Contacts of the helix formed by residues 442 - 452 (chain A) in PDB entry 4I2C
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 ARG 442 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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385A PHE* 3.6 31.1 - - + -
386A GLU 5.1 0.6 + - - -
387A LYS* 2.8 48.3 + - - +
388A PHE* 5.6 0.4 - - - -
401A PHE* 4.0 17.0 - - + -
438A CYS* 4.2 1.8 - - - -
439A PRO* 3.0 13.7 + - + +
441A ASP* 1.4 107.0 + - - +
443A ARG* 1.4 63.9 + - - +
444A ALA 3.2 2.7 - - - -
445A PHE* 3.1 16.2 + - - +
446A ALA* 3.0 21.1 + - - +
475A HIS* 3.0 32.5 + - - +
476A ALA* 3.9 11.6 - - - +
485A PHE* 5.9 1.2 - - - -
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Residues in contact with ARG 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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327A LEU* 4.9 5.3 - - - +
347A LEU* 3.6 6.9 - - + +
349A THR* 3.9 22.7 - - + +
438A CYS* 3.7 14.1 - - - -
439A PRO 3.5 2.4 + - - -
440A TYR* 2.9 71.6 + - - +
441A ASP* 3.5 4.8 + - - +
442A ARG* 1.4 76.7 - - - +
444A ALA* 1.3 59.7 + - + +
447A LEU* 3.0 31.2 + - - +
488A ALA 5.0 0.6 + - - +
489A GLU* 3.0 66.0 + - - +
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Residues in contact with ALA 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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442A ARG 3.2 1.0 - - - -
443A ARG* 1.3 78.6 - - - +
445A PHE* 1.3 61.0 + - + +
447A LEU* 3.8 7.2 - - - +
448A LEU* 3.1 29.1 + - - +
488A ALA* 3.9 16.6 + - + +
489A GLU 4.0 2.7 - - - +
490A SER* 3.6 44.6 - - - +
491A GLU* 4.1 3.9 - - - +
494A ILE* 3.4 10.6 - - + +
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Residues in contact with PHE 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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441A ASP 4.4 10.8 - - - -
442A ARG* 3.1 19.4 + - - +
444A ALA* 1.3 72.5 - - - +
446A ALA* 1.3 61.0 + - - +
448A LEU* 3.6 3.8 + - - +
449A GLY* 3.0 22.5 + - - -
472A LEU* 4.2 9.2 - - + -
473A ASP 3.9 3.7 - - - +
474A ASN* 3.2 29.1 - - - +
475A HIS 3.8 14.4 - - - -
476A ALA* 3.8 19.1 - - - -
477A LEU* 3.6 27.4 - - + -
486A LEU 3.4 22.9 - - - -
487A GLU* 5.0 1.1 - - - -
488A ALA* 3.8 28.7 - - + -
494A ILE* 3.6 25.4 - - + -
497A HIS* 5.9 0.2 - + - -
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Residues in contact with ALA 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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347A LEU* 3.7 26.5 - - + -
401A PHE* 3.8 18.4 - - + -
438A CYS* 3.8 12.3 - - + -
442A ARG 3.0 13.3 + - - +
443A ARG 3.9 1.3 - - - +
445A PHE* 1.3 73.9 - - - +
447A LEU* 1.4 54.0 + - - +
449A GLY 3.3 0.9 + - - -
450A TRP* 2.8 46.3 + - + +
474A ASN* 3.0 10.8 + - - -
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Residues in contact with LEU 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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329A THR* 3.9 15.7 - - + +
331A THR* 3.7 21.1 - - + -
335A ARG* 3.6 42.2 - - - +
347A LEU* 3.5 14.0 - - + +
443A ARG 3.0 20.0 + - - +
444A ALA* 3.8 6.5 - - - +
446A ALA* 1.4 74.9 - - - +
448A LEU* 1.3 56.1 + - - +
450A TRP* 3.4 2.4 + - - -
451A THR* 2.7 40.8 + - - +
491A GLU* 3.7 15.0 - - + +
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Residues in contact with LEU 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 ALA 3.1 18.0 + - - +
445A PHE* 3.8 4.5 - - - +
447A LEU* 1.3 76.9 - - - +
449A GLY* 1.3 55.9 + - - +
451A THR* 3.5 7.1 + - - -
452A GLY 3.8 1.0 + - - -
456A PHE* 4.8 1.6 - - + -
457A GLU* 2.6 26.6 - - - +
460A LEU* 3.9 29.2 - - + -
472A LEU* 4.6 11.0 - - + -
491A GLU* 3.2 14.5 + - + +
494A ILE* 3.7 37.7 - - + -
495A PHE* 3.7 23.8 - - + -
508A ARG* 3.7 23.2 + - - +
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Residues in contact with GLY 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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445A PHE 3.0 12.4 + - - -
446A ALA 3.3 2.4 + - - -
448A LEU* 1.3 77.3 - - - +
450A TRP* 1.4 59.9 + - - +
451A THR 3.6 0.2 + - - -
457A GLU* 3.2 21.0 - - - +
461A ARG* 4.2 1.6 - - - -
474A ASN* 3.2 25.6 - - - +
602A APC 3.2 26.3 + - - -
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Residues in contact with TRP 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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331A THR* 3.5 27.4 + - + +
332A GLY 2.9 17.7 + - - -
345A ASP* 4.4 5.2 - - + -
346A PHE 5.4 1.6 - - - -
347A LEU* 5.3 4.3 - - + -
399A ASP* 2.7 24.3 + - + -
403A LYS* 3.7 23.8 - - + -
405A PHE* 5.3 0.7 - + - -
434A ASP* 4.4 13.2 - - + -
436A VAL* 3.2 40.3 - - + +
446A ALA* 2.8 37.9 + - + +
447A LEU 3.7 0.7 - - - +
449A GLY* 1.4 70.3 - - - +
451A THR* 1.3 59.1 + - - +
474A ASN* 3.4 12.1 - - - +
602A APC 2.8 90.6 - + - +
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Residues in contact with THR 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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331A THR* 4.4 0.7 - - - -
332A GLY 3.5 10.6 - - - +
335A ARG* 2.9 40.1 + - + +
336A ARG* 2.8 46.6 + - + +
447A LEU* 2.7 23.7 + - - +
448A LEU 3.5 2.4 + - - -
449A GLY 3.4 0.6 - - - -
450A TRP* 1.3 77.4 - - - +
452A GLY* 1.3 56.4 + - - +
505A PRO* 4.0 11.9 - - + -
508A ARG* 3.7 22.7 - - - +
602A APC 4.5 0.2 - - - -
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Residues in contact with GLY 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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336A ARG* 3.7 4.3 - - - -
450A TRP 3.4 2.6 - - - -
451A THR* 1.3 81.6 - - - +
453A SER* 1.4 70.4 + - - -
456A PHE* 4.0 3.0 - - - +
457A GLU* 3.3 21.8 + - - +
508A ARG* 3.5 27.2 - - - +
602A APC 3.5 14.2 + - - -
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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