Contacts of the helix formed by residues 438 - 450 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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427A LYS* 4.1 37.0 - - + -
430A PHE* 3.8 29.4 - + + -
431A ALA* 3.6 22.7 - - + +
435A LYS* 3.2 35.8 + - + +
436A PRO 3.6 14.4 - - - -
437A GLY* 1.3 82.9 - - - +
439A GLU* 1.3 63.4 + - - +
440A GLU 3.4 2.4 + - - -
441A LEU* 3.4 8.3 + - + -
442A LYS* 3.2 17.8 + - - +
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Residues in contact with GLU 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434A GLY* 5.3 2.7 - - - +
435A LYS 4.5 2.6 + - - +
436A PRO* 3.4 11.6 - - - +
437A GLY* 3.1 33.1 + - - -
438A PHE* 1.3 79.0 + - - +
440A GLU* 1.3 62.4 + - - +
442A LYS* 3.1 21.9 + - + +
443A ALA* 3.3 12.6 + - - +
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Residues in contact with GLU 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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438A PHE 3.4 0.8 - - - -
439A GLU* 1.3 77.6 - - - +
441A LEU* 1.3 63.9 + - - +
443A ALA* 3.3 8.0 + - - +
444A GLU* 3.3 25.3 + - + +
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Residues in contact with LEU 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427A LYS* 3.3 52.9 - - + +
428A ASN* 3.6 14.6 - - - +
431A ALA* 3.7 7.9 - - + -
438A PHE* 3.4 13.3 + - + +
439A GLU 3.3 0.4 - - - -
440A GLU* 1.3 79.5 - - - +
442A LYS* 1.3 62.0 + - - +
444A GLU* 3.3 25.8 + - - +
445A LEU* 3.0 40.0 + - + +
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Residues in contact with LYS 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431A ALA* 3.2 34.7 - - - +
432A LEU* 4.1 14.8 - - - +
433A LEU 5.1 0.2 - - - -
434A GLY* 4.2 15.7 - - - -
438A PHE 3.2 9.7 + - - +
439A GLU* 3.1 17.2 + - + +
440A GLU 3.1 0.6 - - - -
441A LEU* 1.3 78.0 - - - +
443A ALA* 1.3 58.9 + - - +
445A LEU* 3.4 0.9 + - - +
446A GLU* 2.5 75.1 + - + +
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Residues in contact with ALA 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439A GLU 3.3 8.1 + - - +
440A GLU* 3.3 9.2 + - - +
442A LYS* 1.3 79.5 - - - +
444A GLU* 1.3 62.6 + - - +
446A GLU* 3.5 8.8 + - - +
447A GLU* 3.1 24.8 + - - +
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Residues in contact with GLU 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440A GLU* 3.3 15.6 + - + +
441A LEU* 3.5 29.8 - - + +
442A LYS 3.3 0.2 - - - -
443A ALA* 1.3 78.7 - - - +
445A LEU* 1.3 66.2 + - + +
447A GLU* 3.4 7.2 + - - +
448A ARG* 3.2 38.1 + - + +
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Residues in contact with LEU 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428A ASN* 3.5 58.6 - - + +
431A ALA* 4.2 2.0 - - + -
432A LEU* 3.8 19.7 - - + -
441A LEU* 3.0 36.4 + - + +
444A GLU* 1.3 76.3 - - + +
446A GLU* 1.3 65.8 + - - +
448A ARG* 3.1 26.0 + - - +
449A LEU* 2.9 28.6 + - - +
372B LEU* 3.8 21.7 - - + +
376B ASP* 5.7 0.2 - - - +
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Residues in contact with GLU 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432A LEU* 3.7 19.3 - - + +
442A LYS* 2.5 62.9 + - - +
443A ALA* 4.0 7.0 - - - +
445A LEU* 1.3 76.7 - - - +
447A GLU* 1.3 52.7 + - - +
449A LEU* 3.2 8.9 + - + +
450A LYS* 2.7 48.1 + - - +
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Residues in contact with GLU 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443A ALA 3.1 18.5 + - - +
444A GLU* 3.6 7.4 - - - +
445A LEU 3.2 0.2 - - - -
446A GLU* 1.3 75.9 - - - +
448A ARG* 1.3 62.9 + - + +
450A LYS* 3.3 49.8 + - - +
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Residues in contact with ARG 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444A GLU* 3.2 27.9 + - + +
445A LEU* 3.1 31.1 + - - +
447A GLU* 1.3 79.3 - - + +
449A LEU* 1.3 60.9 + - - +
450A LYS 4.6 1.9 - - - +
11B LYS* 4.7 9.5 - - - +
372B LEU* 3.8 35.9 + - + +
375B SER* 4.9 4.9 - - - -
376B ASP* 3.0 42.0 + - - -
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Residues in contact with LEU 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432A LEU* 4.0 19.7 - - + -
445A LEU 2.9 21.3 + - - +
446A GLU* 3.2 7.2 + - + +
448A ARG* 1.3 75.5 - - - +
450A LYS* 1.3 69.7 + - - +
11B LYS* 4.2 28.0 + - - +
368B GLU* 3.8 48.9 - - + +
371B LEU* 5.7 2.2 - - + -
372B LEU* 3.8 24.9 - - + -
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Residues in contact with LYS 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446A GLU* 2.7 26.6 + - - +
447A GLU* 3.3 44.8 + - - +
448A ARG 4.6 1.7 - - - +
449A LEU* 1.3 85.8 - - - +
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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