Contacts of the helix formed by residues 442 - 448 (chain A) in PDB entry 2IUK
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 TYR 442 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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438A ALA 4.2 8.7 - - - -
439A PHE 2.9 11.4 + - - +
441A PRO* 1.3 82.3 - - + +
443A LEU* 1.3 58.6 + - - +
444A THR 3.5 2.7 - - - -
445A ARG* 3.8 10.9 + - + +
446A ILE* 2.9 33.9 + - + +
588A TYR* 4.0 33.0 - + + -
591A GLU* 2.9 46.1 + - - +
592A MET* 3.6 44.4 - - + -
595A SER* 2.7 33.1 + - - -
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Residues in contact with LEU 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 PHE* 3.1 20.7 + - + +
440A ILE* 3.2 12.2 + - + +
442A TYR* 1.3 77.0 - - - +
444A THR* 1.3 59.2 + - - +
446A ILE* 3.8 24.9 - - + -
447A ASN* 2.9 42.4 + - - +
454A ALA* 4.3 15.5 - - + +
455A TYR* 3.7 9.6 - - - +
456A ALA* 3.5 24.2 - - + +
477A SER 3.4 24.9 - - - +
478A LYS* 4.1 11.0 - - + -
479A PRO* 4.0 12.0 - - + +
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Residues in contact with THR 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 ILE 4.6 1.5 + - - -
441A PRO 5.3 2.6 + - - -
442A TYR 3.5 0.2 - - - -
443A LEU* 1.3 75.6 - - - +
445A ARG* 1.3 79.8 - - - +
447A ASN* 3.8 3.0 - - - +
448A SER* 3.2 26.3 + - - -
479A PRO* 3.3 25.8 + - - +
482A ASP 5.2 7.9 + - - +
483A GLY* 5.4 1.4 - - - -
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Residues in contact with ARG 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 PRO 5.4 3.6 + - - +
442A TYR* 3.8 16.3 + - + +
444A THR* 1.3 90.7 + - - +
446A ILE* 1.3 62.8 + - - +
448A SER* 2.9 49.2 + - - -
449A LEU* 3.6 4.0 + - - +
587A LYS* 5.3 1.8 - - - +
588A TYR* 3.1 56.1 + - + +
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Residues in contact with ILE 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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439A PHE* 4.0 21.1 - - + -
442A TYR* 2.9 43.0 + - + +
443A LEU* 4.0 21.1 - - + -
445A ARG* 1.3 70.4 - - - +
447A ASN* 1.3 67.9 + - - +
449A LEU* 3.1 28.2 + - + +
452A ALA* 3.7 7.0 - - + +
454A ALA* 4.8 0.2 - - + -
584A LEU* 3.7 38.6 - - + +
585A PRO* 3.7 30.5 - - + +
588A TYR* 4.4 9.6 - - + -
592A MET* 4.2 0.4 - - + -
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Residues in contact with ASN 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 LEU* 2.9 25.8 + - - +
444A THR* 3.3 3.5 + - - +
446A ILE* 1.3 79.3 - - - +
448A SER* 1.3 58.6 + - - +
449A LEU 3.3 2.2 - - - +
452A ALA 3.4 16.0 - - - +
453A LYS* 3.5 9.4 + - - +
454A ALA* 2.9 47.1 + - - +
478A LYS* 3.7 22.6 - - - +
479A PRO* 6.0 0.2 - - - +
740A PHE* 3.7 8.8 - - + -
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Residues in contact with SER 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 THR* 3.2 10.3 + - - -
445A ARG* 2.9 44.1 + - - -
447A ASN* 1.3 76.1 - - - +
449A LEU* 1.3 64.9 + - - +
450A PRO* 3.8 1.4 - - - +
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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