Contacts of the helix formed by residues 366 - 373 (chain B) in PDB entry 3Q36
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 SER 366 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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364B PRO 3.7 1.0 + - - -
365B PHE* 1.3 74.5 - - - +
367B CYS* 1.3 66.4 + - - +
368B LEU* 4.1 4.0 + - - +
369B LYS* 3.1 20.7 + - - +
370B ILE* 3.1 23.5 + - - +
442B ASN* 3.6 10.1 - - - -
443B HIS* 3.3 24.2 + - - -
444B PRO* 3.7 3.1 - - - -
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Residues in contact with CYS 367 (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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366B SER* 1.3 70.5 - - - +
368B LEU* 1.3 58.5 + - - +
370B ILE* 3.1 3.6 + - - +
371B ILE* 2.8 35.6 + - + +
421B GLN* 3.5 23.3 - - + +
441B LEU* 4.0 12.1 - - - -
442B ASN 3.0 33.0 + - - +
443B HIS* 3.5 11.0 - - - -
444B PRO* 3.7 1.3 - - - +
458B SF4 2.5 43.5 - - - -
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Residues in contact with LEU 368 (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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366B SER* 3.5 4.5 + - - +
367B CYS* 1.3 78.3 - - - +
369B LYS* 1.3 54.3 + - - +
371B ILE* 4.3 9.4 - - + -
372B LEU* 2.7 63.5 + - + +
421B GLN* 4.0 25.1 - - - +
442B ASN* 4.5 2.3 + - + +
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Residues in contact with LYS 369 (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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362B TYR* 6.6 0.4 - - - -
363B THR 5.5 0.7 - - - +
365B PHE* 2.9 68.7 - - + -
366B SER* 3.1 21.6 + - - +
367B CYS 3.1 0.8 - - - -
368B LEU* 1.3 77.9 - - - +
370B ILE* 1.3 55.8 + - - +
372B LEU* 4.9 0.7 - - - -
373B SER* 2.8 48.8 + - - +
374B ASN* 5.7 4.4 + - - +
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Residues in contact with ILE 370 (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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288B MET* 3.9 7.0 - - + -
308B GLN* 3.3 39.5 - - + +
365B PHE* 3.8 21.5 - - + -
366B SER 3.1 11.0 + - - +
367B CYS 3.6 4.7 - - - +
369B LYS* 1.3 75.4 - - - +
371B ILE* 1.3 59.7 + - - +
373B SER 3.1 20.0 - - - +
383B GLY* 3.3 29.6 - - - +
384B CYS* 3.7 5.6 - - + +
388B HIS* 3.4 11.4 - - - -
444B PRO* 3.7 31.0 - - + -
458B SF4 4.2 9.4 - - - -
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Residues in contact with ILE 371 (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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367B CYS* 2.8 32.7 + - + +
368B LEU* 3.9 10.1 - - + +
370B ILE* 1.3 77.1 - - - +
372B LEU* 1.3 67.1 + - + +
384B CYS* 3.7 31.6 - - + -
387B ARG* 3.7 27.8 + - + +
388B HIS* 3.9 17.8 + - - -
420B TYR* 4.0 29.6 - - + -
421B GLN* 4.2 18.4 - - + +
458B SF4 4.7 1.3 - - - -
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Residues in contact with LEU 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B LEU* 2.7 52.1 + - + +
369B LYS* 4.9 0.7 - - - -
371B ILE* 1.3 84.2 - - + +
373B SER* 1.3 62.8 + - - +
375B PRO* 5.5 2.1 - - - +
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Residues in contact with SER 373 (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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369B LYS* 2.8 34.0 + - - +
370B ILE* 3.1 18.7 - - - +
372B LEU* 1.3 81.5 - - - +
374B ASN* 1.3 77.3 + - - +
375B PRO* 3.7 2.2 - - - -
382B HIS* 5.4 0.2 - - - -
388B HIS* 5.0 0.7 - - - -
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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