Contacts of the helix formed by residues 391 - 398 (chain C) in PDB entry 1JIQ
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 PHE 391 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339C LEU* 4.0 12.8 - - + -
380C TRP* 3.5 34.8 - + - -
382C GLU* 3.9 25.6 - - + -
387C GLY* 3.1 27.7 + - - -
390C ALA* 1.3 83.4 - - + +
392C TYR* 1.3 87.6 + + - +
393C GLN* 3.1 4.0 - - - -
394C LEU* 3.1 16.9 + - - +
395C ILE* 3.6 13.1 + - + +
353D GLN* 3.8 41.1 - - + +
357D MET* 3.8 19.0 - - + +
358D GLU 5.0 1.1 - - - +
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Residues in contact with TYR 392 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339C LEU* 3.6 26.7 - - + +
341C TYR* 2.9 40.8 + - - -
382C GLU 5.3 0.2 + - - -
384C GLY* 4.8 1.9 - - - -
387C GLY* 3.2 14.3 + - - -
388C GLN* 3.4 45.0 + - + +
390C ALA 3.8 1.2 - - - -
391C PHE* 1.3 96.8 - + - +
393C GLN* 1.3 65.0 + - - +
395C ILE* 2.9 14.6 + - + -
396C HIS* 2.8 38.7 + + + -
406C PHE* 3.7 10.1 - + - -
432C GLN* 3.2 26.9 - - + +
436C LEU* 6.0 1.6 - - + -
515D VAL* 6.1 3.1 - - + -
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Residues in contact with GLN 393 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388C GLN 5.3 0.4 + - - -
390C ALA 5.2 0.2 + - - -
391C PHE 3.1 0.2 - - - -
392C TYR* 1.3 77.6 - - - +
394C LEU* 1.3 57.3 + - - +
396C HIS* 3.8 0.7 - - - +
397C GLN* 2.8 54.1 + - - +
357D MET 4.3 0.2 - - - +
358D GLU* 3.5 48.1 + - + +
361D GLY 3.0 24.4 + - - +
362D LYS* 3.4 18.1 - - - +
512D GLN* 3.3 14.0 - - - +
514D GLY* 2.7 34.9 + - - -
515D VAL* 4.0 7.7 + - + +
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Residues in contact with LEU 394 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391C PHE 3.1 10.3 + - - +
392C TYR 3.1 0.4 - - - -
393C GLN* 1.3 77.0 - - - +
395C ILE* 1.3 64.1 + - - +
398C GLY* 2.8 30.7 + - - +
400C LYS* 4.7 13.3 - - + +
402C ILE* 3.7 25.6 - - + +
357D MET* 3.7 34.0 + - + +
361D GLY* 3.6 31.0 - - - -
376D GLY 3.5 24.5 - - - +
377D PRO 3.6 17.0 - - - +
378D ILE* 4.2 6.5 - - + -
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Residues in contact with ILE 395 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337C ALA* 5.4 0.4 - - + -
339C LEU* 4.6 3.1 - - + -
380C TRP* 4.5 9.4 - - + -
391C PHE* 4.0 34.1 - - + +
392C TYR* 2.9 26.3 + - + +
394C LEU* 1.3 78.3 - - + +
396C HIS* 1.3 52.5 + - + +
400C LYS 4.8 3.7 - - - +
402C ILE* 4.1 29.8 - - + +
404C CYS* 4.1 28.7 - - - -
406C PHE* 6.2 0.2 - - + -
436C LEU* 3.4 27.6 - - + -
472C ARG* 2.8 33.3 + - + +
357D MET* 5.8 0.2 - - + -
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Residues in contact with HIS 396 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392C TYR* 2.8 35.1 + - + +
393C GLN 3.9 2.2 - - - +
395C ILE* 1.3 79.4 - - + +
397C GLN* 1.3 63.7 + - + +
432C GLN* 2.8 30.6 + - - -
435C ALA* 3.7 27.7 + - + -
436C LEU* 3.8 29.1 + - + +
468C PHE* 3.9 26.6 - + + +
469C GLU 4.9 5.5 + - - -
470C GLY 5.2 0.9 + - - -
472C ARG* 3.3 25.3 + - - +
363D TYR* 5.6 0.2 - - - -
514D GLY 3.8 23.8 - - - +
515D VAL* 5.7 0.7 - - - -
518D GLY 5.1 3.6 + - - -
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Residues in contact with GLN 397 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393C GLN* 2.8 38.5 + - - +
396C HIS* 1.3 80.6 - - + +
398C GLY* 1.3 62.1 + - - +
465C HIS 3.0 25.0 + - - +
467C VAL 3.0 19.0 - - - +
468C PHE* 3.9 14.9 - - + -
472C ARG* 4.3 1.6 - - - +
361D GLY 3.7 4.3 - - - -
362D LYS* 3.1 24.9 - - - +
363D TYR* 3.2 27.7 - - + -
513D TRP* 3.7 4.6 - - - +
514D GLY* 3.0 28.0 - - - +
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Residues in contact with GLY 398 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394C LEU* 2.8 30.4 + - - -
396C HIS 3.8 0.6 - - - -
397C GLN* 1.3 77.1 - - - +
399C THR* 1.3 64.7 + - - +
400C LYS 3.5 2.9 - - - -
472C ARG* 3.3 17.6 + - - +
361D GLY* 3.8 19.1 - - - -
362D LYS 4.0 1.8 - - - -
363D TYR* 4.3 4.9 - - - +
370D ARG* 4.9 3.6 + - - -
375D THR* 4.7 0.2 - - - -
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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