Contacts of the strand formed by residues 418 - 425 (chain A) in PDB entry 2E3M
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 418 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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392A TRP* 4.0 2.4 - - - -
395A VAL* 5.8 1.3 - - + -
403A VAL* 3.9 23.8 - - + -
404A TYR 3.6 10.1 - - - +
405A ARG* 4.6 10.5 - - + +
416A ASP 3.3 3.5 + - - +
417A PRO* 1.3 73.1 - - - +
419A LYS* 1.3 72.2 + - - +
420A ALA* 4.4 2.7 - - + +
553A TYR* 4.0 19.7 - - + -
554A VAL* 3.4 5.9 - - - +
555A ALA* 2.9 42.6 + - + +
556A ASN* 5.5 0.5 + - - -
572A ALA* 4.9 9.2 - - + +
573A LYS* 6.1 0.9 - - - -
576A TYR* 3.7 49.8 - - + -
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Residues in contact with LYS 419 (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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381A TYR 5.3 0.9 - - - -
382A SER* 2.7 33.0 + - - +
383A LEU 4.5 3.8 + - - -
384A GLN 3.4 21.9 + - - -
385A ASP* 5.3 1.0 - - - +
386A VAL* 3.7 31.3 - - + +
392A TRP* 3.6 22.6 - - + -
403A VAL* 3.6 0.5 - - - +
404A TYR* 2.6 46.3 + - + +
418A LEU* 1.3 78.5 - - - +
420A ALA* 1.3 62.6 + - - +
421A THR* 4.1 15.3 - - + +
552A THR* 3.4 18.2 + - + +
553A TYR 3.4 3.8 - - - +
554A VAL* 3.8 14.6 - - + -
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Residues in contact with ALA 420 (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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401A MET* 5.1 0.7 - - + -
402A LYS 3.2 11.2 - - - +
403A VAL* 4.2 10.5 - - + -
404A TYR* 4.9 0.4 - - - -
418A LEU* 4.5 6.3 - - + -
419A LYS* 1.3 75.0 - - - +
421A THR* 1.3 66.4 + - - +
422A HIS* 6.2 0.2 - - + -
551A ILE* 4.0 0.6 - - - +
552A THR* 3.4 5.7 - - - +
553A TYR* 2.8 39.3 + - + +
580A LEU* 3.4 33.0 - - + -
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Residues in contact with THR 421 (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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386A VAL* 6.2 0.7 - - + -
400A GLU 4.2 2.1 + - - -
401A MET* 3.4 4.3 - - - +
402A LYS* 2.9 50.9 + - - +
404A TYR* 4.1 11.7 + - + -
419A LYS* 4.1 15.9 - - + +
420A ALA* 1.3 77.0 - - - +
422A HIS* 1.3 65.8 + - - +
550A LYS* 6.4 0.7 - - - -
551A ILE* 3.3 5.6 - - - +
552A THR* 3.9 17.7 - - - +
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Residues in contact with HIS 422 (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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400A GLU* 3.6 16.7 - - + +
401A MET* 3.8 29.8 - - + -
420A ALA* 6.2 0.4 - - + -
421A THR* 1.3 75.2 - - - +
423A ALA* 1.3 83.1 + - - +
424A VAL* 4.1 8.3 - - + -
550A LYS* 3.7 6.6 + - - +
551A ILE* 2.8 48.7 + - + +
580A LEU* 4.3 9.6 - - + -
581A LYS* 3.1 33.7 - - - -
584A THR* 3.6 30.0 + - + -
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Residues in contact with ALA 423 (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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400A GLU* 3.6 35.0 - - + +
422A HIS* 1.3 89.4 + - - +
424A VAL* 1.3 61.1 + - - +
425A LYS* 4.3 3.3 + - - +
548A LEU* 3.9 24.9 - - + -
549A CYS 3.5 6.1 - - - +
550A LYS* 4.5 12.6 - - + +
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Residues in contact with VAL 424 (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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422A HIS* 4.0 13.5 - - + +
423A ALA* 1.3 77.8 - - - +
425A LYS* 1.3 63.0 + - - +
426A GLY 3.6 0.5 + - - -
427A VAL* 3.7 23.8 - - + +
432A VAL* 5.7 0.4 - - + -
548A LEU* 3.6 3.5 - - - +
549A CYS* 2.9 41.4 + - + +
551A ILE* 3.8 25.4 - - + -
584A THR* 4.0 24.2 - - - +
587A VAL* 6.0 0.7 - - + -
588A GLN* 3.7 31.0 - - + +
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Residues in contact with LYS 425 (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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400A GLU* 4.4 24.2 + - - +
423A ALA* 4.2 3.8 + - - +
424A VAL* 1.3 74.0 - - - +
426A GLY* 1.3 62.9 + - - +
427A VAL 3.5 0.5 + - - -
544A ARG 5.6 0.2 - - - +
547A ILE 3.7 6.7 - - - +
548A LEU* 3.6 25.7 - - + +
588A GLN* 3.2 28.6 + - - +
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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