Contacts of the strand formed by residues 446 - 452 (chain A) in PDB entry 2A8B
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
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Residue Dist Surf HB Arom Phob DC
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410A ILE* 4.8 5.4 - - + -
412A ILE* 3.8 24.0 - - + -
415A HIS* 3.5 36.4 - + + -
418A LYS* 3.8 24.1 - - + +
419A ASN* 2.6 35.8 + - - -
426A PRO* 3.0 39.2 - - + +
431A ARG* 3.7 12.6 - - - +
434A LEU* 3.7 10.4 - - - +
442A SER 4.1 4.0 - - - +
443A LEU* 3.1 26.3 + - + +
444A SER 3.4 0.2 - - - -
445A THR* 1.3 78.7 + - - +
447A ILE* 1.3 65.5 + - - +
448A ASN* 4.0 10.0 - - - +
475A ASP* 4.1 9.7 - - - +
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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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418A LYS* 5.6 2.5 - - - -
426A PRO* 4.0 7.4 - - - +
431A ARG* 4.9 1.7 - - - +
432A VAL* 3.2 28.4 + - + +
434A LEU* 3.7 20.9 - - + -
445A THR 3.7 0.8 + - - -
446A TYR* 1.3 83.4 - - - +
448A ASN* 1.3 64.7 + - - +
449A ALA* 2.9 31.1 + - + +
465A THR* 4.4 3.8 - - - +
466A GLN* 6.3 1.6 - - + +
472A THR* 4.9 5.8 - - - +
475A ASP* 3.7 38.1 - - + +
476A PHE* 3.7 14.6 - - + +
479A MET* 4.1 13.7 - - + -
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Residues in contact with ASN 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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418A LYS 4.2 3.4 + - - +
419A ASN* 2.9 28.1 + - - +
421A TYR 4.6 0.2 + - - -
424A ILE* 2.7 27.3 + - - +
426A PRO* 3.5 18.1 - - - +
446A TYR* 4.0 4.8 - - - -
447A ILE* 1.3 70.8 - - - +
449A ALA* 1.3 52.6 + - - +
465A THR* 2.6 25.7 + - - -
466A GLN* 3.3 41.4 + - + +
590A ALA 5.5 0.2 + - - -
627A ARG* 2.9 35.0 + - - +
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Residues in contact with ALA 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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426A PRO* 3.8 2.1 - - - +
431A ARG* 3.3 7.4 - - - +
432A VAL* 3.0 27.8 + - + -
447A ILE* 2.9 15.9 + - + +
448A ASN* 1.3 77.7 + - - +
450A ASN* 1.3 63.4 + - - +
463A ILE* 4.0 1.3 - - + -
464A ALA 3.2 9.2 - - - +
465A THR* 3.4 15.0 - - - +
479A MET* 3.6 26.9 - - - -
627A ARG* 3.6 1.5 - - - +
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Residues in contact with ASN 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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426A PRO* 3.1 12.9 - - - +
427A ASN 2.7 27.2 + - - +
430A SER* 2.7 28.2 + - - +
431A ARG* 3.3 3.4 - - - +
432A VAL* 3.9 5.4 - - - -
449A ALA* 1.3 74.5 - - - +
451A TYR* 1.3 63.9 + - - +
452A ILE* 3.6 1.2 - - + +
463A ILE* 3.2 3.3 - - - -
464A ALA 3.0 31.0 + - - -
626A ASP 3.3 18.2 - - - +
627A ARG* 2.9 42.0 + - + +
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Residues in contact with TYR 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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430A SER* 2.7 38.4 + - - +
431A ARG 3.8 16.2 - - - -
432A VAL* 3.9 17.5 - - + +
433A CYS 4.4 4.1 + - - -
450A ASN* 1.3 74.2 - - - +
452A ILE* 1.3 59.5 + - - +
453A ARG* 4.2 0.7 - - - -
460A LYS* 3.5 58.2 + - + +
462A PHE 3.5 4.3 - - - +
463A ILE* 3.8 15.7 - - + -
482A GLN* 4.6 0.3 + - - -
483A GLU* 2.6 46.0 + - - -
583A PRO* 4.4 1.3 - - + -
626A ASP* 3.6 17.0 - - - +
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Residues in contact with ILE 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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450A ASN* 3.9 2.9 - - + +
451A TYR* 1.3 78.8 - - - +
453A ARG* 1.3 69.6 + - - +
460A LYS 3.8 2.1 + - - -
461A ALA 3.1 8.8 + - - -
462A PHE* 2.7 42.7 + - + +
464A ALA* 3.6 39.7 - - + +
599A ILE* 3.9 11.0 - - + -
623A LEU* 3.2 33.4 - - + +
626A ASP* 3.5 23.6 - - + +
627A ARG* 3.9 13.0 - - + -
630A MET* 3.9 11.2 - - + -
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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