Contacts of the helix formed by residues 405 - 417 (chain D) in PDB entry 6PB4
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 GLU 405 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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390D LEU* 4.5 3.6 - - - +
400D MET* 3.5 47.5 + - - +
403D ARG* 4.6 10.7 - - + +
404D GLU* 1.3 78.7 - - - +
406D ALA* 1.3 67.0 + - - +
407D VAL* 3.6 26.4 - - + +
408D VAL* 3.0 30.3 + - + +
409D TRP* 3.5 5.7 - - - -
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Residues in contact with ALA 406 (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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193B GLU* 4.3 20.7 - - + +
194B GLN* 3.6 26.4 - - - +
404D GLU 4.0 1.8 + - - -
405D GLU* 1.3 71.6 - - - +
407D VAL* 1.3 65.8 + - + +
409D TRP* 2.9 26.5 + - - +
410D ASP* 3.3 13.7 + - - +
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Residues in contact with VAL 407 (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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385D LEU* 5.7 2.5 - - + -
388D ARG* 6.2 0.2 - - - +
390D LEU* 4.7 15.7 - - + -
400D MET* 5.9 0.2 - - + -
405D GLU* 3.6 30.1 - - + +
406D ALA* 1.3 77.0 - - + +
408D VAL* 1.3 58.7 + - + +
410D ASP* 2.9 14.1 + - - +
411D ILE* 2.5 57.4 + - + +
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Residues in contact with VAL 408 (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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374D LEU* 4.4 22.9 - - + -
381D ILE* 5.2 13.0 - - + +
385D LEU* 6.2 4.5 - - + -
400D MET* 4.7 10.5 - - + +
401D VAL* 5.1 17.7 - - + -
404D GLU* 5.2 2.2 - - - +
405D GLU* 3.0 35.0 - - + +
407D VAL* 1.3 78.0 - - + +
409D TRP* 1.3 62.1 + - + +
411D ILE* 3.0 13.2 + - + +
412D LEU* 2.3 39.1 + - + +
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Residues in contact with TRP 409 (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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191B ARG* 3.3 15.1 + - - +
193B GLU 5.1 10.1 - - - +
194B GLN* 5.6 2.2 - - - -
370D LYS* 4.2 36.3 - - + -
371D LYS* 5.5 6.1 - - + -
374D LEU* 4.1 23.6 - - + -
404D GLU* 2.6 42.8 + - - +
405D GLU 3.5 16.7 + - - -
406D ALA* 2.9 16.3 + - - +
408D VAL* 1.3 79.7 - - + +
410D ASP* 1.3 55.8 + - - +
412D LEU* 3.2 35.7 - - + +
413D ASP* 2.5 36.9 + - - +
441D LEU* 5.9 1.9 - - + +
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Residues in contact with ASP 410 (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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191B ARG* 2.4 38.6 + - - +
193B GLU* 3.7 24.0 - - - +
406D ALA* 3.7 11.8 - - - +
407D VAL* 2.9 14.0 + - - +
409D TRP* 1.3 73.2 - - - +
411D ILE* 1.3 53.1 + - + +
413D ASP* 3.0 4.3 + - - +
414D GLU* 2.4 40.1 + - - +
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Residues in contact with ILE 411 (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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381D ILE* 4.3 22.2 - - + +
384D LYS* 3.3 28.7 - - + +
385D LEU* 4.3 20.0 - - + -
388D ARG* 4.2 27.8 - - + +
390D LEU* 6.0 2.0 - - + -
407D VAL* 2.5 51.1 + - + +
408D VAL* 3.1 10.8 - - + +
410D ASP* 1.3 71.4 - - + +
412D LEU* 1.3 53.5 + - - +
414D GLU* 2.9 9.1 + - - +
415D VAL* 2.7 34.7 + - - +
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Residues in contact with LEU 412 (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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370D LYS* 4.9 4.3 - - + +
373D ALA* 4.5 5.2 - - + +
374D LEU* 3.4 42.4 - - + +
377D PHE* 4.6 4.0 - - + -
381D ILE* 3.9 24.7 - - + -
408D VAL* 2.3 30.9 + - + +
409D TRP* 3.0 31.4 + - + +
411D ILE* 1.3 66.9 - - - +
413D ASP* 1.3 65.9 + - - +
415D VAL* 3.0 8.9 + - + +
416D ILE* 2.9 51.4 + - + +
441D LEU* 5.0 8.1 - - + -
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Residues in contact with ASP 413 (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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191B ARG* 3.2 32.1 + - - +
409D TRP 2.5 11.6 + - - +
410D ASP 3.3 4.8 - - - +
412D LEU* 1.3 72.4 - - - +
414D GLU* 1.3 67.0 + - - +
416D ILE* 2.9 21.0 + - - +
417D ARG* 3.3 25.3 + - - +
441D LEU* 5.0 12.1 - - + +
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Residues in contact with GLU 414 (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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384D LYS* 4.9 11.0 - - - -
388D ARG* 4.8 14.4 - - - +
410D ASP 2.4 27.1 + - - +
411D ILE* 2.9 13.9 + - - +
413D ASP* 1.3 77.7 - - - +
415D VAL* 1.3 60.6 + - - +
417D ARG* 2.5 51.3 + - - +
43E ASN* 4.0 7.8 + - - +
45E LYS* 4.1 5.9 - - - +
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Residues in contact with VAL 415 (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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377D PHE* 4.7 7.2 - - + -
380D PHE* 3.5 41.1 - - + -
381D ILE* 4.2 13.2 - - + -
384D LYS* 3.4 31.9 - - + +
411D ILE 2.7 17.4 + - - +
412D LEU* 3.0 8.7 + - + +
414D GLU* 1.3 79.4 - - - +
416D ILE* 1.3 71.9 + - + +
417D ARG 3.0 3.3 + - - +
419D HIS* 4.3 4.0 - - + +
45E LYS* 2.8 33.6 + - - +
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Residues in contact with ILE 416 (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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373D ALA* 4.5 6.7 - - + -
377D PHE* 3.8 28.5 - - + -
412D LEU* 2.9 49.4 + - + +
413D ASP* 2.9 8.2 + - - +
415D VAL* 1.3 77.7 - - + +
417D ARG* 1.3 67.5 + - - +
418D GLU 3.3 0.5 + - - -
419D HIS* 3.0 21.1 + - - +
439D PRO* 3.8 35.4 - - + +
441D LEU* 3.9 24.2 - - + -
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Residues in contact with ARG 417 (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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413D ASP* 3.3 17.0 + - - +
414D GLU* 2.5 61.4 + - - +
415D VAL 3.0 4.3 + - - +
416D ILE* 1.3 77.8 - - - +
418D GLU* 1.3 70.4 + - + +
419D HIS* 2.8 12.3 + - - +
438D GLU* 5.2 0.2 - - - -
3E ARG* 4.2 12.3 - - - +
43E ASN* 3.3 45.1 + - - +
44E ASP* 3.9 10.0 + - - +
45E LYS* 2.8 30.3 - - + +
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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