Contacts of the helix formed by residues 438 - 450 (chain E) in PDB entry 3IFS
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 PHE 438 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427E LYS* 3.9 41.1 - - + -
430E PHE* 3.9 21.3 - + + -
431E ALA* 3.5 22.0 - - + -
435E LYS* 3.3 35.6 + - + +
436E PRO 3.5 16.8 - - - -
437E GLY* 1.3 79.0 - - - +
439E GLU* 1.3 59.4 + - - +
440E GLU* 3.3 2.9 - - - -
441E LEU* 3.1 13.7 + - + +
442E LYS* 2.9 27.6 + - - +
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Residues in contact with GLU 439 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434E GLY 5.5 0.7 - - - +
435E LYS 4.4 2.2 + - - +
436E PRO* 4.1 7.1 - - - +
437E GLY* 2.6 45.4 + - - +
438E PHE* 1.3 77.2 - - - +
440E GLU* 1.3 62.5 + - - +
442E LYS* 3.4 13.4 - - + +
443E ALA* 3.1 23.2 + - - +
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Residues in contact with GLU 440 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437E GLY 5.2 2.6 + - - +
438E PHE 3.3 1.5 - - - -
439E GLU* 1.3 80.1 - - - +
441E LEU* 1.3 67.8 + - - +
443E ALA* 3.4 6.4 + - - +
444E GLU* 3.3 26.1 + - - +
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Residues in contact with LEU 441 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427E LYS* 3.4 40.8 - - + +
428E ASN* 3.9 10.8 - - - +
431E ALA* 3.7 18.4 - - + -
438E PHE* 3.1 15.5 + - + +
440E GLU* 1.3 81.4 - - + +
442E LYS* 1.3 56.4 + - - +
444E GLU* 3.2 25.7 + - - +
445E LEU* 2.8 51.7 + - + +
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Residues in contact with LYS 442 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431E ALA* 3.2 35.6 - - - +
432E LEU* 4.0 11.0 - - - +
434E GLY* 3.9 19.3 - - - -
438E PHE 2.9 11.4 + - - +
439E GLU* 3.4 17.5 - - + +
441E LEU* 1.3 76.6 - - - +
443E ALA* 1.3 62.2 + - - +
445E LEU* 3.3 3.2 + - - +
446E GLU* 2.7 65.5 + - - +
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Residues in contact with ALA 443 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439E GLU 3.1 10.1 + - - +
440E GLU* 3.6 10.1 - - - +
442E LYS* 1.3 79.5 - - - +
444E GLU* 1.3 63.8 + - - +
446E GLU* 3.3 10.6 + - - +
447E GLU* 3.1 22.7 + - - +
450E LYS* 5.3 0.7 + - - -
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Residues in contact with GLU 444 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440E GLU* 3.3 17.2 + - - +
441E LEU* 3.2 27.7 + - + +
443E ALA* 1.3 76.6 - - - +
445E LEU* 1.3 72.6 + - + +
447E GLU* 3.3 8.2 + - - +
448E ARG* 3.3 33.0 + - + +
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Residues in contact with LEU 445 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428E ASN* 3.5 56.3 - - + +
431E ALA* 4.2 1.8 - - + -
432E LEU* 3.7 22.7 - - + -
441E LEU* 2.8 41.3 + - + +
444E GLU* 1.3 78.1 - - + +
446E GLU* 1.3 57.8 + - - +
448E ARG* 3.1 24.5 + - - +
449E LEU* 3.0 32.7 + - - +
372F LEU* 3.9 21.9 - - + +
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Residues in contact with GLU 446 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432E LEU* 3.9 18.2 - - + +
442E LYS* 2.7 59.4 + - - +
443E ALA* 3.7 7.5 - - - +
445E LEU* 1.3 72.9 - - - +
447E GLU* 1.3 67.1 + - - +
449E LEU* 3.1 10.6 + - + +
450E LYS* 2.9 33.1 + - + +
365F LYS* 5.8 1.7 + - - -
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Residues in contact with GLU 447 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443E ALA 3.1 12.7 + - - +
444E GLU* 3.5 11.9 - - - +
445E LEU 3.2 0.4 - - - -
446E GLU* 1.3 74.3 - - - +
448E ARG* 1.3 65.5 + - + +
450E LYS* 2.4 63.9 + - - +
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Residues in contact with ARG 448 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428E ASN* 5.7 0.2 - - - +
444E GLU* 3.5 24.2 + - + +
445E LEU* 3.1 29.3 + - - +
447E GLU* 1.3 79.5 - - + +
449E LEU* 1.3 61.3 + - - +
450E LYS* 3.7 4.3 + - - +
11F LYS* 4.1 14.0 - - - +
372F LEU* 3.6 38.5 + - + +
375F SER* 4.7 5.9 - - - -
376F ASP* 2.8 43.4 + - - -
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Residues in contact with LEU 449 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432E LEU* 4.0 33.9 - - + -
445E LEU 3.0 19.6 + - - +
446E GLU* 3.1 9.6 + - + +
448E ARG* 1.3 75.0 - - - +
450E LYS* 1.3 67.8 + - - +
11F LYS* 4.2 23.0 + - + +
368F GLU* 4.0 35.4 - - + +
371F LEU* 5.7 3.1 - - + -
372F LEU* 3.8 25.6 - - + -
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Residues in contact with LYS 450 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443E ALA 5.3 0.6 + - - -
446E GLU* 2.9 17.1 + - + +
447E GLU* 2.4 59.6 + - - +
448E ARG 4.1 3.6 - - - +
449E LEU* 1.3 81.5 - - - +
11F LYS* 5.5 3.8 + - - -
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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