Contacts of the helix formed by residues 341 - 362 (chain D) in PDB entry 3OS8
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 341 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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342D MET* 1.3 70.7 + - - +
343D MET* 3.1 7.3 - - - +
344D GLY* 2.8 18.4 + - - +
345D LEU* 2.9 20.3 + - - +
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Residues in contact with MET 342 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341D SER* 1.3 80.8 + - - +
343D MET* 1.3 58.2 + - - +
345D LEU* 3.1 12.4 + - - +
346D LEU* 2.9 46.4 + - + +
404D PHE* 4.9 5.4 - - - -
408D LEU* 5.9 2.9 - - - -
410D LEU* 3.2 34.5 - - + -
414D GLN 4.2 7.6 - - - +
418D VAL* 3.4 50.7 - - + -
421D MET* 3.9 13.5 - - + +
425D PHE* 4.8 7.9 - - + -
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Residues in contact with MET 343 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D KN0 3.5 39.0 - - + -
341D SER 3.1 4.8 - - - +
342D MET* 1.3 75.6 - - + +
344D GLY* 1.3 62.6 + - - +
346D LEU* 4.1 2.6 - - - +
347D THR* 2.6 37.2 + - - +
418D VAL* 5.7 0.4 - - + -
421D MET* 3.2 31.2 - - + -
524D HIS* 4.9 4.7 - - - -
525D LEU* 3.8 9.6 - - + -
528D MET* 4.9 13.5 - - + -
530D CYS* 3.6 33.9 - - + -
533D VAL* 5.0 2.5 - - + -
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Residues in contact with GLY 344 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341D SER* 2.8 14.0 + - - +
343D MET* 1.3 79.8 - - - +
345D LEU* 1.3 62.9 + - - +
347D THR* 3.8 4.4 - - - -
348D ASN* 3.2 23.6 + - - +
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Residues in contact with LEU 345 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329D SER* 3.8 16.1 + - - +
330D GLU 5.1 2.2 - - - +
331D TYR* 4.4 20.4 - - + +
332D ASP 4.0 20.9 - - - +
341D SER* 2.9 17.0 + - - +
342D MET* 3.1 12.5 + - - +
344D GLY* 1.3 77.7 - - - +
346D LEU* 1.3 67.5 + - + +
348D ASN* 3.4 7.8 + - + +
349D LEU* 3.0 25.8 + - - +
408D LEU* 3.7 36.1 - - + +
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Residues in contact with LEU 346 (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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1D KN0 3.6 74.1 + - + +
342D MET* 2.9 30.1 + - + +
343D MET* 4.1 1.3 - - - +
345D LEU* 1.3 76.8 - - + +
347D THR* 1.3 54.9 + - - +
349D LEU* 3.2 6.3 + - + +
350D ALA* 2.7 39.2 + - - +
404D PHE* 3.5 39.3 - - + -
408D LEU* 5.8 2.5 - - + -
421D MET* 4.3 15.9 - - + -
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Residues in contact with THR 347 (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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1D KN0 3.4 22.4 - - - -
343D MET* 2.6 26.0 + - - +
344D GLY* 3.8 6.2 - - - -
346D LEU* 1.3 76.9 - - - +
348D ASN* 1.3 62.0 + - - +
350D ALA* 4.1 0.2 - - - +
351D ASP* 3.0 44.9 + - - +
533D VAL* 4.0 22.4 - - + +
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Residues in contact with ASN 348 (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 SER* 4.6 2.1 + - - -
330D GLU* 2.8 48.8 + - - +
344D GLY 3.2 15.7 + - - +
345D LEU* 3.8 8.3 - - + +
347D THR* 1.3 81.7 - - - +
349D LEU* 1.3 61.4 + - - +
351D ASP* 3.8 5.8 + - - +
352D ARG* 2.9 45.1 + - - +
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Residues in contact with LEU 349 (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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1D KN0 4.3 10.3 - - + +
327D LEU* 4.1 29.8 - - + +
328D TYR 4.2 8.1 - - - +
329D SER* 4.4 8.1 - - - +
345D LEU 3.0 17.4 + - - +
346D LEU* 3.7 5.8 - - + +
348D ASN* 1.3 76.0 - - - +
350D ALA* 1.3 60.5 + - - +
352D ARG* 3.2 24.3 + - - +
353D GLU* 2.9 51.3 + - - +
404D PHE* 3.4 39.0 - - + +
405D ALA* 4.7 2.7 - - + -
408D LEU* 5.4 2.0 - - + -
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Residues in contact with ALA 350 (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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1D KN0 3.2 39.0 + - + +
346D LEU 2.7 21.4 + - - +
347D THR 4.1 1.3 - - - +
349D LEU* 1.3 73.4 - - - +
351D ASP* 1.3 58.9 + - - +
353D GLU* 3.1 10.3 + - - +
354D LEU* 2.9 32.4 + - - +
383D TRP* 5.0 2.5 - - + -
387D LEU* 4.0 13.5 - - + +
533D VAL* 5.7 0.2 - - + -
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Residues in contact with ASP 351 (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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347D THR* 3.0 41.1 + - - +
348D ASN* 3.9 7.5 - - - +
350D ALA* 1.3 79.1 - - - +
352D ARG* 1.3 62.9 + - + +
354D LEU* 3.6 14.4 + - - +
355D VAL* 3.6 17.2 - - - +
533D VAL* 4.7 11.1 - - - +
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Residues in contact with ARG 352 (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 LEU* 3.8 27.6 - - + +
328D TYR 2.7 32.5 + - - +
329D SER* 3.8 3.6 - - - +
330D GLU* 3.3 33.4 + - - +
348D ASN* 2.9 35.6 + - - +
349D LEU* 3.2 20.9 + - - +
351D ASP* 1.3 77.8 - - + +
353D GLU* 1.3 64.3 + - - +
354D LEU 3.5 0.3 + - - -
355D VAL* 3.6 14.4 + - - +
356D HIS* 3.4 18.4 - - + -
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Residues in contact with GLU 353 (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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1D KN0 2.7 39.3 + - - -
327D LEU* 3.9 22.7 + - + +
349D LEU* 2.9 34.7 + - + +
350D ALA 3.1 4.0 + - - +
352D ARG* 1.3 75.7 - - - +
354D LEU* 1.3 59.2 + - - +
356D HIS* 3.0 9.1 + - - +
357D MET* 2.8 27.8 + - - +
387D LEU* 3.9 20.0 - - + +
394D ARG* 3.7 16.4 + - - -
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Residues in contact with LEU 354 (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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350D ALA 2.9 16.0 + - - +
351D ASP* 3.7 11.0 - - - +
352D ARG 3.3 0.4 - - - -
353D GLU* 1.3 76.4 - - - +
355D VAL* 1.3 65.1 + - + +
357D MET* 3.0 25.1 + - + +
358D ILE* 2.9 52.4 + - + +
379D LEU* 6.0 0.2 - - + -
383D TRP* 4.9 7.2 - - + -
387D LEU* 5.3 0.2 - - - +
535D PRO* 4.0 28.5 - - + -
539D LEU* 4.4 7.4 - - + -
540D LEU* 4.2 10.5 - - + -
543D MET* 3.3 27.8 - - + -
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Residues in contact with VAL 355 (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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351D ASP 3.6 17.9 - - - +
352D ARG* 3.7 10.8 - - - +
353D GLU 3.2 0.6 - - - -
354D LEU* 1.3 79.4 - - + +
356D HIS* 1.3 64.4 + - + +
358D ILE* 3.6 6.6 + - - +
359D ASN* 2.9 38.1 + - - +
543D MET* 5.3 10.8 - - - -
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Residues in contact with HIS 356 (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 PRO* 3.9 19.6 - - + +
325D PRO* 3.5 27.4 - - + +
327D LEU* 3.6 31.1 - - + +
352D ARG* 3.4 22.4 - - + -
353D GLU* 3.0 7.4 + - - +
355D VAL* 1.3 78.2 - - + +
357D MET* 1.3 54.4 - - - +
359D ASN* 3.2 7.5 + - - +
360D TRP* 2.7 36.2 + - - +
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Residues in contact with MET 357 (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 PRO* 5.2 4.0 - - - +
353D GLU 2.8 11.2 + - - +
354D LEU* 3.0 23.3 + - + +
356D HIS* 1.3 77.1 - - - +
358D ILE* 1.3 52.7 + - - +
360D TRP* 3.1 23.3 + - + +
361D ALA* 2.7 37.3 + - - +
379D LEU* 4.2 17.5 - - + -
383D TRP* 3.5 44.4 - - + +
386D ILE* 4.0 21.1 - - + -
387D LEU* 3.6 29.2 - - + -
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Residues in contact with ILE 358 (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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354D LEU* 2.9 53.3 + - + +
355D VAL* 3.7 9.2 - - - +
357D MET* 1.3 76.8 - - + +
359D ASN* 1.3 64.0 + - - +
361D ALA* 3.4 7.1 + - - +
362D LYS* 3.1 47.0 + - + +
379D LEU* 4.3 18.6 - - + -
540D LEU* 4.2 7.9 - - + -
543D MET* 4.1 43.5 - - + +
544D LEU* 4.3 9.9 - - + +
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Residues in contact with ASN 359 (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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355D VAL* 2.9 30.5 + - - +
356D HIS* 3.2 9.4 + - - +
357D MET 3.2 0.6 - - - -
358D ILE* 1.3 81.1 - - - +
360D TRP* 1.3 65.4 + - - +
362D LYS* 3.6 23.5 + - - +
363D ARG* 3.3 28.8 + - - +
547D HIS* 4.1 12.3 - - - +
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Residues in contact with TRP 360 (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 LEU* 4.9 6.5 + - - +
322D ALA* 3.3 42.1 - - + +
323D GLU* 4.2 8.9 + - - -
324D PRO* 4.3 13.0 - - + -
356D HIS 2.7 21.5 + - - +
357D MET* 3.4 21.3 - - + +
359D ASN* 1.3 72.0 - - - +
361D ALA* 1.3 67.9 + - + +
363D ARG* 2.9 24.0 + - - +
364D VAL* 3.3 28.0 + - + +
379D LEU* 5.5 0.2 - - + -
386D ILE* 3.8 28.7 - - + -
446D VAL* 5.2 2.0 + - - +
449D LYS* 3.8 51.8 - - + +
450D SER* 4.1 13.2 + - - -
453D LEU* 3.9 23.3 - - + -
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Residues in contact with ALA 361 (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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357D MET 2.7 19.9 + - - +
358D ILE* 3.6 5.8 - - - +
360D TRP* 1.3 83.1 - - + +
362D LYS* 1.3 58.2 + - - +
363D ARG 2.9 5.2 + - - -
364D VAL* 3.0 12.1 + - - +
367D PHE* 3.2 33.7 - - + +
379D LEU* 4.0 19.3 - - + -
453D LEU* 3.9 20.9 - - + -
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Residues in contact with LYS 362 (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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358D ILE* 3.1 34.7 + - + +
359D ASN* 3.9 16.6 + - - +
360D TRP 3.3 0.8 - - - -
361D ALA* 1.3 76.2 - - - +
363D ARG* 1.3 61.1 + - + +
364D VAL 3.5 2.6 - - - +
367D PHE* 4.0 1.8 - - + -
368D VAL* 3.1 36.9 - - + +
375D GLN* 4.6 5.6 - - - +
543D MET 4.4 4.6 + - - -
544D LEU* 3.4 36.0 + - + -
547D HIS* 3.3 45.4 - - - +
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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