Contacts of the helix formed by residues 450 - 457 (chain A) in PDB entry 5Q1B
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 HIS 450 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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365A TYR* 4.0 18.5 - + + -
446A THR* 3.1 28.7 + - - +
447A PHE 3.5 2.0 - - - -
448A ASN 3.2 0.2 - - - -
449A HIS* 1.3 97.4 - + - +
451A HIS* 1.3 63.6 + - - +
452A ALA 3.4 2.9 - - - -
453A GLU* 2.9 34.0 + - - +
454A MET* 3.0 37.2 + - + +
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Residues in contact with HIS 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A VAL* 3.7 32.1 - - + +
333A PHE* 5.1 0.2 - - + -
447A PHE 2.9 15.3 + - - +
448A ASN* 2.7 32.6 + - - -
449A HIS 3.6 0.6 - - - -
450A HIS* 1.3 75.9 - - - +
452A ALA* 1.3 63.2 + - + +
454A MET* 3.3 10.2 - - + +
455A LEU* 3.0 37.6 + - + +
472A ILE 5.1 1.6 - - - -
473A TRP* 3.5 21.8 - + + -
474A ASP* 3.1 49.7 + - + -
501A 9N7 3.8 9.6 - - + -
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Residues in contact with ALA 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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449A HIS 5.3 2.0 + - - +
450A HIS 3.4 0.6 - - - -
451A HIS* 1.3 93.0 + - + +
453A GLU* 1.3 58.3 + - + +
455A LEU* 3.2 8.5 + - - +
456A MET* 2.9 36.4 + - + +
474A ASP* 3.9 27.4 - - + +
475A VAL* 4.6 3.4 - - + -
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Residues in contact with GLU 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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365A TYR* 3.2 24.3 + - - +
449A HIS* 3.8 5.5 - - - +
450A HIS* 2.9 42.3 + - - +
451A HIS 3.4 0.2 - - - -
452A ALA* 1.3 77.2 - - + +
454A MET* 1.3 53.2 + - - +
456A MET* 4.2 4.7 - - - +
457A SER* 2.8 38.6 + - - -
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Residues in contact with MET 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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333A PHE* 3.9 23.3 - - + -
361A ILE* 3.4 17.9 - - + +
365A TYR* 3.3 39.4 - - + +
369A MET* 4.6 8.1 - - - -
447A PHE* 3.4 48.2 - - + +
450A HIS* 3.0 29.6 + - + +
451A HIS* 3.3 11.4 - - - +
453A GLU* 1.3 75.9 - - - +
455A LEU* 1.3 60.9 + - - +
457A SER* 3.3 16.2 + - - -
458A TRP* 3.5 9.8 + - - +
501A 9N7 3.7 13.7 - - - -
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Residues in contact with LEU 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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288A PHE* 4.0 11.5 - - + -
291A LEU* 3.8 18.2 - - + -
451A HIS* 3.0 25.1 + - + +
452A ALA 3.2 5.4 + - - +
454A MET* 1.3 76.6 - - - +
456A MET* 1.3 61.1 + - - +
458A TRP* 3.2 14.4 - - + +
463A HIS* 3.1 21.5 - - - -
465A PHE* 4.6 7.2 - - + -
473A TRP* 3.4 52.9 - - + -
475A VAL* 4.0 20.9 - - + -
501A 9N7 3.7 24.0 - - + -
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Residues in contact with MET 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 ALA* 2.9 22.4 + - + +
453A GLU* 4.2 5.4 - - - +
455A LEU* 1.3 75.1 - - - +
457A SER* 1.3 57.0 - - - +
458A TRP 3.2 1.5 - - - +
463A HIS* 3.0 48.6 + - + +
465A PHE* 3.7 29.6 - - + -
475A VAL* 4.1 13.0 - - + -
476A GLN 5.9 0.7 - - - -
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Residues in contact with SER 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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360A GLY 4.2 2.1 - - - +
361A ILE* 4.3 0.9 - - - +
362A SER* 3.2 31.9 + - - -
364A GLU* 4.8 3.1 - - - -
365A TYR* 3.5 16.2 - - - -
453A GLU* 2.8 23.0 + - - -
454A MET 3.3 8.8 + - - -
456A MET* 1.3 73.1 - - - +
458A TRP* 1.3 63.8 + - - +
459A ARG* 3.3 8.3 + - - +
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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