Contacts of the helix formed by residues 446 - 458 (chain A) in PDB entry 2I88
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 ASP 446 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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421A TYR* 3.9 29.3 + - + +
424A TRP* 3.6 12.6 + - - -
444A GLY 3.7 3.5 + - - +
445A TYR* 1.3 82.9 - - - +
447A VAL* 1.3 57.7 + - - +
448A VAL* 3.3 19.9 + - - +
449A SER* 2.8 40.0 + - - +
450A ASP 4.0 0.7 + - - -
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Residues in contact with VAL 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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424A TRP* 3.7 23.8 - - + -
445A TYR* 3.5 25.5 + - + +
446A ASP* 1.3 72.4 + - - +
448A VAL* 1.3 59.3 + - + +
450A ASP* 2.8 22.0 + - - +
451A ILE* 3.0 24.8 + - + +
463A LEU* 4.1 15.9 - - + -
467A LEU* 4.7 3.6 - - + -
482A LEU* 3.3 37.2 - - + +
483A LEU* 4.4 14.1 - - + -
486A LEU* 5.2 4.9 - - + -
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Residues in contact with VAL 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A LEU* 3.6 39.9 - - + +
419A VAL* 4.8 11.4 - - + +
424A TRP* 3.8 27.8 - - + +
446A ASP* 3.2 9.3 - - - +
447A VAL* 1.3 75.9 - - + +
449A SER* 1.3 62.0 + - - +
451A ILE* 3.5 9.0 + - + +
452A LEU* 3.0 31.1 + - + +
486A LEU* 3.9 27.4 - - + -
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Residues in contact with SER 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A ASP* 2.8 32.4 + - - +
448A VAL* 1.3 77.3 - - - +
450A ASP* 1.3 67.5 + - - +
452A LEU* 3.5 13.3 + - - +
453A LYS* 3.3 31.8 + - - +
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Residues in contact with ASP 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A TYR* 2.5 37.6 + - - +
447A VAL 2.8 11.0 + - - +
449A SER* 1.3 86.7 + - - +
451A ILE* 1.3 64.7 + - - +
453A LYS* 3.3 40.0 + - - +
454A ILE* 3.7 9.9 - - - +
463A LEU* 3.9 15.1 - - + +
466A THR* 3.7 16.3 + - - +
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Residues in contact with ILE 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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413A PHE* 3.3 18.1 - - + -
416A LEU* 3.9 26.9 - - + -
447A VAL* 3.0 28.3 + - + +
448A VAL* 3.9 8.5 - - - +
450A ASP* 1.3 74.6 - - - +
452A LEU* 1.3 63.2 + - - +
454A ILE* 3.0 31.8 + - + +
460A TRP* 5.0 9.0 - - + -
463A LEU* 4.2 23.1 - - + -
483A LEU* 5.5 4.0 - - + -
486A LEU* 4.6 17.9 - - + -
500A VAL* 5.6 7.2 - - + -
503A ILE* 5.7 5.2 - - + -
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Residues in contact with LEU 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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413A PHE* 3.3 38.6 - - + +
416A LEU* 4.0 17.5 - - + +
417A ALA* 4.0 14.6 - - + +
448A VAL* 3.0 41.2 + - + +
449A SER* 3.6 11.0 - - - +
450A ASP 3.2 0.2 - - - -
451A ILE* 1.3 75.9 - - + +
453A LYS* 1.3 63.1 + - + +
455A LYS* 3.0 23.0 + - + +
456A ASP* 4.3 1.9 + - - +
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Residues in contact with LYS 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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449A SER* 3.3 20.1 + - - +
450A ASP* 3.3 29.2 + - - +
451A ILE 3.2 0.4 - - - -
452A LEU* 1.3 77.3 - - - +
454A ILE* 1.3 61.2 + - + +
455A LYS 3.2 0.7 + - - -
456A ASP* 3.2 16.0 + - - +
457A THR* 3.6 18.6 + - + +
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Residues in contact with ILE 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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413A PHE* 4.2 8.6 - - + -
450A ASP 3.7 8.7 - - - +
451A ILE* 3.0 25.0 + - - +
453A LYS* 1.3 73.8 - - + +
455A LYS* 1.3 65.5 + - - +
457A THR* 3.8 7.0 - - - -
458A GLY* 2.8 38.7 + - - +
459A ASP 3.8 14.6 - - - +
460A TRP* 3.4 66.9 - - + +
463A LEU* 4.2 12.8 - - + -
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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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406A LYS* 5.4 6.4 - - - +
410A ASP* 3.9 27.4 - - - +
413A PHE* 3.7 45.6 - - + -
414A ASN* 2.9 31.5 + - - +
452A LEU* 3.0 15.1 + - + +
454A ILE* 1.3 77.5 - - - +
456A ASP* 1.3 72.4 + - - +
458A GLY 4.9 0.3 + - - -
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Residues in contact with ASP 456 (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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452A LEU 5.1 1.9 - - - +
453A LYS* 3.2 10.2 + - - +
454A ILE 3.0 0.4 - - - -
455A LYS* 1.3 96.0 - - - +
457A THR* 1.3 67.1 + - + +
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Residues in contact with THR 457 (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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453A LYS* 3.6 13.1 + - + +
454A ILE* 3.3 8.9 + - - -
456A ASP* 1.3 82.0 - - + +
458A GLY* 1.3 62.3 + - - +
459A ASP* 3.1 31.6 + - - +
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Residues in contact with GLY 458 (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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394A GLU* 5.3 1.6 - - - +
397A LYS* 5.0 6.4 + - - -
454A ILE* 2.8 30.8 + - - -
455A LYS 5.6 0.2 - - - -
456A ASP 3.7 0.4 - - - -
457A THR* 1.3 72.7 + - - +
459A ASP* 1.3 55.5 + - - +
460A TRP* 3.5 15.2 + - - -
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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