Contacts of the strand formed by residues 423 - 430 (chain A) in PDB entry 4J15
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 GLU 423 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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370A THR* 6.0 3.4 - - + +
373A GLU* 5.3 2.9 - - - -
374A LYS* 4.8 13.0 - - + -
419A PHE* 3.2 3.8 - - - -
420A MET 2.9 30.9 + - - +
421A ARG* 3.6 11.1 - - - +
422A GLY* 1.3 83.6 - - - +
424A GLU* 1.3 64.8 + - - +
425A ILE* 3.4 3.2 + - - +
475A ARG* 3.8 21.4 + - - +
478A MET* 4.8 5.6 - - - +
479A LEU* 3.6 30.0 - - + +
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Residues in contact with GLU 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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373A GLU* 4.0 17.2 + - - +
417A ASP* 3.5 25.5 - - + +
418A MET 3.5 7.4 - - - +
419A PHE* 3.5 17.0 - - + -
423A GLU* 1.3 72.2 - - - +
425A ILE* 1.3 63.0 + - - +
426A LEU* 3.4 31.6 + - - +
427A SER* 3.9 9.3 + - - -
475A ARG* 3.0 33.4 + - - +
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Residues in contact with ILE 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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310A MET* 4.0 22.0 - - + -
388A PHE* 4.2 11.4 - - + -
418A MET* 2.8 22.2 + - + +
420A MET* 3.7 36.6 - - + +
423A GLU 3.7 4.0 - - - +
424A GLU* 1.3 81.2 - - - +
426A LEU* 1.3 65.7 + - + +
470A GLY 3.2 12.3 - - - +
471A ILE* 3.5 24.6 - - + +
472A GLY 4.5 1.9 + - - -
475A ARG* 4.6 9.1 - - + +
476A VAL* 4.2 12.6 - - + -
479A LEU* 3.5 32.3 - - + -
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Residues in contact with LEU 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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291A ILE* 6.1 0.9 - - + -
306A ILE* 3.5 28.0 - - + -
310A MET* 5.7 2.5 - - + -
416A TYR* 3.9 22.7 - - + -
417A ASP* 3.0 8.7 - - - +
418A MET* 2.9 49.7 + - + +
424A GLU* 3.4 5.4 + - - +
425A ILE* 1.3 86.5 - - + +
427A SER* 1.3 64.3 + - - +
428A GLY* 3.6 17.0 - - - +
469A GLY* 4.1 8.3 - - - +
470A GLY* 3.5 31.6 - - - +
471A ILE* 4.2 9.9 - - + -
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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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399A ARG* 3.2 14.9 + - - -
416A TYR 3.5 0.2 - - - -
417A ASP* 2.9 24.1 + - - -
424A GLU* 3.9 12.9 + - - -
426A LEU* 1.3 78.3 - - - +
428A GLY* 1.3 57.8 + - - +
431A ARG* 5.2 2.9 + - - -
469A GLY* 4.6 5.7 - - - -
470A GLY 4.4 3.7 + - - +
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Residues in contact with GLY 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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399A ARG* 3.0 11.1 + - - -
416A TYR* 2.8 44.4 + - - -
426A LEU* 3.6 5.9 - - - +
427A SER* 1.3 75.3 - - - +
429A ALA* 1.3 61.5 + - - +
431A ARG* 4.7 4.0 - - - -
468A GLY 3.2 18.4 - - - -
469A GLY* 4.3 2.5 - - - -
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Residues in contact with ALA 429 (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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399A ARG* 5.1 0.7 - - - +
402A TYR* 5.8 0.7 - - + -
403A THR* 3.8 18.2 - - + +
414A ASN 3.3 14.1 - - - +
415A SER* 3.7 11.7 - - - -
416A TYR* 3.6 7.5 - - - -
428A GLY* 1.3 77.2 - - - +
430A GLN* 1.3 72.2 + - - +
431A ARG* 3.5 19.4 - - - +
467A ALA* 3.3 22.3 - - - +
468A GLY 3.4 9.0 + - - -
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Residues in contact with GLN 430 (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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295A PHE* 3.4 16.3 - - + -
299A TYR* 3.7 14.3 - - + +
403A THR* 3.8 0.9 - - - -
404A MET* 3.0 42.0 + - + +
414A ASN* 2.9 34.0 + - + +
416A TYR* 4.4 2.4 - - - -
429A ALA* 1.3 78.7 - - - +
431A ARG* 1.3 69.8 + - - +
433A HIS* 4.4 0.7 - - - -
465A PRO* 4.3 4.5 - - - +
466A HIS 3.5 12.1 - - - +
467A ALA* 3.6 6.5 - - - +
35B ILE 3.1 23.4 - - - +
36B GLN 3.6 3.8 - - - -
37B SER* 2.6 29.9 + - - -
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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