Contacts of the strand formed by residues 417 - 423 (chain B) in PDB entry 1JEQ
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 417 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451A LYS* 3.1 39.7 + - + +
452A ILE 4.7 2.1 - - - +
453A MET* 3.5 5.8 - - - +
364B VAL 4.6 0.2 - - - +
365B PHE* 3.6 13.7 - - - -
377B LEU* 4.9 2.1 - - - +
378B SER* 2.7 30.3 + - - -
381B ILE* 3.6 16.7 - - + +
382B HIS* 2.5 32.9 + - - -
411B HIS 3.6 8.7 - - - +
412B ILE* 3.6 6.6 - - + +
416B TYR* 1.3 82.2 - - - +
418B CYS* 1.3 67.1 + - - +
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Residues in contact with CYS 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363B LYS* 4.0 24.5 - - - -
364B VAL 2.9 23.1 - - - +
365B PHE* 3.7 12.1 - - + -
377B LEU* 4.8 0.7 - - - -
381B ILE* 3.2 20.4 - - - +
410B PRO* 3.8 1.0 - - - +
411B HIS* 3.0 58.6 + - - +
416B TYR* 4.1 7.4 - - - -
417B GLU* 1.3 77.2 - - - +
419B LEU* 1.3 64.0 + - - +
420B VAL* 4.9 0.2 - - - -
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Residues in contact with LEU 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251B LEU* 3.7 29.8 - - + -
340B PHE* 5.1 1.1 - - + -
362B LEU 3.7 0.2 - - - +
363B LYS* 3.5 3.3 - - - -
364B VAL* 2.8 43.5 + - + +
377B LEU* 4.2 8.3 - - + -
380B LEU* 4.2 12.1 - - + -
381B ILE* 3.8 24.7 - - + +
384B LEU* 3.9 26.0 - - + -
391B ALA* 6.0 0.9 - - + -
408B ALA* 4.1 26.0 - - + +
409B PHE 3.4 15.7 - - - +
410B PRO* 3.9 2.2 - - + -
418B CYS* 1.3 75.4 - - - +
420B VAL* 1.3 62.7 + - - +
421B TYR 3.7 0.6 + - - -
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Residues in contact with VAL 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359A HIS* 3.9 15.7 - - + -
361B VAL* 3.3 34.3 - - + -
362B LEU 3.4 3.8 - - - +
363B LYS* 4.7 10.5 - - + +
407B VAL 3.3 4.9 - - - +
408B ALA* 4.2 1.1 - - - -
409B PHE* 3.0 65.3 + - + -
411B HIS* 3.9 26.9 - - + -
418B CYS* 4.9 0.2 - - - -
419B LEU* 1.3 73.9 - - - +
421B TYR* 1.3 59.7 + - - +
422B VAL* 3.9 5.2 - - + -
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Residues in contact with TYR 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340B PHE* 4.1 20.9 - + + -
360B GLN* 5.3 6.3 - - + -
361B VAL* 3.8 2.4 - - - +
362B LEU* 2.7 62.6 + - + +
364B VAL* 4.5 5.6 - - + -
393B VAL* 3.5 30.7 - - + -
395B TYR* 3.3 30.1 - + + +
404B GLN* 3.0 32.6 + - - +
406B GLY* 3.8 16.7 + - - -
407B VAL 3.2 14.6 - - - -
408B ALA* 4.4 1.8 - - + +
419B LEU 3.7 1.6 + - - -
420B VAL* 1.3 70.3 - - - +
422B VAL* 1.3 69.9 + - - +
423B GLN* 3.7 23.2 - - + -
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Residues in contact with VAL 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358A LYS 5.4 0.7 - - - +
359A HIS* 5.7 0.2 - - - -
361A TYR* 3.8 30.3 - - + -
356B PHE* 3.8 29.6 - - + -
357B MET 4.1 2.7 - - - +
360B GLN 4.5 5.4 - - - +
361B VAL* 4.4 8.5 - - + -
407B VAL* 2.9 39.4 + - + +
409B PHE* 3.8 24.9 - - + -
420B VAL* 3.9 9.2 - - + -
421B TYR* 1.3 88.5 - - - +
423B GLN* 1.3 67.6 + - - +
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Residues in contact with GLN 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A LYS* 5.8 8.8 - - - +
356B PHE* 3.7 5.0 - - - -
357B MET* 2.8 44.1 + - + +
358B GLY* 3.6 20.2 - - - -
360B GLN 5.1 1.8 + - - -
404B GLN* 2.9 52.6 + - - +
405B VAL 3.8 4.4 + - - +
406B GLY* 3.9 0.2 - - - -
421B TYR* 3.7 14.2 - - + +
422B VAL* 1.3 77.1 - - - +
424B LEU* 1.3 76.2 + - - +
426B PHE* 5.0 11.3 - - - -
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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