Contacts of the helix formed by residues 447 - 452 (chain A) in PDB entry 1XJP
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 LYS 447 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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328A VAL* 5.5 11.5 - - - +
329A PHE 5.6 2.2 + - - -
330A ASN* 4.8 19.1 - - + +
444A ARG* 5.8 2.7 - - - +
445A HIS* 3.3 18.4 + - + +
446A GLY* 1.3 70.1 - - - -
448A LEU* 1.3 60.7 + - - +
449A ARG* 6.1 0.2 - - + -
450A PRO* 2.6 43.3 - - + +
451A PHE* 3.4 8.6 + - - +
53B ASN* 3.4 29.6 + - - +
55B THR* 5.4 2.2 - - - +
339B VAL* 3.4 20.8 - - + +
340B GLN* 5.1 5.8 + - - +
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Residues in contact with LEU 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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89A PHE* 6.6 0.7 - - + -
446A GLY* 3.3 19.7 - - - +
447A LYS* 1.3 72.4 - - - +
449A ARG* 1.3 61.9 + - + +
451A PHE* 3.3 11.5 + - + +
452A GLU* 2.8 32.3 + - - +
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Residues in contact with ARG 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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331A ALA* 3.1 32.9 + - - +
333A LYS* 5.5 9.9 - - - +
447A LYS* 6.1 0.2 - - + -
448A LEU* 1.3 74.1 - - + +
450A PRO* 1.3 75.4 - - + +
452A GLU* 4.8 0.7 - - - -
453A ARG* 2.8 43.4 + - - +
55B THR* 5.2 9.2 - - + -
56B GLU* 5.4 5.6 - - + +
57B GLU* 1.9 48.8 + - - +
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Residues in contact with PRO 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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447A LYS* 2.6 47.6 - - + +
449A ARG* 1.3 100.1 - - + +
451A PHE* 1.3 54.0 + - - +
453A ARG* 3.1 3.3 + - - -
454A ASP* 3.1 24.0 + - - -
53B ASN* 4.7 5.6 - - - +
54B ILE 4.0 15.9 - - - +
55B THR* 5.0 5.9 - - - +
339B VAL* 3.8 21.1 - - - +
341B LYS* 3.1 24.8 - - + +
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Residues in contact with PHE 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 GLU* 2.3 33.9 - - - -
97A VAL* 3.0 51.5 - - + +
98A VAL* 5.5 4.0 - - + -
447A LYS 3.4 10.5 + - - +
448A LEU* 3.3 15.4 + - + +
450A PRO* 1.3 79.2 - - - +
452A GLU* 1.3 61.8 + - - +
453A ARG 3.3 1.0 + - - -
454A ASP* 3.5 17.3 + - + +
457A ASN* 4.5 12.0 + - + -
338B ASN* 6.1 2.9 - - + -
339B VAL* 4.7 25.0 - - + +
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Residues in contact with GLU 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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92A THR* 4.1 19.6 - - + +
93A GLU* 3.4 24.3 - - + +
96A ASN* 3.1 31.7 + - - +
448A LEU 2.8 19.6 + - - +
449A ARG* 4.8 0.4 - - - -
450A PRO 3.5 0.2 - - - -
451A PHE* 1.3 73.2 - - - +
453A ARG* 1.4 81.8 + - - +
454A ASP 3.7 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