Contacts of the strand formed by residues 406 - 413 (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 MET 406 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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404A PRO* 4.5 17.7 - - + +
405A VAL* 1.3 85.0 - - - +
407A ASP* 1.3 77.8 + - - +
408A LEU 3.2 3.8 + - - -
421A TRP* 3.6 1.4 - - - +
422A THR* 2.7 49.7 + - + +
424A PRO* 6.2 3.6 - - + -
486A GLU* 5.8 2.2 - - - +
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Residues in contact with ASP 407 (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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405A VAL 4.4 0.2 + - - -
406A MET* 1.3 79.9 - - - +
408A LEU* 1.3 67.6 + - - +
409A LYS* 3.4 10.4 + - - +
420A GLU 3.7 6.6 - - - +
421A TRP* 4.0 2.9 - - - -
422A THR* 2.6 28.2 + - - +
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Residues in contact with LEU 408 (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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405A VAL* 4.1 22.4 - - + +
406A MET 3.2 2.8 - - - -
407A ASP* 1.3 78.4 - - - +
409A LYS* 1.3 75.7 + - - +
419A VAL* 3.7 24.5 - - + -
420A GLU 3.6 13.5 - - - +
421A TRP* 4.2 5.2 - - + -
472A ILE 4.8 0.9 - - - +
474A VAL* 4.0 12.6 - - + +
486A GLU* 3.4 32.3 - - + +
487A SER 3.7 10.8 - - - +
488A ILE* 3.7 35.5 - - + +
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Residues in contact with LYS 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A ASP 3.7 8.7 - - - +
408A LEU* 1.3 81.3 - - - +
410A ALA* 1.3 62.2 + - - +
411A PHE* 4.6 6.0 - - + -
418A TRP 4.0 0.3 - - - +
419A VAL* 3.5 2.9 - - - -
420A GLU* 3.0 61.7 + - + +
488A ILE* 3.6 11.0 - - + -
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Residues in contact with ALA 410 (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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409A LYS* 1.3 77.0 - - - +
411A PHE* 1.3 64.1 + - - +
412A PRO* 4.7 0.7 - - - +
417A LEU* 5.0 2.0 - - + -
418A TRP 3.1 10.5 - - - +
419A VAL* 4.0 4.0 - - + -
472A ILE* 3.8 28.7 - - + -
488A ILE* 3.7 17.1 - - + +
490A ALA* 3.8 24.9 - - + +
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Residues in contact with PHE 411 (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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409A LYS* 4.6 5.2 - - + -
410A ALA* 1.3 81.7 - - - +
412A PRO* 1.3 80.6 - - + +
413A LYS* 4.3 27.1 - - + -
417A LEU* 3.8 5.1 - - - +
418A TRP* 2.9 57.5 + + + +
420A GLU* 3.2 43.1 - - + -
457A ARG* 5.6 2.0 - - - -
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Residues in contact with PRO 412 (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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410A ALA 4.7 1.1 - - - +
411A PHE* 1.3 91.0 - - + +
413A LYS* 1.3 64.9 + - - +
415A ASN* 6.1 0.7 - - - +
416A MET 3.4 8.3 - - - +
417A LEU* 3.7 6.3 - - + -
490A ALA* 5.8 1.1 - - + -
491A TYR 3.6 15.7 - - - +
492A LEU* 3.0 32.5 - - + +
493A LYS* 5.7 0.2 - - - -
494A GLN* 6.1 3.4 - - - +
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Residues in contact with LYS 413 (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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411A PHE* 3.7 24.8 + - + -
412A PRO* 1.3 77.4 - - - +
414A ASP* 1.3 88.7 + - - +
415A ASN 3.3 1.5 - - - +
416A MET* 2.8 31.0 + - - +
418A TRP* 3.7 34.6 + - + +
457A ARG* 6.0 2.6 - - - +
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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