Contacts of the helix formed by residues 441 - 456 (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 GLN 441 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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393D TRP* 3.7 3.1 - - - -
439D ASN* 2.6 32.7 + - - +
440D LEU* 1.3 77.1 + - - +
442D GLY* 1.3 60.9 + - - +
443D GLU* 3.9 15.6 - - + +
444D GLU* 2.9 33.1 + - + +
445D PHE* 2.8 29.3 + - - +
503D ARG* 4.7 1.1 - - - +
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Residues in contact with GLY 442 (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 LEU* 4.6 7.9 - - - -
393D TRP* 3.4 27.6 - - - -
441D GLN* 1.3 73.0 + - - +
443D GLU* 1.3 66.4 + - - +
445D PHE* 3.2 4.0 + - - +
446D VAL* 3.0 28.9 + - - +
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Residues in contact with GLU 443 (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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316D VAL* 3.6 25.2 - - + +
320D LEU* 4.3 14.0 - - + +
441D GLN* 3.2 17.5 - - + +
442D GLY* 1.3 78.9 + - - +
444D GLU* 1.3 61.7 + - + +
446D VAL* 3.1 23.7 - - - +
447D CYS* 3.4 14.0 - - - -
489D LEU* 3.8 29.4 - - + -
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Residues in contact with GLU 444 (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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440D LEU* 3.4 13.7 - - + +
441D GLN* 2.9 34.2 + - + +
443D GLU* 1.3 74.5 - - + +
445D PHE* 1.3 66.1 + - - +
447D CYS* 3.1 5.5 + - - +
448D LEU* 3.0 24.7 + - - +
486D LEU* 4.0 22.8 - - + +
489D LEU* 4.6 13.9 - - + +
490D MET* 4.1 14.7 - - + +
503D ARG* 2.7 49.7 + - - -
507D LEU* 4.5 5.6 - - + -
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Residues in contact with PHE 445 (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 GLU* 3.6 21.1 - - - -
389D ILE* 3.6 33.0 - - + -
390D GLY* 4.1 11.2 - - - -
393D TRP* 3.5 62.6 - + + -
435D PHE* 4.7 0.2 - + - -
440D LEU* 4.1 13.4 - - + +
441D GLN 2.8 13.2 + - - +
442D GLY* 3.4 8.7 - - - +
444D GLU* 1.3 78.2 - - - +
446D VAL* 1.3 73.0 + - + +
448D LEU* 3.1 6.1 + - + +
449D LYS* 3.0 46.3 + - + +
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Residues in contact with VAL 446 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316D VAL* 4.8 4.0 - - + +
319D LEU* 3.7 30.5 - - + +
320D LEU* 4.1 17.9 - - + +
323D GLU* 3.7 37.9 - - + +
360D TRP* 5.2 2.0 + - - +
442D GLY 3.0 13.5 + - - +
443D GLU* 3.1 23.3 - - - +
445D PHE* 1.3 82.5 - - + +
447D CYS* 1.3 61.0 + - - +
449D LYS* 3.5 8.1 + - - +
450D SER* 3.0 28.6 + - - -
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Residues in contact with CYS 447 (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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315D MET* 5.4 0.2 - - - -
316D VAL* 4.8 2.7 - - - -
319D LEU* 4.1 16.4 - - - -
443D GLU 3.4 15.0 - - - -
444D GLU 3.1 8.9 + - - +
446D VAL* 1.3 80.4 - - - +
448D LEU* 1.3 59.9 + - - +
450D SER* 3.3 3.5 + - - -
451D ILE* 2.9 33.8 + - - +
482D ILE* 3.8 19.0 - - + +
485D THR* 3.9 28.0 - - - -
486D LEU* 3.8 23.1 - - + -
489D LEU* 4.3 4.0 - - - -
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Residues in contact with LEU 448 (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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389D ILE* 4.1 19.7 - - + -
435D PHE* 4.7 8.3 - - + -
440D LEU* 4.4 17.0 - - + -
444D GLU 3.0 15.9 + - - +
445D PHE* 3.1 7.8 + - - +
447D CYS* 1.3 76.8 - - + +
449D LYS* 1.3 63.5 + - - +
451D ILE* 3.0 11.1 + - + +
452D ILE* 2.9 27.6 + - - +
486D LEU* 4.8 6.5 - - + -
507D LEU* 4.0 54.7 - - + +
508D LEU* 4.4 9.4 - - + -
510D ILE* 6.0 0.7 - - + -
511D LEU* 4.3 19.8 - - + +
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Residues in contact with LYS 449 (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 GLU* 2.6 37.6 + - - -
324D PRO* 3.7 18.6 - - - +
360D TRP* 3.8 33.3 - - + +
386D ILE* 4.1 21.6 - - + +
389D ILE* 3.8 21.4 - - + +
390D GLY* 5.2 2.2 - - - +
445D PHE* 3.0 37.8 + - + +
446D VAL* 3.7 7.6 - - - +
448D LEU* 1.3 76.2 - - - +
450D SER* 1.3 62.3 + - - +
452D ILE* 3.2 12.7 + - - +
453D LEU* 3.1 17.2 + - - +
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Residues in contact with SER 450 (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* 3.3 28.6 - - - +
360D TRP* 4.1 9.5 - - - -
364D VAL* 4.1 17.3 - - - +
446D VAL 3.0 15.9 + - - -
447D CYS 3.5 7.9 - - - -
449D LYS* 1.3 72.7 - - - +
451D ILE* 1.3 66.4 + - - +
453D LEU* 3.2 7.0 + - - +
454D LEU* 3.1 26.5 + - - +
482D ILE* 3.9 18.6 - - - -
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Residues in contact with ILE 451 (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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509B LEU* 3.7 28.7 - - + -
447D CYS 2.9 21.1 + - - +
448D LEU* 3.4 11.2 - - + +
450D SER* 1.3 75.2 - - - +
452D ILE* 1.3 58.9 + - - +
454D LEU 3.3 1.4 + - - -
455D ASN* 2.8 36.0 + - + +
479D LEU* 4.0 19.1 - - + +
482D ILE* 3.7 25.4 - - + -
483D THR* 5.5 3.8 - - - +
486D LEU* 3.8 21.5 - - + -
508D LEU* 3.9 16.2 - - + -
511D LEU* 3.7 19.5 - - + -
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Residues in contact with ILE 452 (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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382D ALA* 3.8 3.9 - - + +
385D GLU* 3.7 28.9 - - + +
386D ILE* 4.0 13.7 - - + -
389D ILE* 3.9 39.0 - - + -
448D LEU 2.9 15.2 + - - +
449D LYS* 3.4 7.4 - - - +
451D ILE* 1.3 77.6 - - - +
453D LEU* 1.3 63.6 + - - +
455D ASN* 4.6 2.0 - - - +
456D SER* 3.0 40.3 + - - +
511D LEU* 4.0 23.8 - - + -
514D ILE* 4.2 18.2 - - + -
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Residues in contact with LEU 453 (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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360D TRP* 3.9 10.5 - - + -
361D ALA* 3.9 13.5 - - + -
364D VAL* 3.7 32.5 - - + -
367D PHE* 3.8 36.6 - - + -
378D LEU* 3.5 31.8 - - + +
379D LEU* 4.0 28.7 - - + +
382D ALA* 4.0 6.3 - - + -
386D ILE* 4.2 10.3 - - + +
449D LYS 3.1 9.3 + - - +
450D SER 3.2 8.9 + - - +
452D ILE* 1.3 81.4 - - - +
454D LEU* 1.3 61.6 + - + +
455D ASN 3.6 0.2 + - - -
456D SER 4.2 1.6 + - - -
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Residues in contact with LEU 454 (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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364D VAL* 4.7 12.1 - - + -
366D GLY 5.4 1.3 - - - -
367D PHE* 4.3 22.7 - - + +
370D LEU* 4.8 3.1 - - + -
378D LEU* 3.9 25.0 - - + +
450D SER 3.1 10.4 + - - +
453D LEU* 1.3 82.4 - - + +
455D ASN* 1.3 60.0 + - - +
458D VAL* 3.5 9.4 - - - +
475D ILE* 3.3 36.7 - - + +
478D VAL* 3.4 37.9 - - + -
479D LEU* 3.9 17.0 - - + -
482D ILE* 3.9 19.7 - - + -
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Residues in contact with ASN 455 (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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509B LEU* 3.4 30.7 - - - +
512B SER* 3.1 24.1 + - - -
513B HIS* 2.6 55.2 + - - -
451D ILE* 2.8 28.1 + - + +
452D ILE* 4.5 1.3 - - - +
454D LEU* 1.3 77.5 - - - +
456D SER* 1.3 57.5 + - - +
457D GLY 3.3 2.9 - - - -
458D VAL* 3.2 9.9 - - - +
459D TYR* 3.7 11.7 + - - -
476D HIS* 5.6 1.0 - - - -
479D LEU* 4.4 11.5 - - + +
511D LEU* 6.0 0.3 - - - +
515D ARG* 4.9 0.3 + - - -
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Residues in contact with SER 456 (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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513B HIS* 3.9 3.3 + - - -
381D CYS* 4.0 11.7 - - - +
382D ALA* 4.2 14.6 - - - -
385D GLU* 2.7 33.6 + - - -
452D ILE* 3.0 22.8 + - - +
453D LEU 4.2 0.4 + - - -
454D LEU 3.8 0.4 - - - -
455D ASN* 1.3 77.9 + - - +
457D GLY* 1.3 58.2 + - - +
459D TYR* 5.1 0.5 + - - +
460D THR* 5.1 1.4 + - - -
515D ARG* 2.9 36.0 + - - +
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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