Contacts of the helix formed by residues 445 - 455 (chain A) in PDB entry 2IFD
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 LEU 445 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201A CL 3.9 5.8 - - + -
443A LEU 3.4 0.9 - - - +
444A PRO* 1.3 79.8 - - + +
446A GLU* 1.3 65.7 + - - +
447A ARG* 3.5 34.1 - - + +
448A ASP* 3.1 31.2 + - - +
449A ALA* 3.0 21.1 + - - +
483A MET* 3.9 2.0 - - - -
543A PHE* 3.4 34.8 - - + -
546A LYS* 3.8 28.5 - - + +
547A THR* 3.9 16.4 - - + -
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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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201A CL 3.3 19.9 - - + +
444A PRO 5.4 0.2 - - - +
445A LEU* 1.3 71.0 - - - +
447A ARG* 1.3 57.8 + - - +
449A ALA* 3.2 0.5 + - - +
450A GLU* 2.9 26.5 + - - +
482A ARG* 4.3 18.4 - - + +
483A MET* 3.8 24.4 - - + +
486A PHE* 3.4 43.4 - - + +
548A ARG* 3.0 33.0 + - - +
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Residues in contact with ARG 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A CL 4.3 2.0 - - - +
445A LEU* 3.5 33.0 - - + +
446A GLU* 1.3 79.4 - - - +
448A ASP* 1.3 67.0 + - - +
450A GLU* 3.9 4.6 - - - +
451A SER* 3.2 26.0 + - - -
546A LYS* 2.8 38.1 + - - +
547A THR 4.6 0.4 - - - -
548A ARG* 3.9 45.8 - - - +
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Residues in contact with ASP 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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443A LEU* 3.9 15.1 - - + +
444A PRO* 5.8 2.1 - - + +
445A LEU* 3.1 39.0 + - + +
447A ARG* 1.3 83.8 + - - +
449A ALA* 1.3 61.1 + - - +
451A SER* 3.4 6.5 + - - -
452A PHE* 3.0 30.5 + - - +
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Residues in contact with ALA 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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424A VAL* 5.4 0.7 - - + -
443A LEU* 4.0 28.4 - - + +
445A LEU 3.0 8.8 + - - +
446A GLU 3.2 4.0 + - - +
448A ASP* 1.3 73.9 - - - +
450A GLU* 1.3 60.8 + - - +
452A PHE* 4.0 0.2 - - - -
453A LEU* 3.0 37.6 + - + +
483A MET* 3.7 32.3 - - + -
487A ILE* 4.2 11.7 - - + -
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Residues in contact with GLU 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 2.9 14.7 + - - +
447A ARG* 3.9 4.7 - - - +
449A ALA* 1.3 78.2 - - - +
451A SER* 1.3 56.2 + - - +
454A LEU* 2.7 56.3 + - + +
455A LYS 3.4 1.2 + - - -
486A PHE* 3.4 20.0 - - + -
487A ILE* 4.4 8.0 - - - +
490A ARG* 3.4 35.5 + - + +
548A ARG* 3.9 13.3 + - - -
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Residues in contact with SER 451 (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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447A ARG 3.2 15.9 + - - -
448A ASP* 3.7 7.9 - - - -
449A ALA 3.3 0.2 - - - -
450A GLU* 1.3 80.8 - - - +
452A PHE* 1.3 62.9 + - - +
455A LYS* 3.0 45.5 + - - +
456A SER 4.5 0.7 + - - -
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Residues in contact with PHE 452 (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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422A VAL* 4.3 17.9 - - + -
441A VAL* 4.1 25.6 - - + -
443A LEU* 3.8 27.6 - - + -
448A ASP 3.0 18.7 + - - +
449A ALA 4.0 2.0 - - - +
451A SER* 1.3 77.4 + - - +
453A LEU* 1.3 80.9 + - + +
455A LYS 5.2 0.2 + - - -
456A SER 4.8 3.8 + - - +
458A ILE* 3.8 18.9 - - + +
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Residues in contact with LEU 453 (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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422A VAL* 4.7 7.4 - - + -
424A VAL* 4.5 14.6 - - + -
443A LEU* 4.5 4.3 - - + -
449A ALA* 3.0 21.8 + - + +
452A PHE* 1.3 102.7 - - + +
454A LEU* 1.3 64.2 + - + +
455A LYS 3.8 0.2 - - - -
456A SER 4.9 0.2 - - - -
457A PRO* 3.4 12.3 - - - +
458A ILE* 4.0 3.9 - - + +
469A LEU* 4.0 36.1 - - + -
471A PHE* 4.6 2.5 - - + -
487A ILE* 3.8 27.1 - - + -
502A TYR* 2.6 41.8 + - + +
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Residues in contact with LEU 454 (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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450A GLU* 2.7 32.7 + - + +
453A LEU* 1.3 76.2 - - + +
455A LYS* 1.3 65.7 + - - +
456A SER 3.2 1.8 - - - -
457A PRO* 3.5 11.9 - - + +
487A ILE* 4.3 17.9 - - + +
490A ARG* 3.5 33.0 - - + +
491A ASP* 4.2 15.7 - - - +
494A VAL* 4.8 8.9 - - + +
501A TYR* 3.9 27.6 - - + -
502A TYR* 3.8 25.1 - - + -
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Residues in contact with LYS 455 (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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450A GLU 3.4 3.2 + - - -
451A SER* 3.0 39.0 + - - +
454A LEU* 1.3 79.0 - - - +
456A SER* 1.3 61.8 + - - +
457A PRO* 3.8 2.8 - - - +
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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