Contacts of the helix formed by residues 391 - 398 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353C GLN* 3.6 33.7 - - + +
357C MET* 3.7 29.1 - - + +
358C GLU 5.0 0.7 - - - +
339D LEU* 3.9 12.1 - - + -
380D TRP* 3.4 33.9 - + - -
382D GLU* 3.8 25.1 - - + -
387D GLY* 3.0 26.1 + - - -
390D ALA* 1.3 84.0 - - + +
392D TYR* 1.3 85.4 + + - +
393D GLN* 3.2 3.4 - - - -
394D LEU* 3.1 19.2 + - - +
395D ILE* 3.6 11.7 + - + +
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Residues in contact with TYR 392 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514C GLY 5.2 0.4 - - - +
515C VAL* 6.2 2.0 - - + -
339D LEU* 3.6 26.1 - - + +
341D TYR* 2.8 41.1 + - - -
382D GLU 5.4 0.3 + - - -
384D GLY* 4.9 2.1 - - - -
387D GLY* 3.3 14.9 + - - -
388D GLN* 3.4 43.6 + - + +
390D ALA 3.8 1.0 - - - -
391D PHE* 1.3 95.3 - + - +
393D GLN* 1.3 66.9 + - - +
394D LEU 3.0 0.2 - - - -
395D ILE* 2.9 14.9 + - + -
396D HIS* 2.9 37.8 + + + +
406D PHE* 3.6 10.9 - + - -
432D GLN* 3.2 27.1 - - + +
436D LEU* 6.0 1.8 - - + -
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Residues in contact with GLN 393 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357C MET 4.3 0.2 - - - +
358C GLU* 3.6 48.7 + - + +
361C GLY 3.1 24.8 + - - +
362C LYS* 3.4 19.6 - - - +
512C GLN* 3.2 15.0 - - - +
513C TRP 4.7 0.2 - - - +
514C GLY* 2.7 35.0 + - - -
515C VAL* 3.9 6.7 + - + +
388D GLN 5.3 0.2 + - - -
391D PHE 3.2 0.8 - - - -
392D TYR* 1.3 76.2 - - - +
394D LEU* 1.3 57.9 + - - +
396D HIS* 3.8 0.5 - - - +
397D GLN* 2.8 57.5 + - - +
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Residues in contact with LEU 394 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357C MET* 3.7 35.4 + - + +
361C GLY* 3.7 27.8 - - - -
376C GLY 3.6 24.5 - - - +
377C PRO 3.7 15.9 - - - +
378C ILE* 4.4 5.8 - - + -
391D PHE 3.1 11.5 + - - +
392D TYR 3.0 0.2 - - - -
393D GLN* 1.3 78.2 - - - +
395D ILE* 1.3 63.0 + - - +
398D GLY* 2.8 31.0 + - - -
400D LYS* 4.5 15.1 - - + +
402D ILE* 3.7 27.1 - - + +
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Residues in contact with ILE 395 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337D ALA* 5.4 0.4 - - + -
339D LEU* 4.7 3.1 - - + -
380D TRP* 4.2 10.8 - - + -
391D PHE* 3.8 39.9 - - + +
392D TYR* 2.9 23.4 + - + +
394D LEU* 1.3 81.1 - - + +
396D HIS* 1.3 50.2 + - - +
400D LYS 4.9 4.1 - - - +
402D ILE* 4.1 27.6 - - + +
404D CYS* 4.2 29.2 - - - -
406D PHE* 6.4 0.2 - - + -
436D LEU* 3.7 22.4 - - + -
472D ARG* 2.7 36.4 + - + +
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Residues in contact with HIS 396 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363C TYR* 5.7 0.2 - - - -
514C GLY 3.7 24.8 + - - +
515C VAL* 5.7 0.2 - - - -
518C GLY 5.1 3.5 + - - -
392D TYR* 2.9 32.0 + + + +
393D GLN 4.0 1.3 - - - +
395D ILE* 1.3 79.2 - - + +
397D GLN* 1.3 63.8 + - + +
432D GLN* 2.8 32.3 + - - -
435D ALA* 3.8 21.1 - - + +
436D LEU* 3.6 34.3 - - + +
468D PHE* 4.0 27.0 - + + +
469D GLU* 4.8 6.6 + - - +
470D GLY 5.1 0.5 + - - -
472D ARG* 3.3 24.3 + - - +
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Residues in contact with GLN 397 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361C GLY 3.7 4.0 - - - -
362C LYS* 3.1 26.4 - - - +
363C TYR* 3.2 29.0 + - + +
513C TRP* 3.6 4.2 - - - +
514C GLY* 3.0 33.7 + - - +
393D GLN* 2.8 28.2 + - - +
396D HIS* 1.3 79.3 - - + +
398D GLY* 1.3 62.3 + - - +
465D HIS 3.0 26.3 + - - +
467D VAL 3.1 23.4 + - - +
468D PHE* 4.1 16.0 - - + -
472D ARG* 4.5 1.3 - - - +
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Residues in contact with GLY 398 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361C GLY* 3.8 18.4 - - - -
362C LYS 4.0 2.2 - - - -
363C TYR* 4.3 5.0 - - - +
370C ARG* 5.1 3.6 + - - -
375C THR* 4.7 0.2 - - - -
393D GLN 3.9 0.2 + - - -
394D LEU* 2.8 30.5 + - - -
396D HIS 3.8 0.8 - - - -
397D GLN* 1.3 77.1 - - - +
399D THR* 1.3 65.2 + - - +
400D LYS 3.5 2.9 - - - -
472D ARG* 3.3 17.4 + - - +
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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