Contacts of the helix formed by residues 447 - 452 (chain A) in PDB entry 1PJS
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 LEU 447 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341A GLY 3.4 5.1 - - - +
343A PRO* 3.5 30.5 - - + -
346A HIS* 3.9 28.5 - - + +
349A TYR* 4.2 26.0 - - + +
444A VAL* 3.3 14.8 - - - +
445A VAL 3.1 0.8 - - - -
446A ALA* 1.3 77.4 - - + +
448A ARG* 1.3 65.4 + - - +
449A ASP 3.2 2.4 + - - -
450A LYS* 3.4 24.5 + - + +
451A LEU* 3.2 34.1 + - + +
315B GLU* 3.9 21.5 - - - +
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Residues in contact with ARG 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A SER 3.2 21.4 + - - +
341A GLY 3.5 11.1 + - - -
342A ILE* 4.3 8.3 - - + -
418A VAL* 3.3 40.1 + - - +
420A HIS* 3.4 42.4 + - + -
444A VAL 4.4 0.4 + - - -
445A VAL* 3.4 17.4 + - + +
446A ALA 3.1 1.8 - - - -
447A LEU* 1.3 76.6 - - - +
449A ASP* 1.3 66.6 + - - +
452A ASN* 2.6 60.4 + - + +
455A SER 5.2 0.4 + - - -
456A ASN 5.5 0.6 - - - -
457A HIS* 2.8 28.1 + - - +
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Residues in contact with ASP 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A ALA 4.3 5.1 + - - -
447A LEU 3.2 1.0 + - - -
448A ARG* 1.3 90.3 + - + +
450A LYS* 1.3 61.1 + - - +
452A ASN* 3.1 33.0 + - - +
318B CYS* 5.9 0.9 - - - -
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Residues in contact with LYS 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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349A TYR* 5.5 2.6 + - - -
446A ALA 5.5 1.6 - - - +
447A LEU* 3.8 26.2 - - + +
449A ASP* 1.3 76.7 - - - +
451A LEU* 1.3 73.5 + - + +
452A ASN 4.0 0.8 - - - +
315B GLU* 3.4 46.8 + - + +
318B CYS* 3.4 34.2 - - - +
324B PHE* 4.3 0.5 - - - -
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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
----------------------------------------------------------
341A GLY* 3.6 13.3 - - - +
343A PRO* 3.8 33.2 - - + -
346A HIS* 6.0 0.2 - - - +
447A LEU* 3.2 28.3 + - + +
448A ARG 3.5 0.7 - - - -
450A LYS* 1.3 101.0 - - + +
452A ASN* 1.3 63.9 + - - +
453A TRP* 3.4 17.8 + - - -
305B PHE* 5.0 6.9 - - + -
311B GLY* 3.9 19.5 - - - +
314B LEU* 3.8 13.8 - - + +
315B GLU* 3.4 35.4 - - + +
324B PHE* 3.5 15.2 - - + -
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Residues in contact with ASN 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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339A TYR 4.6 2.4 - - - +
340A SER* 4.3 12.1 - - - +
341A GLY* 4.2 5.8 - - - -
448A ARG* 2.6 46.0 + - + +
449A ASP* 3.1 19.4 + - - +
450A LYS 4.0 1.0 - - - +
451A LEU* 1.3 73.0 - - - +
453A TRP* 1.3 68.8 + - - +
454A PHE 3.8 5.0 + - - -
455A SER 3.1 27.3 + - - +
456A ASN* 5.0 2.2 - - - +
318B CYS* 6.0 1.9 - - - -
324B PHE* 4.3 6.4 - - - -
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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