Contacts of the strand formed by residues 412 - 421 (chain A) in PDB entry 5EQX
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 THR 412 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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408A ILE* 3.9 0.3 - - - -
409A VAL* 3.1 26.3 + - - +
410A ASN* 3.1 17.0 + - + +
411A LYS* 1.3 103.6 - - + +
413A ILE* 1.3 75.4 + - - +
414A THR* 4.4 7.4 + - - -
433A TYR* 5.2 9.8 - - + -
434A VAL 3.4 13.0 - - - -
435A ARG* 3.9 18.6 - - + +
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Residues in contact with ILE 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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382A ASP 6.0 1.1 - - - +
385A TYR* 4.4 23.6 - - + -
386A LEU* 4.8 7.0 - - + -
397A PHE* 4.2 26.0 - - + -
407A PHE 3.2 24.0 - - - +
408A ILE* 4.0 22.9 - - + -
409A VAL* 5.0 3.4 - - - -
412A THR* 1.3 80.7 - - - +
414A THR* 1.3 66.3 + - - +
432A VAL 3.5 2.6 - - - +
433A TYR* 3.6 0.5 - - - -
434A VAL* 3.0 52.3 + - + +
436A VAL* 4.8 8.7 - - + -
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Residues in contact with THR 414 (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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380A ARG* 4.0 18.9 + - - +
382A ASP* 4.5 11.4 + - - +
386A LEU* 5.5 0.9 - - - -
407A PHE 5.3 0.2 + - - -
409A VAL* 5.8 3.6 - - - +
412A THR* 4.4 5.4 + - - -
413A ILE* 1.3 80.3 + - - +
415A ALA* 1.3 64.5 + - - +
431A THR* 3.4 29.8 - - + -
432A VAL 3.4 3.6 - - - +
433A TYR* 3.6 30.6 - - + +
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Residues in contact with ALA 415 (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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378A MET* 4.6 4.0 - - + -
380A ARG 3.7 11.0 - - - +
381A ASN* 3.9 20.0 - - - +
386A LEU* 3.8 27.3 - - + +
414A THR* 1.3 75.2 - - - +
416A GLU* 1.3 65.6 - - - +
431A THR* 3.5 6.1 - - - +
432A VAL* 2.6 41.5 + - + +
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Residues in contact with GLU 416 (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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378A MET* 3.8 8.1 - - - +
379A GLY* 2.8 41.6 + - - +
380A ARG* 3.8 24.3 + - + +
415A ALA* 1.3 75.8 - - - +
417A VAL* 1.3 67.8 + - - +
418A LEU* 4.9 2.8 - - + +
429A THR* 3.9 12.7 - - + +
430A GLY 3.2 7.2 - - - +
431A THR* 4.5 3.8 - - + +
612A MAN 1.3 44.9 + - - +
613A MAN 3.2 18.3 + - - +
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Residues in contact with VAL 417 (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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334A PHE* 3.3 29.8 - - + -
360A TYR* 3.8 6.7 - - + -
377A VAL 3.5 3.1 - - - +
378A MET* 3.6 30.7 - - + -
388A ILE* 3.7 22.2 - - + -
395A ILE* 4.3 4.3 - - + -
416A GLU* 1.3 72.9 - - - +
418A LEU* 1.3 63.8 + - - +
429A THR* 3.5 1.7 - - - -
430A GLY 2.6 53.9 + - - +
432A VAL* 3.7 22.9 - - + -
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Residues in contact with LEU 418 (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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334A PHE* 4.3 1.3 - - - -
375A LYS 3.5 0.9 - - - +
376A TYR* 3.4 6.4 - - - -
377A VAL* 2.6 50.3 + - + +
378A MET 3.4 8.1 - - - +
379A GLY* 3.3 37.9 - - - +
416A GLU* 4.8 2.5 - - + +
417A VAL* 1.3 74.3 - - - +
419A ALA* 1.3 60.0 + - - +
420A ILE* 4.0 6.1 - - + -
427A THR* 3.6 26.5 - - + -
428A SER 3.5 0.7 - - - +
429A THR* 3.4 35.7 - - + +
612A MAN 4.1 8.5 - - - +
614A MAN 4.7 8.3 - - - +
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Residues in contact with ALA 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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332A ILE* 4.9 6.2 - - + +
334A PHE* 3.6 25.1 - - + -
362A ALA* 3.9 11.2 - - + -
374A VAL* 4.9 5.8 - - + -
375A LYS 3.5 4.9 - - - -
376A TYR* 3.9 19.1 - - + -
418A LEU* 1.3 73.2 - - - +
420A ILE* 1.3 62.8 + - - +
421A ASP 3.9 0.5 + - - -
426A LYS 3.7 1.6 - - - +
428A SER* 2.9 37.6 + - - +
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Residues in contact with ILE 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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374A VAL* 3.1 6.3 - - - -
375A LYS* 2.8 52.3 + - + +
377A VAL* 4.2 29.4 - - + -
418A LEU* 4.8 5.4 - - + -
419A ALA* 1.3 75.4 - - - +
421A ASP* 1.3 73.9 + - - +
422A GLU* 3.7 0.7 + - - +
425A GLY* 4.0 19.5 - - - -
426A LYS 4.5 2.9 - - - -
427A THR* 3.8 20.9 - - + +
614A MAN 4.2 24.7 - - - +
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Residues in contact with ASP 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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332A ILE* 3.2 31.2 - - + +
372A SER 4.6 0.9 - - - +
373A ASN* 3.9 8.4 - - - +
374A VAL* 4.2 2.9 - - - +
419A ALA 3.9 2.6 + - - -
420A ILE* 1.3 81.6 - - - +
422A GLU* 1.3 61.9 + - - +
423A TYR* 2.7 48.4 + - - +
424A THR* 3.3 24.8 + - + +
425A GLY 3.5 14.7 + - - -
426A LYS* 4.2 10.2 + - + +
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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