Contacts of the helix formed by residues 336 - 347 (chain D) in PDB entry 4JF7
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 ASN 336 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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334D SER 3.7 0.7 + - - +
335D GLN* 1.3 77.9 - - - +
337D GLN* 1.3 66.5 + - - +
338D ALA* 3.2 10.7 - - + +
339D THR* 3.1 32.7 + - - +
340D GLN* 3.1 11.1 + - - +
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Residues in contact with GLN 337 (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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323D TYR* 5.4 1.2 + - - -
325D ILE* 4.7 11.9 - - - +
330D ALA* 5.4 7.4 - - - +
335D GLN 3.6 1.8 + - - -
336D ASN* 1.3 72.8 - - - +
338D ALA* 1.3 56.3 + - - +
340D GLN* 3.3 18.2 + - - +
341D VAL* 3.0 56.0 + - + +
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Residues in contact with ALA 338 (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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336D ASN* 3.2 9.0 - - + +
337D GLN* 1.3 78.3 - - - +
339D THR* 1.3 58.7 + - - +
341D VAL* 3.8 5.4 - - - +
342D GLN* 2.9 30.9 + - - +
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Residues in contact with THR 339 (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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335D GLN* 4.2 20.4 - - + +
336D ASN* 3.1 33.7 + - - +
338D ALA* 1.3 75.2 - - - +
340D GLN* 1.3 61.4 + - - +
342D GLN* 3.8 10.6 + - - +
343D ASN* 2.9 55.7 + - - +
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Residues in contact with GLN 340 (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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325D ILE* 4.1 15.4 - - + +
329D VAL* 3.9 18.7 - - - +
330D ALA* 4.8 9.1 + - - +
333D CYS* 3.1 52.4 + - - +
335D GLN* 3.4 19.7 + - + +
336D ASN 3.1 11.1 + - - +
337D GLN* 3.6 22.2 + - - +
339D THR* 1.3 76.5 - - - +
341D VAL* 1.3 57.6 + - - +
343D ASN* 4.7 0.4 - - - -
344D ALA* 2.9 31.0 + - - +
455D PRO* 3.4 22.7 - - + +
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Residues in contact with VAL 341 (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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323D TYR* 3.5 32.0 - - + +
325D ILE* 4.4 2.5 - - + -
337D GLN* 3.0 39.8 + - + +
338D ALA* 3.8 5.6 - - - +
340D GLN* 1.3 73.4 - - - +
342D GLN* 1.3 68.6 + - - +
344D ALA* 3.2 6.6 + - - +
345D LYS* 2.9 53.0 + - + +
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Residues in contact with GLN 342 (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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338D ALA 2.9 18.9 + - - +
339D THR* 3.8 10.3 - - - +
341D VAL* 1.3 80.2 - - - +
343D ASN* 1.3 71.1 + - - +
345D LYS* 3.4 10.2 + - - +
346D SER* 3.3 22.2 + - - -
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Residues in contact with ASN 343 (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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335D GLN* 4.3 8.3 + - - +
339D THR* 2.9 40.6 + - - +
342D GLN* 1.3 87.1 - - - +
344D ALA* 1.3 60.1 + - - +
346D SER* 2.9 20.8 + - - -
347D SER* 3.2 12.6 + - - -
455D PRO* 3.1 35.4 + - + +
456D GLY* 3.9 11.0 + - - +
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Residues in contact with ALA 344 (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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323D TYR* 3.7 26.0 - - + -
324D PHE 4.7 4.9 - - - +
325D ILE* 3.8 15.7 - - + -
340D GLN 2.9 17.8 + - - +
341D VAL 3.2 4.2 + - - +
343D ASN* 1.3 72.8 - - - +
345D LYS* 1.3 64.3 + - - +
346D SER 3.1 0.2 - - - -
347D SER* 2.8 24.0 + - - -
348D TYR* 3.0 14.0 - - - -
409D TRP* 4.7 4.0 - - - +
455D PRO* 3.8 8.9 - - + +
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Residues in contact with LYS 345 (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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321D ASN* 2.9 58.2 + - - +
322D LYS 4.2 6.1 - - - +
323D TYR* 3.7 23.8 - - + +
341D VAL* 2.9 39.5 + - + +
342D GLN* 3.6 11.4 - - - +
344D ALA* 1.3 78.9 - - - +
346D SER* 1.3 59.0 + - - +
347D SER 3.6 0.5 + - - -
348D TYR* 3.7 7.4 - - - -
349D TYR* 3.3 24.1 - - + -
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Residues in contact with SER 346 (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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342D GLN* 3.3 8.8 + - - -
343D ASN* 2.9 25.8 + - - +
344D ALA 3.1 0.4 - - - -
345D LYS* 1.3 75.6 - - - +
347D SER* 1.3 60.7 + - - +
348D TYR 3.1 6.9 + - - -
349D TYR* 3.3 27.2 + - - +
456D GLY* 5.1 0.2 - - - -
457D PHE* 3.9 13.1 + - - +
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Residues in contact with SER 347 (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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343D ASN 3.2 7.6 + - - -
344D ALA* 2.8 23.4 + - - -
346D SER* 1.3 76.9 - - - +
348D TYR* 1.3 66.6 + - - +
349D TYR 3.3 0.9 - - - -
387D MET* 3.3 29.5 + - - +
408D SER* 3.8 13.4 + - - -
409D TRP* 3.9 10.7 + - - -
456D GLY 3.2 24.2 - - - -
457D PHE* 3.5 18.0 - - - +
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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