Contacts of the helix formed by residues 448 - 455 (chain A) in PDB entry 5XJY
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 PHE 448 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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262A LEU* 5.5 11.4 - - + -
444A ASP 2.8 23.7 + - - +
445A ASN* 4.3 1.3 - - - -
447A HIS* 1.3 75.4 - - - +
449A TRP* 1.3 60.1 + - - +
451A GLN* 3.1 4.5 + - - +
452A GLN* 2.9 30.7 + - - +
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Residues in contact with TRP 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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262A LEU* 5.9 9.4 - - + +
439A LEU 4.6 5.6 - - - +
440A LEU* 5.3 6.1 - - - +
445A ASN* 2.7 34.4 + - + +
448A PHE* 1.3 76.2 - - - +
450A GLU* 1.3 49.7 + - - +
452A GLN* 4.5 3.7 - - - +
453A LEU* 2.7 38.9 + - - +
462A ASP* 5.9 2.9 - - + -
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Residues in contact with GLU 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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445A ASN 3.0 3.4 + - - +
446A ASP* 2.5 28.7 + - + +
449A TRP* 1.3 74.9 - - - +
451A GLN* 1.3 54.7 + - - +
453A LEU* 4.1 6.3 - - - -
454A ASP* 2.6 38.4 - - + +
462A ASP* 4.6 17.0 - - + -
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Residues in contact with GLN 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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447A HIS 2.5 26.7 + - - +
448A PHE* 3.1 6.9 + - - +
450A GLU* 1.3 78.1 - - - +
452A GLN* 1.3 58.7 + - - +
454A ASP* 4.0 2.0 - - - +
455A GLY* 2.9 25.3 + - - -
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Residues in contact with GLN 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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262A LEU 5.4 2.9 - - - +
263A HIS* 6.4 0.2 - - - -
266A GLY* 4.4 25.2 - - - +
270A GLN* 5.5 0.2 - - - +
448A PHE 2.9 14.3 + - - +
449A TRP* 4.5 3.6 - - - +
451A GLN* 1.3 77.0 - - - +
453A LEU* 1.3 53.6 + - - +
455A GLY* 3.4 2.7 - - - -
456A LEU* 2.7 30.1 + - - +
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Residues in contact with LEU 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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266A GLY* 5.9 0.4 - - - -
269A ALA* 5.2 12.6 - - + -
449A TRP 2.7 24.1 + - - +
450A GLU* 4.1 3.4 - - - -
452A GLN* 1.3 76.9 - - - +
454A ASP* 1.3 62.6 + - - +
455A GLY 3.2 1.3 - - - -
456A LEU* 3.1 21.4 + - + +
457A ASP 3.6 9.0 - - - +
459A THR* 4.2 13.3 - - - -
461A GLN 6.3 1.1 - - - -
462A ASP* 5.8 7.6 - - + +
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Residues in contact with ASP 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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450A GLU* 2.6 27.5 + - + +
451A GLN* 4.0 3.1 - - - +
453A LEU* 1.3 76.7 - - - +
455A GLY* 1.3 57.5 + - - +
457A ASP* 3.6 13.8 + - - +
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Residues in contact with GLY 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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451A GLN 2.9 18.9 + - - -
452A GLN* 3.4 4.3 - - - -
454A ASP* 1.3 75.2 - - - +
456A LEU* 1.3 64.0 + - - +
457A ASP* 4.7 0.4 - - - -
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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