Contacts of the helix formed by residues 319 - 327 (chain Z) in PDB entry 5LN3
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 GLU 319 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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316Z ASP* 3.3 34.2 + - + +
317Z LEU* 3.4 0.8 - - - -
318Z THR* 1.3 76.7 + - - +
320Z ILE* 1.4 64.6 + - - +
321Z MET 3.2 1.1 - - - -
322Z SER* 3.2 23.8 + - - -
323Z ASN* 3.4 34.9 + - - +
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Residues in contact with ILE 320 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279Z GLU* 4.2 39.5 - - + +
282Z PHE* 3.7 41.1 - - + -
283Z THR* 5.1 3.8 - - - +
305Z LEU* 5.6 1.3 - - + -
317Z LEU* 3.6 19.4 + - - +
318Z THR 3.3 0.2 - - - -
319Z GLU* 1.4 76.3 - - - +
321Z MET* 1.3 73.9 + - + +
323Z ASN* 3.7 5.9 + - + +
324Z VAL* 3.4 33.6 + - + +
330Z PHE* 5.7 3.1 - - + -
340Z MET* 5.5 4.5 - - + -
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Residues in contact with MET 321 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282Z PHE* 3.7 30.5 - - - -
291Z GLN* 5.1 0.9 - - - +
295Z ALA* 6.2 0.2 - - + -
305Z LEU* 5.7 2.5 - - + -
318Z THR 3.5 12.8 + - - +
319Z GLU 3.2 0.2 - - - -
320Z ILE* 1.3 86.2 - - + +
322Z SER* 1.4 62.9 + - - +
324Z VAL 3.6 0.2 + - - -
325Z GLN* 2.8 32.4 + - - +
332Z ALA* 3.9 19.4 - - + +
333Z LEU 4.4 1.8 - - - +
336Z GLU* 4.3 13.0 - - + +
337Z LEU* 3.8 53.2 - - + +
340Z MET* 4.0 30.5 - - + +
341Z GLU* 5.3 0.9 - - - +
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Residues in contact with SER 322 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318Z THR 4.0 4.0 + - - -
319Z GLU* 3.2 24.8 + - - +
321Z MET* 1.4 78.2 - - - +
323Z ASN* 1.3 67.4 + - - +
325Z GLN* 3.5 20.4 + - - +
326Z LEU* 3.7 15.0 - - - +
337Z LEU* 6.0 1.9 - - - +
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Residues in contact with ASN 323 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319Z GLU* 3.5 41.0 + - - +
320Z ILE* 3.8 6.4 - - - +
322Z SER* 1.3 77.8 - - - +
324Z VAL* 1.3 67.1 + - + +
325Z GLN 3.5 0.5 + - - -
326Z LEU* 3.6 29.5 + - - +
327Z ASN 4.4 2.8 + - - +
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Residues in contact with VAL 324 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282Z PHE* 4.2 7.4 - - + -
320Z ILE* 3.4 20.0 + - + +
323Z ASN* 1.3 83.0 - - + +
325Z GLN* 1.4 57.3 + - - +
326Z LEU 3.5 0.2 - - - -
327Z ASN 3.1 22.0 - - - +
328Z SER* 3.4 5.0 - - - -
329Z ASN* 3.8 9.6 - - + +
330Z PHE* 3.6 57.7 - - + +
331Z LEU 4.2 0.2 - - - +
332Z ALA* 3.6 29.1 - - + +
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Residues in contact with GLN 325 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321Z MET* 2.8 38.0 + - - +
322Z SER* 3.5 12.6 + - - +
323Z ASN 3.3 0.4 - - - -
324Z VAL* 1.4 77.6 - - - +
326Z LEU* 1.3 60.1 + - + +
327Z ASN* 3.5 1.2 + - - -
328Z SER* 4.5 4.9 + - - -
332Z ALA* 3.6 23.3 - - + +
333Z LEU 3.8 16.4 - - - +
334Z ALA* 3.7 24.2 - - - +
337Z LEU* 3.6 30.1 - - - +
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Residues in contact with LEU 326 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322Z SER 3.7 10.5 - - - +
323Z ASN* 3.6 23.6 - - - +
324Z VAL 3.5 0.4 - - - -
325Z GLN* 1.3 75.3 - - + +
327Z ASN* 1.4 77.7 + - + +
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Residues in contact with ASN 327 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323Z ASN 4.4 1.9 + - - +
324Z VAL* 3.1 11.1 + - - +
326Z LEU* 1.4 92.8 + - + +
328Z SER* 1.4 65.0 + - - +
329Z ASN* 3.4 20.6 + - - +
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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