Contacts of the helix formed by residues 433 - 448 (chain D) in PDB entry 5LS6
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 433 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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269D ALA* 6.1 0.4 - - - -
432D TRP* 1.3 76.2 - - - +
434D GLY* 1.3 65.1 + - - +
435D ALA* 3.4 9.8 + - - +
436D GLU* 2.9 39.6 + - - +
437D ALA* 3.0 23.9 + - - +
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Residues in contact with GLY 434 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269D ALA 3.5 17.5 + - - -
270D LYS 3.8 4.5 - - - -
271D SER* 3.6 24.5 - - - -
433D SER* 1.3 73.3 - - - +
435D ALA* 1.3 54.5 + - - +
437D ALA 3.3 0.5 + - - -
438D SER* 2.7 38.9 + - - -
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Residues in contact with ALA 435 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264D ILE* 3.5 43.6 - - + +
269D ALA* 3.5 17.1 - - + +
270D LYS 5.1 0.4 - - - -
433D SER* 3.2 8.3 + - - +
434D GLY* 1.3 72.3 - - - +
436D GLU* 1.3 61.0 + - + +
438D SER* 4.2 3.1 - - - -
439D MET* 3.2 26.3 + - - +
654F ARG* 4.4 12.9 - - - +
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Residues in contact with GLU 436 (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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431D GLU 3.8 0.5 - - - +
432D TRP* 3.5 20.2 - - + -
433D SER* 2.9 42.3 + - - +
435D ALA* 1.3 77.0 - - + +
437D ALA* 1.3 54.3 + - - +
439D MET* 3.5 4.1 + - - +
440D PHE* 2.8 35.2 + - - +
458D ILE* 4.2 8.4 - - + +
460D THR* 2.8 48.8 + - + +
461D LYS* 2.9 33.2 + - - +
654F ARG* 6.1 1.8 - - - +
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Residues in contact with ALA 437 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271D SER* 3.3 24.2 - - - +
432D TRP* 4.0 5.1 - - + -
433D SER 3.0 17.1 + - - +
434D GLY 3.3 1.5 + - - +
436D GLU* 1.3 73.6 - - - +
438D SER* 1.3 60.9 + - - +
440D PHE* 3.5 2.9 - - - +
441D ARG* 3.0 35.9 + - - +
469D PHE* 3.8 31.0 - - + -
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Residues in contact with SER 438 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264D ILE* 4.8 8.1 - - - -
270D LYS 3.0 8.6 + - - -
271D SER* 4.6 0.2 + - - -
272D VAL* 2.8 42.5 + - - +
277D SER* 3.5 15.5 - - - -
434D GLY 2.7 21.1 + - - -
435D ALA* 4.5 4.0 - - - -
437D ALA* 1.3 73.6 - - - +
439D MET* 1.3 56.4 + - - +
441D ARG* 3.1 3.8 + - - +
442D VAL* 2.8 40.2 + - - +
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Residues in contact with MET 439 (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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264D ILE* 4.9 8.2 - - + +
435D ALA 3.2 19.7 + - - +
436D GLU* 3.9 4.5 - - - +
438D SER* 1.3 75.0 - - - +
440D PHE* 1.3 65.0 + - - +
442D VAL* 3.5 14.3 - - + +
443D LEU* 3.1 65.4 + - + +
458D ILE* 4.7 12.8 - - + -
654F ARG* 4.2 19.3 - - + +
657F MET* 3.4 54.5 - - + +
658F LEU* 4.4 12.1 - - - -
661F VAL* 4.8 1.6 - - + -
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Residues in contact with PHE 440 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432D TRP* 3.9 12.6 - + + -
436D GLU 2.8 20.6 + - - +
437D ALA 3.5 4.5 - - - +
439D MET* 1.3 75.4 - - - +
441D ARG* 1.3 68.9 - - + +
443D LEU* 2.6 26.0 + - - +
444D ILE* 3.1 46.6 + - + +
451D PHE* 5.1 0.4 - + - -
454D ILE* 3.8 17.0 - - + -
458D ILE* 4.0 10.3 - - + +
466D VAL* 3.7 28.3 - - + -
469D PHE* 3.3 30.3 - + - -
470D ARG* 3.8 27.6 - - + -
473D GLU* 4.0 15.7 - - + -
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Residues in contact with ARG 441 (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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271D SER* 2.7 32.9 + - - -
272D VAL* 3.4 29.3 + - - +
273D GLN* 3.9 32.6 - - - +
274D ARG* 3.5 23.8 - - - +
437D ALA* 3.0 27.1 + - - +
438D SER 3.5 5.8 - - - +
440D PHE* 1.3 80.2 - - + +
442D VAL* 1.3 60.6 + - - +
444D ILE* 3.6 21.6 - - + +
469D PHE* 4.3 3.4 - - - -
473D GLU* 3.2 39.6 + - - +
58J GLN* 5.9 0.8 + - - -
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Residues in contact with VAL 442 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264D ILE* 5.5 0.2 - - + -
274D ARG* 2.7 39.2 + - + +
277D SER* 3.7 27.6 - - - -
278D LEU* 4.3 7.6 - - + -
438D SER 2.8 30.6 + - - +
439D MET* 3.5 11.0 - - + +
440D PHE 3.0 0.2 + - - -
441D ARG* 1.3 73.8 - - - +
443D LEU* 1.3 65.8 + - + +
445D GLY* 3.1 5.0 + - - -
446D THR* 3.7 2.3 + - - +
658F LEU* 4.1 18.4 - - + -
661F VAL* 3.7 37.5 - - + -
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Residues in contact with LEU 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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439D MET* 3.1 52.0 + - + +
440D PHE 2.6 11.7 + - - +
442D VAL* 1.3 72.4 - - - +
444D ILE* 1.3 54.0 + - - +
446D THR* 3.1 4.1 + - + +
447D TYR* 2.6 63.8 + - + +
454D ILE* 3.7 20.4 - - + +
457D LEU* 3.8 27.8 - - + -
458D ILE* 4.0 19.1 - - + +
661F VAL* 4.3 15.3 - - + -
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Residues in contact with ILE 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 PHE* 3.1 51.3 + - + +
441D ARG* 3.6 21.5 - - + +
443D LEU* 1.3 75.0 - - - +
445D GLY* 1.3 63.3 + - - +
447D TYR 4.8 0.2 - - - -
448D TYR* 2.9 37.0 + - - +
449D ASP* 4.8 13.9 - - - +
451D PHE* 5.0 7.4 - - + -
454D ILE* 4.8 7.6 - - + -
470D ARG* 4.9 17.9 - - - +
473D GLU* 5.8 2.5 - - + +
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Residues in contact with GLY 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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274D ARG* 3.5 29.9 + - - -
441D ARG 3.9 0.6 + - - -
442D VAL 3.1 4.4 + - - -
443D LEU 3.1 1.4 - - - -
444D ILE* 1.3 84.5 - - - +
446D THR* 1.3 56.5 + - - +
448D TYR* 3.4 28.2 + - - -
665F ASP* 5.6 0.2 - - - +
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Residues in contact with THR 446 (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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274D ARG* 3.8 13.9 - - - -
442D VAL 3.7 1.4 + - - -
443D LEU* 3.1 17.7 + - + +
445D GLY* 1.3 76.5 - - - +
447D TYR* 1.3 86.9 + - + +
448D TYR* 3.7 9.8 - - - -
661F VAL* 4.5 15.7 - - + -
664F HIS* 2.7 41.6 + - + -
665F ASP* 4.2 2.4 + - - -
671F ILE* 3.1 16.9 - - + +
674F ILE* 5.5 2.2 - - + -
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Residues in contact with TYR 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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443D LEU* 2.6 34.5 + - + +
446D THR* 1.3 96.9 - - + +
448D TYR* 1.3 70.5 + - - +
449D ASP 3.9 0.2 - - - -
450D ASN* 3.5 24.3 - - + +
453D ALA* 3.7 26.5 - - + -
454D ILE* 3.3 21.1 - - + -
457D LEU* 3.4 33.4 - - + +
671F ILE* 3.3 43.7 + - + -
674F ILE* 3.6 11.2 - - + +
675F ASP* 3.8 10.9 + - + +
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Residues in contact with TYR 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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309D LYS 5.0 2.6 + - - -
310D ASN* 3.1 57.4 + - + -
339D THR* 6.0 8.1 - - + -
443D LEU 3.9 0.2 + - - -
444D ILE* 2.9 25.4 + - - +
445D GLY* 3.4 25.1 + - - -
446D THR* 4.4 8.7 - - - -
447D TYR* 1.3 83.4 - - - +
449D ASP* 1.3 71.0 + - + +
450D ASN* 2.9 5.5 + - - +
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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