Contacts of the helix formed by residues 320 - 334 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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318D LEU 4.0 1.0 + - - -
319D PRO* 1.3 76.2 - - - +
321D TYR* 1.3 64.3 + - - +
322D SER* 3.5 11.5 + - - -
323D LYS* 3.0 24.7 + - - +
324D ILE* 3.0 21.5 + - - +
479D GLY* 3.3 18.8 - - - -
480D ASN* 3.8 13.4 - - - +
481D ALA 4.8 0.2 - - - -
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Residues in contact with TYR 321 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320D SER* 1.3 71.6 - - - +
322D SER* 1.3 56.9 + - - +
324D ILE* 3.2 7.9 + - + +
325D PHE* 2.9 28.8 + - - +
451D PRO* 5.1 1.3 - - + -
452D SER 4.1 0.9 + - - -
453D ASP* 3.5 21.6 - - - -
454D GLU* 3.8 22.5 + - + -
457D CYS* 4.2 17.1 - - + -
476D TYR* 3.5 39.5 - - + -
477D PRO* 3.6 32.1 - - + +
479D GLY 3.1 24.2 + - - +
480D ASN 3.5 19.3 - - - -
481D ALA* 3.7 15.8 - - + -
482D VAL* 4.2 5.0 + - - +
513D THR* 3.3 26.7 - - + +
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Residues in contact with SER 322 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320D SER* 3.1 10.1 + - - -
321D TYR* 1.3 78.4 - - - +
323D LYS* 1.3 58.2 + - - +
325D PHE* 3.4 4.8 + - - +
326D GLY* 3.0 24.4 + - - -
348D GLU 5.4 0.4 - - - -
349D GLY 3.5 14.4 + - - -
350D SER 3.4 19.9 - - - +
351D GLY* 4.0 7.5 - - - +
419D ASP* 2.7 28.8 + - - -
420D ARG* 3.5 7.4 + - - -
476D TYR* 4.5 1.7 - - - -
478D ARG* 5.7 1.0 - - - -
479D GLY 5.8 1.0 + - - -
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Residues in contact with LYS 323 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319D PRO* 4.2 17.5 - - + -
320D SER* 3.0 22.6 + - - +
322D SER* 1.3 77.3 - - - +
324D ILE* 1.3 66.3 + - - +
326D GLY 3.3 0.9 + - - +
327D ASP* 2.9 62.8 + - - +
351D GLY* 5.1 5.6 - - - -
354D GLU* 4.1 13.9 + - - -
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Residues in contact with ILE 324 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319D PRO* 3.9 23.3 - - + -
320D SER 3.0 19.0 + - - +
321D TYR* 3.4 14.4 - - + +
323D LYS* 1.3 76.7 - - - +
325D PHE* 1.3 63.5 + - - +
327D ASP* 3.7 9.2 - - - +
328D TRP* 3.1 21.7 + - - +
454D GLU* 3.8 37.9 - - + +
457D CYS* 4.5 15.0 - - + -
458D ARG* 3.9 27.4 + - + +
461D LEU* 5.2 1.3 - - + -
481D ALA* 5.0 0.4 - - + -
486D LEU* 4.7 15.9 - - + -
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Residues in contact with PHE 325 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321D TYR 2.9 14.1 + - - +
322D SER* 3.5 6.5 - - - +
323D LYS 3.2 0.2 - - - -
324D ILE* 1.3 75.1 - - - +
326D GLY* 1.3 66.7 + - - +
328D TRP* 3.0 14.6 + + - +
329D LEU* 2.9 59.7 + - + +
341D ALA* 5.8 0.4 - - + -
350D SER* 3.6 18.4 - - - -
352D MSE 4.1 6.3 - - + -
388D ILE* 4.1 11.7 - - + -
390D ALA* 3.8 24.0 - - + -
417D ALA* 3.5 24.2 - - + -
457D CYS* 5.8 0.4 - - - -
461D LEU* 3.9 27.4 - - + -
476D TYR* 3.5 25.6 - - + +
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Residues in contact with GLY 326 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322D SER 3.0 12.1 + - - -
323D LYS 3.9 1.1 - - - -
325D PHE* 1.3 79.9 - - - +
327D ASP* 1.3 63.1 + - - +
329D LEU* 3.3 14.2 + - - +
330D CYS* 3.2 29.0 + - - -
351D GLY 3.4 24.9 - - - -
352D MSE 4.9 1.6 - - - -
354D GLU* 5.9 1.8 - - - -
355D PHE* 4.5 1.9 - - - +
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Residues in contact with ASP 327 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323D LYS* 2.9 60.2 + - - +
324D ILE* 3.7 9.4 + - - +
326D GLY* 1.3 77.0 - - - +
328D TRP* 1.3 58.6 + - - +
330D CYS* 3.3 8.8 + - - +
331D GLU* 3.0 36.6 + - - +
354D GLU* 4.6 11.1 - - - +
458D ARG* 5.3 2.2 - - - +
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Residues in contact with TRP 328 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324D ILE 3.1 11.6 + - - +
325D PHE* 3.0 17.9 + + - +
327D ASP* 1.3 77.9 - - - +
329D LEU* 1.3 78.4 + - + +
331D GLU* 3.6 3.8 - - - +
332D THR* 2.8 49.9 + - + -
339D LEU* 4.7 1.3 - - + -
388D ILE* 3.4 35.2 - - + -
415D LEU* 3.8 4.7 - - + -
458D ARG* 4.2 27.1 - - + +
461D LEU* 3.4 51.8 - - + -
462D TYR* 3.9 17.3 - + - +
465D TYR* 3.7 24.5 - + + -
489D LEU* 4.1 24.0 - - + +
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Residues in contact with LEU 329 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325D PHE* 2.9 46.3 + - + +
326D GLY* 3.5 10.5 - - - +
327D ASP 3.2 0.4 - - - -
328D TRP* 1.3 103.8 - - + +
330D CYS* 1.3 57.7 + - - +
332D THR* 3.8 0.9 - - - -
333D ALA* 2.9 33.3 + - - +
339D LEU* 4.1 8.5 - - + +
341D ALA* 4.0 21.8 - - + -
352D MSE 4.1 14.4 - - + -
355D PHE* 3.6 27.3 - - + -
388D ILE* 3.7 16.2 - - + -
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Residues in contact with CYS 330 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326D GLY 3.2 16.4 + - - -
327D ASP* 3.3 8.9 + - - +
329D LEU* 1.3 82.0 - - - +
331D GLU* 1.3 63.2 + - - +
333D ALA 3.7 0.2 + - - -
334D ALA* 3.4 19.4 + - - +
354D GLU* 3.8 26.5 - - - +
355D PHE* 3.7 30.7 - - - -
358D LYS* 4.3 12.8 - - + -
359D PHE* 3.9 18.0 - - + -
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Residues in contact with GLU 331 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327D ASP* 3.0 20.2 + - - +
328D TRP* 3.6 9.2 - - + +
330D CYS* 1.3 76.9 - - - +
332D THR* 1.3 63.6 + - - +
334D ALA* 3.3 14.7 + - - +
335D LYS* 3.3 27.1 + - - +
458D ARG* 2.6 48.3 + - - -
489D LEU* 4.0 9.9 - - + +
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Residues in contact with THR 332 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328D TRP* 2.8 40.5 + - + -
331D GLU* 1.3 72.8 - - - +
333D ALA* 1.3 57.8 + - - +
334D ALA 2.9 4.9 - - - -
335D LYS* 2.8 39.6 + - + +
336D ASP* 3.5 8.6 + - - +
339D LEU* 3.5 25.4 - - + -
462D TYR* 5.8 2.3 - - + -
465D TYR* 3.5 33.4 - - + +
466D HIS* 5.8 2.2 - - + -
489D LEU* 5.5 0.5 - - - +
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Residues in contact with ALA 333 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329D LEU 2.9 20.5 + - - +
332D THR* 1.3 71.3 - - - +
334D ALA* 1.3 58.3 + - - +
335D LYS 3.2 0.4 - - - -
336D ASP 3.0 5.5 - - - +
339D LEU* 4.0 10.2 - - + +
355D PHE* 3.8 21.8 - - + -
359D PHE* 3.9 24.5 - - + -
362D ARG* 2.5 44.5 + - - +
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Residues in contact with ALA 334 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330D CYS 3.4 11.5 + - - +
331D GLU* 3.3 14.1 + - - +
332D THR 2.9 1.2 - - - -
333D ALA* 1.3 78.7 - - - +
335D LYS* 1.3 60.8 + - + +
336D ASP 3.6 0.4 - - - -
359D PHE* 4.4 12.3 - - + -
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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