Contacts of the helix formed by residues 446 - 451 (chain A) in PDB entry 4I6J
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 446 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259A ALA 5.9 0.7 - - - +
262A LEU* 3.8 32.5 - - + -
263A LEU* 4.6 9.2 - - + -
357A TRP* 3.8 18.8 - + - -
360A ALA* 3.3 30.7 + - + -
361A ILE* 3.2 43.2 - - + +
364A GLN* 2.9 29.8 + - - -
375A ALA* 5.0 1.4 - - - +
441A ASP* 3.4 24.3 + - + +
444A GLY 3.2 0.2 - - - -
445A ASP* 1.3 75.9 - - - +
447A ILE* 1.3 68.6 + - + +
449A ARG* 3.0 19.3 + - - +
450A TYR* 3.6 26.4 - + - +
463A TYR* 5.0 0.7 - - - +
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Residues in contact with ILE 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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356A PRO* 3.3 37.5 - - + -
357A TRP* 3.5 6.1 - - - +
360A ALA* 4.2 17.9 - - + -
444A GLY 3.2 7.7 + - - +
446A TYR* 1.3 81.9 - - + +
448A ARG* 1.3 56.8 + - - +
449A ARG 3.0 0.9 + - - -
450A TYR 3.2 0.2 + - - -
451A LEU* 2.8 47.6 + - + +
454A LEU* 4.0 4.3 - - + -
462A ILE* 3.9 25.8 - - + +
463A TYR* 3.3 44.2 - - + -
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Residues in contact with ARG 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 SER 2.4 32.5 + - - -
444A GLY 3.0 12.4 + - - +
445A ASP* 3.3 29.0 + - - +
446A TYR 3.2 0.2 - - - -
447A ILE* 1.3 75.8 - - - +
449A ARG* 1.3 56.4 + - - +
451A LEU 4.5 5.6 - - - -
452A PRO* 4.5 4.4 - - - +
454A LEU 3.9 0.9 - - - +
455A LYS* 3.0 67.9 + - + +
457A PHE 2.8 29.1 + - - -
458A PRO* 4.4 0.4 - - - +
459A SER* 3.4 16.6 + - - +
462A ILE* 3.5 28.1 - - + +
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Residues in contact with ARG 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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263A LEU* 4.0 30.8 - - + +
368A GLU* 4.9 4.4 + - - -
445A ASP 3.3 9.3 + - - +
446A TYR* 3.0 12.9 + - - +
447A ILE 3.0 1.4 - - - -
448A ARG* 1.3 79.2 - - - +
450A TYR* 1.3 91.1 + - + +
452A PRO* 5.0 6.9 - - - +
455A LYS* 5.2 1.6 - - - +
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Residues in contact with TYR 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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263A LEU* 4.2 11.1 - - + +
264A ALA 5.6 0.2 + - - -
360A ALA* 3.9 18.6 - - - +
363A THR* 3.7 18.0 - - + +
364A GLN* 3.4 41.3 + - + +
367A GLN* 3.7 24.9 + - - +
368A GLU* 2.6 37.0 + - - -
446A TYR* 3.6 38.8 - + - +
447A ILE 3.2 1.0 + - - -
449A ARG* 1.3 106.2 + - + +
451A LEU* 1.3 70.4 + - - +
452A PRO* 3.3 13.2 - - - +
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Residues in contact with LEU 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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351A GLY 5.3 2.9 - - - +
356A PRO* 3.4 45.3 - - + +
359A ASP* 3.7 14.1 - - + -
360A ALA* 3.6 13.9 - - - +
363A THR* 4.2 13.5 - - - +
447A ILE* 2.8 19.7 + - + +
448A ARG* 4.5 0.3 - - - -
450A TYR* 1.3 87.0 - - - +
452A PRO* 1.3 64.7 - - + +
453A LYS* 3.2 3.6 - - - -
454A LEU* 3.1 29.4 + - + +
484A TYR* 3.8 19.7 - - + -
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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