Contacts of the helix formed by residues 438 - 450 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427B LYS* 3.8 42.2 - - + -
430B PHE* 4.1 17.9 - + + -
431B ALA* 3.4 23.0 - - + +
435B LYS* 3.2 42.6 + - + +
436B PRO 3.6 11.7 - - - -
437B GLY* 1.3 81.2 - - - +
439B GLU* 1.3 58.4 + - - +
440B GLU 3.5 2.2 - - - -
441B LEU* 3.5 9.3 + - + +
442B LYS* 2.9 31.1 + - - +
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Residues in contact with GLU 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434B GLY 5.3 0.9 - - - +
435B LYS 4.1 1.6 - - - +
436B PRO* 3.5 10.3 - - - +
437B GLY* 3.0 34.1 + - - -
438B PHE* 1.3 77.4 - - - +
440B GLU* 1.3 63.0 + - - +
442B LYS* 3.3 12.6 + - + +
443B ALA* 3.2 22.2 + - - +
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Residues in contact with GLU 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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438B PHE 3.5 0.2 - - - -
439B GLU* 1.3 78.0 - - - +
441B LEU* 1.3 64.1 + - - +
443B ALA* 3.4 7.6 + - - +
444B GLU* 3.2 37.9 + - + +
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Residues in contact with LEU 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B LYS* 3.7 36.6 - - + +
428B ASN* 3.9 13.0 - - - +
431B ALA* 3.8 14.6 - - + -
438B PHE* 3.5 15.3 + - + +
440B GLU* 1.3 78.6 - - - +
442B LYS* 1.3 64.7 + - - +
444B GLU* 3.1 24.8 + - - +
445B LEU* 2.9 51.0 + - + +
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Residues in contact with LYS 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431B ALA* 3.1 33.4 - - - +
432B LEU* 3.9 14.3 + - - +
433B LEU 4.8 0.2 - - - -
434B GLY* 3.7 21.3 - - - -
438B PHE 2.9 18.8 + - - +
439B GLU* 3.4 14.1 - - + +
441B LEU* 1.3 76.2 - - - +
443B ALA* 1.3 61.7 + - - +
445B LEU* 3.4 1.4 + - - +
446B GLU* 2.7 64.6 + - - +
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Residues in contact with ALA 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439B GLU 3.2 9.2 + - - +
440B GLU* 3.8 8.3 - - - +
441B LEU 3.3 0.2 - - - -
442B LYS* 1.3 80.4 - - - +
444B GLU* 1.3 62.3 + - + +
446B GLU* 3.5 11.6 + - - +
447B GLU* 3.3 27.5 + - - +
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Residues in contact with GLU 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440B GLU* 3.2 34.7 + - + +
441B LEU* 3.1 27.3 + - + +
443B ALA* 1.3 76.3 - - - +
445B LEU* 1.3 62.7 + - + +
447B GLU* 3.2 19.3 - - - +
448B ARG* 3.4 16.8 + - - +
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Residues in contact with LEU 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372A LEU* 3.7 22.9 - - + +
428B ASN* 3.6 56.3 - - + +
431B ALA* 4.1 5.2 - - + -
432B LEU* 3.8 15.3 - - + -
441B LEU* 2.9 40.4 + - + +
442B LYS 3.8 2.9 - - - +
444B GLU* 1.3 77.2 - - + +
446B GLU* 1.3 64.1 + - - +
448B ARG* 2.9 35.2 + - - +
449B LEU* 3.2 15.8 + - - +
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Residues in contact with GLU 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432B LEU* 3.7 18.3 - - + +
442B LYS* 2.7 60.4 + - - +
443B ALA* 4.0 11.6 - - - +
444B GLU 3.4 0.2 - - - -
445B LEU* 1.3 75.4 - - - +
447B GLU* 1.3 62.0 + - - +
449B LEU* 3.2 22.6 + - + +
450B LYS 3.3 14.8 + - - +
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Residues in contact with GLU 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443B ALA 3.3 13.5 + - - +
444B GLU* 3.2 15.0 - - - +
446B GLU* 1.3 78.1 - - - +
448B ARG* 1.3 59.8 + - + +
450B LYS* 3.1 27.9 + - - +
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Residues in contact with ARG 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A LYS* 4.2 5.9 - - - +
372A LEU* 4.0 33.9 + - + +
375A SER* 4.6 6.5 - - - -
376A ASP* 2.7 43.7 + - - -
444B GLU* 3.5 16.8 - - - +
445B LEU* 2.9 31.2 + - - +
447B GLU* 1.3 76.5 - - + +
449B LEU* 1.3 57.4 + - - +
450B LYS* 3.1 27.2 - - - +
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Residues in contact with LEU 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A LYS* 3.6 21.5 + - - +
367A TYR* 6.4 0.2 - - + -
368A GLU* 3.7 50.7 - - + +
371A LEU* 5.1 4.7 - - + -
372A LEU* 3.7 27.4 - - + -
432B LEU* 4.4 13.7 - - + -
445B LEU 3.6 13.7 - - - +
446B GLU* 3.2 18.9 + - + +
448B ARG* 1.3 76.1 - - - +
450B LYS* 1.3 77.2 + - - +
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Residues in contact with LYS 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A SER* 3.0 35.6 + - - -
11A LYS* 3.5 17.4 - - - +
446B GLU 3.3 12.5 + - - +
447B GLU* 3.1 16.8 + - - +
448B ARG* 3.1 27.7 - - - +
449B LEU* 1.3 89.9 - - - +
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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