Contacts of the strand formed by residues 449 - 454 (chain A) in PDB entry 2DH3
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 449 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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312A GLU* 4.0 16.5 - - - +
315A LYS* 4.4 5.4 - - - +
445A ALA* 3.9 25.2 - - + +
446A GLY* 3.1 24.0 + - - +
448A GLY* 1.3 79.8 - - - +
450A PHE* 1.3 63.7 + - - +
451A SER* 4.5 4.0 - - - +
465A VAL* 4.2 13.9 - - + -
466A LEU 3.3 15.7 - - - +
467A ASN* 3.8 15.0 - - + +
473A LEU* 3.8 26.9 - - + -
474A SER 4.6 3.1 - - - +
475A ALA* 3.7 35.7 - - + +
515A LEU* 4.7 6.1 - - + -
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Residues in contact with PHE 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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312A GLU* 6.3 0.2 - - - -
314A THR* 4.7 1.6 - - + -
315A LYS* 3.5 53.2 - - + +
318A VAL* 4.3 20.2 - - + -
319A THR* 5.3 1.1 - - + -
355A MET* 4.0 19.5 - - - -
359A LEU* 4.4 11.0 - - + -
440A PHE* 4.4 5.2 - + - -
442A ALA* 4.3 15.5 - - + -
449A LEU* 1.3 75.9 - - - +
451A SER* 1.3 63.9 + - - +
452A TYR* 3.8 30.8 - + - -
464A VAL 4.1 0.3 - - - +
465A VAL* 3.9 0.7 - - - -
466A LEU* 3.2 48.7 + - + +
468A PHE* 4.0 18.8 - + + -
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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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442A ALA* 3.4 5.0 - - - +
443A PHE* 2.9 50.7 + - - +
445A ALA* 4.6 7.4 - - - +
449A LEU* 4.5 5.7 - - - +
450A PHE* 1.3 78.1 + - - +
452A TYR* 1.3 68.2 + - - +
463A LEU* 4.8 1.1 - - - -
464A VAL 3.1 11.7 - - - -
465A VAL* 3.5 29.0 - - - +
477A LEU* 4.8 7.3 - - - +
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Residues in contact with TYR 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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355A MET* 3.6 21.0 + - - +
358A THR* 2.5 39.3 + - - -
359A LEU* 4.0 6.5 - - + -
440A PHE* 3.3 27.4 - + + -
441A HIS 3.1 15.9 - - - +
442A ALA* 3.9 1.8 - - - -
443A PHE* 3.9 4.6 - - - -
450A PHE* 3.8 41.7 - + - -
451A SER* 1.3 80.5 - - - +
453A ILE* 1.3 65.8 + - - +
454A ARG* 4.3 7.6 - - + -
462A PHE 3.9 0.5 - - - +
463A LEU* 3.5 5.2 - - - +
464A VAL* 3.0 62.4 + - + +
466A LEU* 4.4 2.2 - - + -
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Residues in contact with ILE 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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439A ASP 3.9 0.2 - - - +
440A PHE* 3.6 5.5 - - - -
441A HIS* 2.8 38.5 + - + +
443A PHE* 3.5 32.5 - - + -
452A TYR* 1.3 73.0 - - - +
454A ARG* 1.3 77.6 + - - +
455A HIS* 4.4 14.1 - - + -
461A ARG* 5.2 5.8 - - + +
462A PHE 3.4 5.6 - - - +
463A LEU* 3.6 23.6 - - + -
482A LEU* 4.6 9.6 - - + -
485A SER 5.5 6.1 - - - +
486A ALA* 6.1 2.7 - - - +
488A LEU* 3.7 25.6 - - + -
525A PHE* 4.5 9.2 - - + -
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Residues in contact with ARG 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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329A TRP* 6.1 0.2 - - - -
358A THR* 2.9 26.2 + - - +
359A LEU 4.0 4.6 + - - -
360A PRO* 3.6 25.9 - - - +
361A GLY 4.7 1.4 - - - +
434A SER* 3.7 17.3 + - - +
435A LEU* 3.6 41.5 + - + +
437A HIS 3.1 28.2 + - - -
438A GLY* 3.7 3.6 - - - -
439A ASP 3.0 31.1 + - - +
440A PHE* 4.0 15.7 - - - +
452A TYR* 4.3 9.6 - - + +
453A ILE* 1.3 82.3 - - - +
455A HIS* 1.3 62.5 + - - +
461A ARG* 3.5 4.7 - - - +
462A PHE* 2.9 41.6 + - + +
464A VAL* 5.4 1.6 - - + -
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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