Contacts of the helix formed by residues 448 - 455 (chain A) in PDB entry 1XV9
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 ASP 448 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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269A CYS 5.0 6.2 + - - +
270A GLN* 5.0 12.5 - - - +
273A ASP* 3.4 24.9 + - + +
446A PRO* 4.1 10.5 - - - +
447A ILE* 1.3 82.5 - - - +
449A THR* 1.3 59.9 + - + +
451A LEU* 3.3 7.4 + - - +
452A MET* 2.8 36.1 + - - +
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Residues in contact with THR 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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273A ASP* 3.8 11.4 + - - -
277A PHE* 4.9 6.1 - - - -
448A ASP* 1.3 70.7 + - - +
450A PHE* 1.3 71.5 + - - +
452A MET* 2.8 19.7 + - - +
453A GLU* 3.1 9.9 + - - +
632E ILE* 3.6 20.1 - - + +
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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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273A ASP* 3.4 7.3 + - - +
276A LEU* 3.2 53.1 - - + +
277A PHE* 3.3 37.7 - + + -
280A VAL* 3.7 22.0 - - + -
449A THR* 1.3 80.5 + - - +
451A LEU* 1.3 63.0 + - - +
453A GLU* 3.6 5.4 + - - +
454A MET* 3.4 26.2 + - + +
632E ILE* 3.3 45.8 - - + +
633E LEU* 3.8 20.9 - - + -
636E LEU* 4.2 13.0 - - + -
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Residues in contact with LEU 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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269A CYS* 3.7 40.8 - - + +
272A ALA* 4.2 14.6 - - + -
273A ASP* 3.3 15.9 + - - +
276A LEU* 3.6 9.8 - - + +
305A TRP* 4.0 31.0 - - + -
436A LEU* 4.8 14.6 - - + -
447A ILE* 3.6 22.9 - - + -
448A ASP 3.5 7.9 - - - +
449A THR 3.1 0.8 - - - -
450A PHE* 1.3 76.3 - - - +
452A MET* 1.3 59.6 + - - +
454A MET* 3.0 15.1 + - - +
455A LEU* 2.8 28.6 - - + +
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Residues in contact with MET 452 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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440A LYS* 3.4 50.5 - - + +
447A ILE* 3.5 33.9 - - + +
448A ASP 2.8 17.8 + - - +
449A THR* 2.8 12.6 + - - +
451A LEU* 1.3 71.6 - - - +
453A GLU* 1.3 61.2 + - - +
455A LEU* 2.9 35.1 + - + +
456A GLU* 4.6 1.6 - - - +
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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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302A ARG* 5.4 0.3 - - - -
449A THR 3.1 6.8 + - - +
450A PHE* 3.8 9.4 - - - +
451A LEU 3.2 0.2 - - - -
452A MET* 1.3 80.0 - - - +
454A MET* 1.3 66.2 + - - +
455A LEU 3.3 0.7 + - - -
456A GLU* 3.2 23.0 - - - +
630E HIS* 2.9 52.7 - - - +
631E LYS* 3.4 5.0 + - - +
632E ILE* 3.0 36.9 + - + +
633E LEU* 3.2 25.0 - - - +
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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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276A LEU* 3.3 33.7 - - + -
301A LEU* 3.8 5.4 - - + +
302A ARG* 3.5 39.5 + - - +
305A TRP* 3.2 70.5 + - + +
450A PHE* 3.4 11.0 - - - +
451A LEU 3.0 9.4 + - - +
453A GLU* 1.3 84.7 - - - +
455A LEU* 1.3 58.1 + - - +
456A GLU* 3.8 2.1 + - - +
630E HIS* 6.5 0.2 - - - -
633E LEU* 4.4 23.3 - - + -
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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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305A TRP* 4.9 8.7 - - + -
433A LEU* 5.0 4.5 - - + -
436A LEU* 3.8 43.1 - - + +
437A PHE* 3.9 24.7 - - + -
440A LYS* 3.5 27.0 + - + -
447A ILE* 4.7 8.7 - - + -
451A LEU* 2.8 40.6 - - + +
452A MET* 2.9 30.8 - - + +
453A GLU 3.2 0.4 - - - -
454A MET* 1.3 76.1 - - - +
456A GLU* 1.3 70.8 + - - +
457A ALA 4.2 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