Contacts of the helix formed by residues 435 - 443 (chain D) in PDB entry 1FSJ
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 PRO 435 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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416D LYS 3.3 8.3 - - - +
418D VAL* 3.9 21.3 - - + -
422D TRP* 3.5 38.6 - - + -
433D PRO 3.4 7.4 - - - +
434D ILE* 1.3 92.0 - - + +
436D ASP* 1.3 67.0 + - - +
437D ARG* 4.4 3.6 - - + +
438D ILE* 3.0 28.9 + - + +
439D ALA* 3.1 10.6 + - - +
457D VAL* 6.2 1.3 - - + -
467D LEU* 3.9 18.4 - - + -
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Residues in contact with ASP 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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414D LYS 3.4 22.1 - - - +
415D GLY 4.4 0.7 - - - +
416D LYS* 2.8 27.0 + - - +
417D PRO* 3.4 26.2 - - + +
418D VAL* 4.7 2.4 + - - +
434D ILE 3.5 0.4 + - - -
435D PRO* 1.3 72.7 - - - +
437D ARG* 1.3 76.4 + - - +
439D ALA* 3.2 2.6 + - - +
440D ASP* 2.9 38.1 + - - +
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Residues in contact with ARG 437 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418D VAL* 5.4 8.7 + - - -
435D PRO* 3.2 1.9 - - + -
436D ASP* 1.3 92.8 + - - +
438D ILE* 1.3 62.2 + - - +
440D ASP* 3.5 11.5 + - - +
441D LYS* 3.1 41.9 + - - +
464D ASP* 2.9 32.5 + - - +
466D GLU* 3.2 36.3 - - - +
467D LEU* 3.8 23.2 - - + +
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Residues in contact with ILE 438 (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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434D ILE* 4.1 14.8 - - + -
435D PRO* 3.0 20.5 + - + +
437D ARG* 1.3 74.6 - - - +
439D ALA* 1.3 68.6 + - - +
441D LYS* 2.9 18.8 + - + +
442D LEU* 3.1 32.7 + - + +
457D VAL* 4.3 13.9 - - + +
460D GLU* 3.6 30.3 - - + +
461D VAL* 3.6 21.5 - - + +
464D ASP* 5.1 2.7 - - + +
467D LEU* 3.6 28.9 - - + -
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Residues in contact with ALA 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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413D GLY 3.9 2.9 - - - +
414D LYS 3.4 34.8 - - - +
415D GLY* 4.0 3.8 - - - +
434D ILE* 4.2 3.1 - - + +
435D PRO 3.1 7.4 + - - +
436D ASP 3.2 2.7 + - - +
438D ILE* 1.3 78.5 - - - +
440D ASP* 1.3 63.1 + - - +
443D ARG* 2.9 34.3 + - - +
516D MET* 3.6 30.1 - - + -
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Residues in contact with ASP 440 (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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414D LYS 5.3 0.5 - - - +
436D ASP* 2.9 23.4 + - - +
437D ARG* 3.5 17.4 - - - +
438D ILE 3.1 0.2 - - - -
439D ALA* 1.3 78.9 - - - +
441D LYS* 1.3 67.0 + - + +
443D ARG* 3.4 36.0 + - - +
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Residues in contact with LYS 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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437D ARG* 3.1 43.1 + - - +
438D ILE* 2.9 11.4 + - + +
440D ASP* 1.3 83.9 + - + +
442D LEU* 1.3 59.3 + - - +
443D ARG 4.9 0.7 - - - +
445D LYS* 3.2 29.4 + - - +
460D GLU* 3.7 37.0 - - + +
464D ASP* 5.0 5.2 + - - -
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Residues in contact with LEU 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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411D ALA* 3.5 10.5 - - + +
438D ILE* 3.1 27.1 + - + +
441D LYS* 1.3 82.1 - - - +
443D ARG* 1.3 68.3 + - - +
444D ASP 3.4 0.3 + - - -
445D LYS* 3.0 30.1 + - + +
447D PHE* 4.0 19.0 - - + -
453D PHE* 3.8 24.9 - - + -
456D ALA* 4.0 11.0 - - + -
457D VAL* 3.8 26.7 - - + +
460D GLU* 4.0 22.2 - - + +
516D MET* 4.1 11.7 - - - -
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Residues in contact with ARG 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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411D ALA 3.7 11.4 - - - +
412D THR* 4.4 8.1 - - + -
413D GLY 3.0 29.2 + - - +
414D LYS* 3.7 17.6 + - - +
439D ALA* 2.9 25.8 + - - +
440D ASP* 3.4 37.9 + - - +
441D LYS 3.7 1.3 - - - +
442D LEU* 1.3 76.7 - - - +
444D ASP* 1.3 90.7 + - - +
445D LYS* 3.3 7.1 + - - +
516D MET* 3.9 8.2 - - + +
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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