Contacts of the helix formed by residues 361 - 368 (chain E) in PDB entry 1LT9
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 MET 361 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3E NAG 3.1 36.5 + - + +
359E GLN 5.7 0.9 - - - -
360E LEU* 1.3 86.9 - - - +
362E GLY* 1.3 70.5 + - - +
363E GLU 3.5 0.3 + - - -
364E ASN* 3.1 18.6 + - - +
365E ARG* 4.0 3.4 - - - +
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Residues in contact with GLY 362 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3E NAG 5.7 1.1 - - - -
361E MET* 1.3 73.2 - - - +
363E GLU* 1.3 55.6 + - - -
364E ASN 2.8 10.9 + - - -
365E ARG* 2.9 17.8 + - - +
366E THR* 3.1 18.5 + - - +
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Residues in contact with GLU 363 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361E MET 3.5 0.4 + - - -
362E GLY* 1.3 69.3 - - - -
364E ASN* 1.3 61.9 + - - +
366E THR* 3.2 11.2 - - - +
367E MET* 2.8 53.5 + - + +
406E ARG* 4.6 10.3 + - - +
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Residues in contact with ASN 364 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3E NAG 1.5 69.9 + - - +
360E LEU* 3.9 24.1 - - + +
361E MET 3.3 5.6 + - - +
362E GLY 2.8 5.7 + - - -
363E GLU* 1.3 79.5 - - - +
365E ARG* 1.3 62.0 + - - +
367E MET* 3.0 30.4 + - - +
368E THR* 3.8 11.3 + - - +
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Residues in contact with ARG 365 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355E ASP* 3.2 31.9 + - - +
356E GLY* 3.5 16.7 + - - -
357E ALA 3.0 24.3 + - - +
358E SER* 2.8 43.6 + - - +
360E LEU* 3.3 29.4 + - - +
361E MET* 3.5 5.0 + - - +
362E GLY 2.9 8.1 + - - +
364E ASN* 1.3 79.7 - - - +
366E THR* 1.3 64.6 + - - +
368E THR* 2.6 25.0 + - - -
439E ASN* 4.9 0.8 + - - -
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Residues in contact with THR 366 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362E GLY* 3.1 12.2 + - - +
363E GLU* 3.2 22.2 + - - +
365E ARG* 1.3 78.9 - - + +
367E MET* 1.3 58.2 + - - +
368E THR 2.9 10.6 + - - -
369E ILE* 3.0 39.0 + - + +
405E ASN* 3.6 4.0 + - - -
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Residues in contact with MET 367 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363E GLU* 2.8 48.5 + - + +
364E ASN* 3.0 28.0 - - - +
366E THR* 1.3 76.1 + - - +
368E THR* 1.3 57.5 + - + +
369E ILE 3.4 0.7 - - - -
385E TRP* 4.9 7.9 - - + -
405E ASN* 3.0 10.7 - - - +
406E ARG* 2.8 100.4 + - + +
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Residues in contact with THR 368 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356E GLY* 3.8 1.4 - - - -
357E ALA* 3.0 17.2 + - - +
360E LEU* 4.4 11.2 - - + -
364E ASN 3.8 10.9 + - - +
365E ARG* 2.6 23.7 + - - -
366E THR 2.9 0.4 - - - -
367E MET* 1.3 82.0 - - + +
369E ILE* 1.3 62.8 + - - +
370E HIS* 3.6 5.9 + - - -
405E ASN* 4.5 3.6 - - - -
406E ARG 4.5 2.2 - - - +
407E CYS 4.4 4.7 - - - +
408E HIS 3.2 37.5 - - - +
409E ALA* 3.4 24.1 + - - +
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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