Contacts of the strand formed by residues 447 - 452 (chain A) in PDB entry 3L5J
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 447 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330A LYS* 5.8 0.7 - - - +
434A GLU* 3.3 1.7 - - - -
435A TRP* 2.9 65.5 + - + +
445A ILE* 3.8 5.4 + - - +
446A THR* 1.3 78.5 - - - +
448A TRP* 1.3 67.7 + - - +
463A ASN 5.1 6.2 - - - +
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Residues in contact with TRP 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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309A SER* 3.8 40.6 - - - -
310A PHE 3.8 2.0 - - - -
311A TRP* 3.8 28.3 - + + -
328A VAL* 3.8 31.1 - - + +
329A TRP* 3.9 16.5 + - - -
330A LYS* 3.0 46.0 + - + +
432A ILE* 4.2 6.3 - - + -
433A LEU 3.0 14.4 - - - +
434A GLU* 4.1 15.3 - - + +
435A TRP* 3.6 11.2 - - - -
446A THR* 4.6 8.1 - - - +
447A ASP* 1.3 83.1 - - - +
449A GLN* 1.3 90.8 + - - +
450A GLN* 4.2 7.0 - - - -
461A ARG 5.2 0.9 - - - +
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Residues in contact with GLN 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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330A LYS* 4.3 2.9 - - - +
432A ILE* 3.7 4.2 - - - +
433A LEU* 3.1 37.0 + - + +
435A TRP* 3.6 14.2 - - + -
448A TRP* 1.3 94.4 - - - +
450A GLN* 1.3 63.1 + - - +
451A GLU* 2.7 28.4 + - - +
458A THR* 4.0 5.5 + - - +
459A TYR 3.1 20.2 + - - -
460A LEU* 3.6 1.9 - - - +
461A ARG* 2.6 53.5 + - + +
589A CL 4.1 8.1 - - + -
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Residues in contact with GLN 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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308A PRO 4.9 2.4 + - - -
309A SER* 3.2 28.1 + - - +
310A PHE 2.9 29.7 + - - +
430A LYS* 3.3 39.6 + - + +
431A TYR 3.5 11.2 - - - +
432A ILE* 4.1 5.6 - - + +
448A TRP* 4.2 1.0 - - + -
449A GLN* 1.3 78.3 - - - +
451A GLU* 1.3 73.2 + - - +
461A ARG* 2.9 19.8 + - - -
589A CL 3.4 5.1 - - - +
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Residues in contact with GLU 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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421A TRP* 5.4 0.2 - - + -
430A LYS* 3.3 9.5 - - - +
431A TYR* 2.9 37.4 + - + -
433A LEU* 3.8 22.7 - - + -
449A GLN* 2.7 26.3 + - - +
450A GLN* 1.3 85.3 - - - +
452A ASP* 1.3 65.6 + - - +
455A VAL* 3.9 26.4 - - + +
458A THR* 2.9 24.0 + - + -
461A ARG* 2.8 17.5 + - - -
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Residues in contact with ASP 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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429A LYS 4.7 1.8 - - - -
430A LYS* 4.6 2.5 - - - +
431A TYR* 3.3 9.6 - - - -
451A GLU* 1.3 80.9 + - - +
453A GLY* 1.3 63.8 + - - +
454A THR* 3.0 22.1 + - + +
455A VAL* 3.1 20.4 + - + +
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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