Contacts of the helix formed by residues 379 - 386 (chain A) in PDB entry 3Q7I
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 379 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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327A LEU* 3.6 20.0 - - + -
368A TRP* 3.5 34.4 - + + -
369A GLY 3.8 11.9 - - - -
370A GLY* 3.7 28.3 - - - -
375A GLY* 3.3 22.0 + - - -
378A ALA* 1.3 82.8 - - + +
380A HIS* 1.3 84.5 + + - +
381A GLN 3.0 0.7 - - - -
382A LEU* 2.9 21.8 + - + +
383A LEU* 3.3 11.6 + - + +
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Residues in contact with HIS 380 (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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327A LEU* 3.6 28.9 - - + +
329A TYR* 3.3 27.8 + + - -
370A GLY 5.5 0.6 + - - -
372A GLY* 5.7 1.4 - - - -
375A GLY* 3.0 38.2 + - - +
376A GLN* 3.5 17.9 + - + +
379A PHE* 1.3 94.1 - + - +
381A GLN* 1.3 64.0 + - - +
383A LEU* 3.1 15.5 + - + +
384A HIS* 2.9 39.1 + - + -
394A PHE* 4.6 3.1 - + - -
418A GLN* 2.8 24.9 + - + +
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Residues in contact with GLN 381 (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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376A GLN 5.0 2.8 + - - -
378A ALA 3.1 15.1 + - - +
379A PHE 3.0 0.2 - - - -
380A HIS* 1.3 78.2 - - - +
382A LEU* 1.3 59.5 + - + +
384A HIS* 3.8 5.8 - - - +
385A GLN* 2.9 71.1 + - - +
386A GLY 3.8 0.2 + - - -
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Residues in contact with LEU 382 (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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368A TRP* 5.4 5.2 - - + -
379A PHE* 2.9 14.0 + - + +
381A GLN* 1.3 77.7 - - + +
383A LEU* 1.3 66.5 + - + +
386A GLY* 2.9 35.1 + - - +
388A ILE* 4.3 20.5 - - + +
390A ILE* 3.6 30.1 - - + -
458A ARG* 3.8 3.3 + - - -
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Residues in contact with LEU 383 (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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325A ALA* 4.5 2.0 - - + -
327A LEU* 4.0 28.5 - - + -
368A TRP* 4.0 18.4 - - + -
379A PHE* 3.3 16.2 + - + +
380A HIS* 3.1 28.3 + - + +
382A LEU* 1.3 77.5 - - + +
384A HIS* 1.3 57.3 + - + +
388A ILE 6.1 0.4 - - - -
390A ILE* 3.9 36.1 - - + +
392A VAL* 4.3 17.3 - - + -
422A LEU* 3.5 19.3 - - + +
458A ARG* 2.9 29.3 + - - +
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Residues in contact with HIS 384 (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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380A HIS* 2.9 32.5 + - + +
381A GLN* 3.9 4.9 - - - +
383A LEU* 1.3 79.9 - - + +
385A GLN* 1.3 61.9 - - + +
418A GLN* 2.8 33.0 + - - -
421A ALA* 4.0 23.9 - - + +
422A LEU* 3.7 32.3 + - + +
454A ILE* 3.7 28.0 - - + +
455A PRO* 3.5 22.0 - - - +
456A GLY 5.1 0.2 + - - -
458A ARG* 3.7 10.0 + - - +
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Residues in contact with GLN 385 (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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381A GLN* 2.9 46.6 + - - +
384A HIS* 1.3 78.2 - - + +
386A GLY* 1.3 68.8 + - - +
451A HIS 3.0 25.6 + - - +
452A LYS* 3.8 3.8 - - - +
453A VAL 2.9 26.1 + - - +
454A ILE* 3.7 24.5 - - + +
455A PRO* 4.7 5.3 - - + +
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Residues in contact with GLY 386 (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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381A GLN 3.8 1.4 + - - -
382A LEU* 2.9 33.9 + - - +
385A GLN* 1.3 79.8 - - - +
387A ASN* 1.3 62.0 + - - +
388A ILE 3.5 2.9 - - - -
458A ARG* 2.8 27.5 + - - -
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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