - -
461A LEU* 4.0 24.9 - - + -
476A TYR* 3.3 27.1 - - + +
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Residues in contact with GLY 326 (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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322A SER 3.0 11.7 + - - -
323A LYS* 3.3 3.3 + - - -
325A PHE* 1.3 79.3 - - - +
327A ASP* 1.3 62.5 + - - +
329A LEU* 3.2 11.6 + - - +
330A CYS* 3.0 28.6 + - - -
351A GLY 3.3 26.0 - - - -
352A MSE 5.2 0.7 - - - -
355A PHE* 4.7 1.3 - - - +
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Residues in contact with ASP 327 (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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319A PRO* 6.1 0.2 - - - +
323A LYS* 2.8 54.2 + - - +
324A ILE* 3.6 8.5 - - + +
326A GLY* 1.3 70.6 - - - +
328A TRP* 1.3 64.2 + - - +
330A CYS* 3.2 7.6 + - - +
331A GLU* 3.1 29.9 + - - +
354A GLU* 4.4 12.0 - - - +
458A ARG* 5.2 3.6 - - - +
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Residues in contact with TRP 328 (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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324A ILE 2.9 14.0 + - - +
325A PHE* 3.5 15.7 - + - +
327A ASP* 1.3 74.7 - - - +
329A LEU* 1.3 80.3 + - + +
331A GLU* 3.2 9.6 - - - +
332A THR* 2.9 57.8 + - + -
339A LEU* 4.8 2.2 - - + -
388A ILE* 3.5 34.1 - - + -
415A LEU* 3.8 16.4 - - + -
458A ARG* 4.0 28.8 - - + +
461A LEU* 3.6 46.2 - - + -
462A TYR* 3.9 13.6 - + - +
465A TYR* 3.7 16.8 - + + -
489A LEU* 4.0 26.1 - - + +
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Residues in contact with LEU 329 (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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325A PHE* 2.8 41.0 + - + +
326A GLY* 3.2 10.5 - - - +
328A TRP* 1.3 104.3 - - + +
330A CYS* 1.3 58.0 + - - +
332A THR* 3.8 2.1 - - - -
333A ALA* 2.9 31.7 + - - +
339A LEU* 4.3 5.9 - - + +
341A ALA* 3.9 21.5 - - + -
352A MSE 4.0 11.0 - - + -
355A PHE* 3.7 36.3 - - + -
388A ILE* 3.8 17.0 - - + -
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Residues in contact with CYS 330 (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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326A GLY 3.0 17.9 + - - -
327A ASP* 3.2 9.4 + - - +
329A LEU* 1.3 77.0 - - - +
331A GLU* 1.3 61.5 + - - +
333A ALA 3.5 0.2 + - - -
334A ALA* 3.2 20.4 + - - +
354A GLU* 4.0 25.4 - - - +
355A PHE* 3.5 37.0 - - - -
358A LYS* 4.7 8.3 - - + -
359A PHE* 3.6 21.5 - - + -
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Residues in contact with GLU 331 (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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327A ASP* 3.1 16.7 + - - +
328A TRP* 3.2 12.8 - - - +
330A CYS* 1.3 77.1 - - - +
332A THR* 1.3 68.2 + - - +
334A ALA* 3.4 12.3 + - - +
335A LYS* 3.2 43.2 + - - +
458A ARG* 3.1 41.8 + - - -
489A LEU* 3.9 6.1 - - - +
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Residues in contact with THR 332 (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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328A TRP* 2.9 47.5 + - + -
329A LEU* 3.8 3.6 - - - -
331A GLU* 1.3 78.5 - - - +
333A ALA* 1.3 60.6 + - - +
335A LYS* 2.9 31.9 + - + +
336A ASP* 3.2 16.3 + - - +
339A LEU* 4.1 11.4 - - + -
462A TYR* 5.7 1.0 - - - -
465A TYR* 3.8 37.0 - - + -
466A HIS* 6.1 0.2 - - - +
489A LEU* 5.4 0.2 - - - +
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Residues in contact with ALA 333 (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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329A LEU 2.9 18.8 + - - +
330A CYS 3.8 5.2 - - - +
331A GLU 3.4 0.2 - - - -
332A THR* 1.3 76.4 - - - +
334A ALA* 1.3 59.2 + - - +
336A ASP 3.5 5.5 + - - +
339A LEU* 4.2 6.9 - - + +
355A PHE* 3.9 15.0 - - + -
359A PHE* 3.8 23.7 - - + -
362A ARG* 2.9 44.5 + - - +
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Residues in contact with ALA 334 (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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330A CYS 3.2 15.0 + - - +
331A GLU* 3.7 9.0 - - - +
332A THR 3.1 0.8 - - - -
333A ALA* 1.3 77.3 - - - +
335A LYS* 1.3 61.4 + - + +
359A PHE* 3.9 13.9 - - + -
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Residues in contact with LYS 335 (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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331A GLU* 3.2 44.7 + - - +
332A THR* 2.9 16.9 + - + +
334A ALA* 1.3 82.3 - - + +
336A ASP* 1.3 62.7 + - + +
462A TYR* 5.3 5.6 - - + -
489A LEU* 4.0 16.0 - - - +
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Residues in contact with ASP 336 (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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332A THR* 3.2 15.2 + - - +
333A ALA 3.5 2.5 - - - +
334A ALA 3.6 0.8 - - - -
335A LYS* 1.3 83.2 - - + +
337A ASN* 1.3 60.5 + - - +
338A LYS* 3.1 31.5 + - - +
339A LEU* 3.7 2.1 + - - +
362A ARG* 3.2 19.0 + - - -
386A LYS* 4.2 1.2 - - - +
465A TYR* 2.9 35.7 + - - -
466A HIS* 6.3 0.4 - - - -
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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