Contacts of the strand formed by residues 450 - 454 (chain A) in PDB entry 2AX1
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 ALA 450 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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446A GLN* 3.1 5.6 - - - -
447A ILE 2.8 33.9 + - - +
448A TYR 3.2 2.2 + - - -
449A GLY* 1.3 78.4 - - - +
451A CYS* 1.3 60.8 + - - +
452A TYR* 3.5 22.3 - - + +
555A TYR* 4.1 22.0 - - + -
560A ILE* 3.7 21.3 - - + -
562A HIS* 4.2 6.1 - - + +
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Residues in contact with CYS 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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93A PRO* 5.3 5.8 - - + -
444A ASP* 3.8 31.4 - - - -
445A CYS* 3.8 3.1 - - - -
446A GLN* 3.0 20.3 + - - +
449A GLY 4.1 0.2 + - - -
450A ALA* 1.3 73.1 - - - +
452A TYR* 1.3 66.0 + - - +
560A ILE 3.0 17.5 + - - +
561A TYR* 3.7 23.6 - - + -
562A HIS* 2.9 32.6 + - - +
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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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443A LEU 3.5 0.9 - - - +
444A ASP* 3.2 7.0 - - - +
445A CYS 3.0 33.6 + - - +
447A ILE* 3.7 35.3 + - + -
450A ALA* 3.5 26.0 - - + +
451A CYS* 1.3 74.0 - - - +
453A SER* 1.3 61.1 + - - +
454A ILE* 3.7 19.2 + - + +
549A SER* 3.3 20.4 + - - -
550A TRP* 3.4 43.8 + + + -
555A TYR* 5.8 0.5 - - - -
561A TYR* 5.3 1.1 - - - -
562A HIS* 3.0 48.7 + - + -
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Residues in contact with SER 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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442A ALA* 3.5 23.2 - - - +
443A LEU 3.6 3.9 + - - -
444A ASP* 3.7 14.7 + - - -
452A TYR* 1.3 73.4 - - - +
454A ILE* 1.3 61.2 + - - +
455A GLU* 4.4 0.3 + - - +
561A TYR* 4.3 16.4 + - - -
562A HIS 5.1 4.4 + - - -
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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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409A LEU* 3.9 21.6 - - + +
413A ILE* 3.5 21.3 - - + -
442A ALA* 4.1 0.2 - - - -
443A LEU* 2.7 38.7 + - - +
445A CYS* 3.2 31.6 - - - -
447A ILE* 4.8 2.0 - - + -
452A TYR* 4.1 16.2 - - + -
453A SER* 1.3 80.8 + - - +
455A GLU* 1.3 76.0 + - - +
456A PRO* 3.6 4.0 - - - +
459A LEU* 5.5 0.7 - - + -
462A ILE* 3.8 21.5 - - + -
550A TRP* 3.7 21.5 - - + -
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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