Contacts of the strand formed by residues 420 - 428 (chain A) in PDB entry 4JWE
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 420 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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412A ILE* 3.8 28.1 - - + +
416A THR* 3.5 26.5 - - + +
417A THR 3.4 12.8 - - - +
418A ILE* 4.0 13.4 - - + +
419A PRO* 1.3 75.5 - - - +
421A LYS* 1.3 67.5 + - - +
422A HIS* 5.9 0.2 - - - +
476A PHE 4.1 0.2 - - - +
477A ASP* 3.5 2.2 - - - -
478A ILE* 2.8 35.8 + - + +
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Residues in contact with LYS 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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412A ILE* 5.3 1.1 - - - -
420A THR* 1.3 82.5 + - - +
422A HIS* 1.3 65.3 + - - +
423A SER* 4.3 3.6 + - - -
475A THR* 3.5 24.3 + - + +
476A PHE 3.3 11.9 - - - +
477A ASP* 3.3 28.7 - - + +
703A SO4 3.9 21.2 + - - +
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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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410A THR 5.4 0.7 - - - -
411A LEU* 3.1 46.1 - - + +
412A ILE* 4.4 8.7 - - + +
420A THR* 5.9 0.4 - - - +
421A LYS* 1.3 75.5 + - - +
423A SER* 1.3 85.4 + - - +
424A GLN* 4.6 10.8 + - + +
475A THR* 3.5 1.1 - - - -
476A PHE* 2.9 32.9 + - - +
703A SO4 2.7 28.5 + - - -
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Residues in contact with SER 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A LEU* 4.4 0.4 - - - -
421A LYS* 4.3 4.5 + - - -
422A HIS* 1.3 87.6 + - - +
424A GLN* 1.3 61.5 + - - +
473A GLU* 3.4 24.5 + - - -
474A VAL 3.2 6.5 - - - -
475A THR* 2.7 31.5 + - - +
703A SO4 3.0 31.1 + - - -
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Residues in contact with GLN 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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409A THR* 4.1 7.0 - - - +
410A THR 3.9 17.3 - - - +
411A LEU* 4.0 10.1 - - + +
422A HIS* 4.6 9.6 + - - +
423A SER* 1.3 75.7 - - - +
425A VAL* 1.3 68.9 + - - +
426A PHE* 3.4 27.0 - - + -
473A GLU* 4.6 1.1 - - - -
474A VAL 2.9 30.3 + - - +
6D ARG 5.3 1.6 + - - -
8D PRO* 3.3 35.6 - - - +
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Residues in contact with VAL 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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424A GLN* 1.3 79.0 - - - +
426A PHE* 1.3 71.4 + - - +
471A GLN* 3.9 26.5 - - + -
472A ILE 3.5 6.1 - - - +
473A GLU* 4.3 12.6 - - + +
491A LYS* 3.9 25.8 - - - +
7D ARG* 3.3 54.0 + - + +
8D PRO* 3.7 13.0 - - - +
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Residues in contact with PHE 426 (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 ILE* 3.6 23.1 - - + -
403A THR* 3.7 26.2 - - + -
409A THR* 3.9 6.7 - - + -
411A LEU* 3.9 17.9 - - + -
424A GLN* 3.4 42.2 - - + -
425A VAL* 1.3 74.9 - - - +
427A SER* 1.3 60.2 + - - +
470A PRO 3.6 4.0 - - - +
471A GLN* 3.8 1.7 - - - -
472A ILE* 2.8 34.4 + - - +
474A VAL* 3.5 20.6 - - + -
7D ARG* 4.4 3.1 - - - -
8D PRO* 3.3 39.9 - - + +
10D LEU* 3.7 23.1 - - + -
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Residues in contact with SER 427 (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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426A PHE* 1.3 75.0 - - - +
428A THR* 1.3 67.3 + - - +
468A GLY* 3.0 36.0 + - - -
469A MET 3.5 0.7 + - - -
470A PRO 2.7 25.8 + - - -
472A ILE* 4.7 6.3 - - - -
7D ARG* 4.4 12.7 - - - +
8D PRO 3.0 7.7 + - - -
9D ARG* 3.3 10.6 - - - -
10D LEU* 2.8 30.2 + - - +
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Residues in contact with THR 428 (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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427A SER* 1.3 78.4 + - - +
429A ALA* 1.3 63.6 + - - +
430A GLU 3.9 3.0 + - - -
433A GLN* 3.7 35.8 - - + +
436A VAL* 4.0 20.6 - - + -
462A ILE* 4.8 4.9 - - + -
465A ALA 5.0 0.7 + - - -
466A PRO 4.2 0.5 + - - -
467A ARG* 3.6 7.4 - - - +
468A GLY 3.4 13.3 + - - -
470A PRO* 3.3 38.6 - - + +
472A ILE* 5.3 0.9 - - + -
9D ARG* 3.3 17.3 - - - -
10D LEU 4.1 3.4 - - - -
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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