Contacts of the helix formed by residues 390 - 397 (chain C) in PDB entry 1JLH
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 390 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338C LEU* 3.9 20.0 - - + -
379C TRP* 3.5 27.4 - + - -
381C GLU* 3.7 23.3 - - + -
386C GLY* 3.0 19.3 + - - -
389C ALA* 1.3 83.5 - - + +
391C TYR* 1.3 87.6 + + - +
392C GLN* 3.1 3.8 - - - +
393C LEU* 3.0 16.7 + - - +
394C ILE* 3.5 21.1 + - + +
352D GLN* 3.6 33.2 - - + +
356D MET* 3.8 29.8 - - + +
357D GLU* 5.0 1.6 - - - +
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Residues in contact with TYR 391 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338C LEU* 3.4 27.1 - - + +
340C TYR* 2.9 38.6 + - - -
381C GLU 5.3 0.7 + - - -
383C GLY* 5.4 1.2 - - - -
386C GLY* 3.2 15.6 + - - -
387C GLN* 3.2 39.0 + - + +
389C ALA 3.9 0.6 - - - -
390C PHE* 1.3 93.3 - + - +
392C GLN* 1.3 65.1 + - - +
394C ILE* 3.0 14.1 + - + -
395C HIS* 2.8 38.3 + + + +
405C PHE* 3.6 11.2 - + - -
431C GLN* 3.1 31.6 - - + +
435C LEU* 5.7 1.3 - - + -
513D GLY 5.0 0.7 - - - +
514D VAL* 5.9 2.9 - - + -
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Residues in contact with GLN 392 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390C PHE 3.1 0.2 - - - -
391C TYR* 1.3 76.6 - - - +
393C LEU* 1.3 59.0 + - - +
395C HIS* 4.0 0.3 - - - +
396C GLN* 2.9 49.5 + - - +
356D MET 4.2 0.2 - - - +
357D GLU* 3.5 49.4 + - + +
360D GLY 3.0 23.7 + - - +
361D LYS* 3.4 18.7 - - - +
511D GLN* 3.3 17.0 - - - +
513D GLY* 2.8 34.1 + - - -
514D VAL* 4.1 7.4 + - + +
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Residues in contact with LEU 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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390C PHE 3.0 10.0 + - - +
392C GLN* 1.3 78.8 - - - +
394C ILE* 1.3 63.6 + - + +
397C GLY* 2.8 27.7 + - - -
399C GLU* 3.4 21.2 - - + +
401C ILE* 3.6 27.6 - - + -
471C ARG* 5.1 0.2 + - - -
356D MET* 3.8 34.7 + - + +
360D GLY* 3.8 28.7 - - - -
375D GLY 3.5 25.6 - - - +
376D PRO 3.6 17.3 - - - +
377D ILE* 4.3 0.9 - - + -
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Residues in contact with ILE 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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336C ALA* 5.3 0.4 - - + -
338C LEU* 4.6 4.3 - - + -
379C TRP* 4.1 10.1 - - + -
390C PHE* 3.7 39.0 - - + +
391C TYR* 3.0 21.8 + - + +
393C LEU* 1.3 81.1 - - + +
395C HIS* 1.3 52.3 + - + +
399C GLU 5.3 2.8 - - - +
401C ILE* 4.3 26.2 - - + +
403C CYS* 4.2 30.1 - - - -
405C PHE* 6.4 0.2 - - + -
435C LEU* 4.2 22.0 - - + -
471C ARG* 2.6 37.0 + - + -
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Residues in contact with HIS 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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391C TYR* 2.8 34.0 + + + +
392C GLN 4.0 1.1 - - - +
394C ILE* 1.3 79.8 - - + +
396C GLN* 1.3 62.6 + - + +
397C GLY 3.7 0.7 - - - -
431C GLN* 2.9 31.7 + - - -
434C ALA* 3.9 22.4 - - + +
435C LEU* 3.1 36.1 + - + +
467C PHE* 3.9 29.1 - + + -
468C GLU 5.0 6.2 + - - -
469C GLY 5.1 1.0 + - - -
471C ARG* 3.3 23.9 + - - +
513D GLY 3.6 22.8 + - - +
516D LEU* 5.2 0.4 - - + -
517D GLY 5.0 3.2 + - - -
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Residues in contact with GLN 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 GLN* 2.9 25.2 + - - +
395C HIS* 1.3 79.2 - - - +
397C GLY* 1.3 64.2 + - - +
464C HIS 3.1 25.2 + - - +
466C VAL 3.2 20.5 + - - +
467C PHE* 3.8 23.3 - - + -
471C ARG* 4.4 1.1 - - - +
360D GLY 3.6 4.3 - - - -
361D LYS* 3.2 24.7 - - + +
362D TYR* 3.3 26.5 - - + -
512D TRP* 3.6 4.0 + - - +
513D GLY* 2.9 35.6 + - - +
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Residues in contact with GLY 397 (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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393C LEU* 2.8 31.3 + - - -
395C HIS 3.7 1.0 - - - -
396C GLN* 1.3 78.7 - - - +
398C THR* 1.3 64.2 + - - +
399C GLU* 3.7 1.8 - - - -
468C GLU* 5.5 0.2 - - - +
471C ARG* 3.4 16.3 + - - +
360D GLY* 3.8 19.5 - - - -
361D LYS 4.1 0.7 - - - -
362D TYR* 4.1 6.4 - - - +
369D ARG* 5.3 3.3 + - - -
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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