Contacts of the helix formed by residues 438 - 449 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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427C LYS* 3.9 36.8 - - + -
430C PHE* 3.8 21.1 - + + -
431C ALA* 3.5 18.8 - - + +
435C LYS* 3.3 40.1 + - + +
436C PRO 3.4 14.8 - - - -
437C GLY* 1.3 80.8 - - - +
439C GLU* 1.3 57.0 + - - +
440C GLU 3.4 2.5 - - - -
441C LEU* 3.4 14.1 + - + +
442C LYS* 2.9 29.5 + - - +
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Residues in contact with GLU 439 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434C GLY 5.6 0.2 - - - +
435C LYS 4.3 1.9 - - - +
436C PRO* 3.6 10.2 - - - +
437C GLY* 3.1 33.9 + - - +
438C PHE* 1.3 77.2 - - - +
440C GLU* 1.3 63.7 + - - +
442C LYS* 3.2 11.6 + - + +
443C ALA* 3.1 22.2 + - - +
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Residues in contact with GLU 440 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437C GLY 5.3 0.2 + - - -
438C PHE 3.4 0.6 - - - -
439C GLU* 1.3 78.8 - - - +
441C LEU* 1.3 63.5 + - - +
443C ALA* 3.4 8.5 + - - +
444C GLU* 3.3 38.0 + - + +
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Residues in contact with LEU 441 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427C LYS* 3.6 44.4 - - + +
428C ASN* 3.9 14.1 - - - +
431C ALA* 3.8 7.0 - - + -
438C PHE* 3.4 17.9 + - + +
439C GLU 3.3 0.2 - - - -
440C GLU* 1.3 79.1 - - - +
442C LYS* 1.3 64.3 + - - +
444C GLU* 3.2 21.6 + - - +
445C LEU* 3.0 47.2 + - + +
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Residues in contact with LYS 442 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431C ALA* 3.3 35.2 - - - +
432C LEU* 4.4 10.4 + - - -
433C LEU 5.2 0.4 - - - -
434C GLY* 4.2 18.2 - - - -
438C PHE 2.9 12.2 + - - +
439C GLU* 3.4 14.4 - - + +
441C LEU* 1.3 76.9 - - - +
443C ALA* 1.3 63.8 + - - +
445C LEU* 3.2 4.7 + - - +
446C GLU* 2.8 59.9 + - + +
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Residues in contact with ALA 443 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439C GLU 3.1 10.0 + - - +
440C GLU* 3.7 9.2 - - - +
441C LEU 3.3 0.4 - - - -
442C LYS* 1.3 80.6 - - - +
444C GLU* 1.3 63.0 + - + +
446C GLU* 3.5 7.0 + - - +
447C GLU* 3.3 24.6 + - - +
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Residues in contact with GLU 444 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440C GLU* 3.3 29.5 + - + +
441C LEU* 3.2 26.4 + - + +
443C ALA* 1.3 80.4 - - + +
445C LEU* 1.3 63.6 + - + +
447C GLU* 3.6 6.4 + - - +
448C ARG* 3.4 27.1 + - - +
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Residues in contact with LEU 445 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428C ASN* 3.5 60.6 - - + +
431C ALA* 3.9 5.6 - - + -
432C LEU* 3.9 16.6 - - + -
441C LEU* 3.0 36.1 + - + +
442C LYS 3.8 2.5 - - - +
444C GLU* 1.3 75.1 - - + +
446C GLU* 1.3 66.9 + - - +
447C GLU 3.1 2.2 - - - -
448C ARG* 3.0 31.7 + - - +
449C LEU* 3.1 16.1 + - - +
372D LEU* 3.9 22.3 - - + +
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Residues in contact with GLU 446 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432C LEU* 3.7 20.0 - - + +
442C LYS* 2.8 59.5 + - - +
443C ALA* 4.1 6.5 - - - +
445C LEU* 1.3 72.3 - - - +
447C GLU* 1.3 60.9 + - - +
449C LEU* 3.2 20.9 + - + +
450C LYS* 3.5 30.0 + - - +
365D LYS* 5.4 5.3 + - - +
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Residues in contact with GLU 447 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443C ALA 3.3 15.2 + - - +
444C GLU* 3.9 7.2 - - - +
445C LEU 3.1 0.6 - - - -
446C GLU* 1.3 78.7 - - - +
448C ARG* 1.3 60.6 + - + +
449C LEU 3.5 0.5 + - - -
450C LYS* 3.5 25.9 + - + +
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Residues in contact with ARG 448 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444C GLU* 3.4 19.3 - - - +
445C LEU* 3.0 26.7 + - - +
447C GLU* 1.3 77.6 - - + +
449C LEU* 1.3 61.9 + - - +
450C LYS 3.4 5.0 + - - +
11D LYS* 3.9 15.1 - - - +
372D LEU* 3.7 36.1 + - + +
375D SER* 4.8 5.1 - - - -
376D ASP* 2.8 42.9 + - - -
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Residues in contact with LEU 449 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432C LEU* 3.9 27.4 - - + -
445C LEU 3.1 10.9 + - - +
446C GLU* 3.2 13.8 + - + +
448C ARG* 1.3 75.6 - - - +
450C LYS* 1.3 64.4 + - - +
11D LYS* 4.1 28.6 + - - +
365D LYS* 5.8 0.4 - - - +
368D GLU* 3.5 48.0 - - + +
371D LEU* 5.6 2.2 - - + -
372D LEU* 3.9 21.3 - - + -
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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