Contacts of the helix formed by residues 323 - 329 (chain I) in PDB entry 1LWU
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 323 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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312I THR 4.3 0.3 + - - -
313I PRO 4.1 6.4 + - - -
316I ASP* 2.9 25.7 + - - +
318I ASP* 3.7 0.9 - - - -
320I TYR* 4.4 0.6 - - - -
322I GLY* 1.3 71.6 - - - -
324I CYS* 1.3 60.6 + - - +
325I ALA* 2.9 9.9 + - - +
326I GLU* 2.9 38.2 + - - +
327I GLN* 2.8 35.5 + - - +
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Residues in contact with CYS 324 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318I ASP* 2.7 16.3 + - - +
320I TYR* 3.8 22.2 - - - -
322I GLY 3.9 0.4 + - - -
323I SER* 1.3 71.6 - - - +
325I ALA* 1.3 62.5 + - - +
327I GLN* 4.2 5.8 - - - +
328I ASP* 3.1 29.6 + - - +
334I MET* 3.4 16.9 - - + +
335I ASN 4.0 0.4 - - - -
337I CYS* 2.0 69.1 - - - -
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Residues in contact with ALA 325 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311I SER* 3.7 17.9 - - - +
312I THR* 3.4 41.3 - - - +
313I PRO* 3.8 4.1 - - + +
318I ASP* 3.9 1.0 + - - +
323I SER* 3.7 5.4 - - - +
324I CYS* 1.3 81.0 - - - +
326I GLU* 1.3 56.6 + - - +
329I GLY* 2.8 21.5 + - - -
330I SER 3.1 16.3 + - - +
334I MET* 3.8 13.4 - - + +
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Residues in contact with GLU 326 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313I PRO* 3.6 28.7 - - + +
323I SER* 2.9 28.7 + - - +
325I ALA* 1.3 75.2 - - - +
327I GLN* 1.3 66.9 + - + +
329I GLY* 3.5 9.7 + - - +
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Residues in contact with GLN 327 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320I TYR* 3.1 44.6 + - - -
322I GLY* 4.8 1.2 - - - -
323I SER 2.8 27.0 + - - +
324I CYS* 3.8 8.4 - - - +
325I ALA 3.4 0.4 - - - -
326I GLU* 1.3 77.0 - - + +
328I ASP* 1.3 65.2 + - - +
337I CYS* 4.8 7.4 - - - -
360I PRO* 5.6 1.4 - - - +
361I TYR* 3.0 65.2 - - + +
363I ASP* 4.6 3.6 - - - +
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Residues in contact with ASP 328 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324I CYS* 3.1 20.7 + - - +
325I ALA 4.7 0.2 - - - +
327I GLN* 1.3 83.0 - - - +
329I GLY* 1.3 65.4 + - - +
330I SER* 4.1 2.5 + - - +
334I MET* 3.4 1.8 - - + +
337I CYS* 4.7 2.8 - - - -
338I HIS* 2.7 38.1 + - - -
341I HIS* 3.5 20.9 - - + -
345I LYS* 3.6 15.3 + - - +
361I TYR* 4.8 2.1 - - - -
362I ASP* 3.5 5.4 + - - +
363I ASP* 2.7 50.2 + - + +
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Residues in contact with GLY 329 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204I PHE* 5.5 0.2 - - - +
205I THR* 3.0 34.4 + - - -
313I PRO* 4.1 6.5 - - - -
325I ALA 2.8 14.0 + - - -
326I GLU 3.9 8.5 - - - -
327I GLN 3.1 3.6 - - - -
328I ASP* 1.3 79.1 - - - +
330I SER* 1.3 64.7 + - - -
345I LYS* 4.7 5.6 - - - +
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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