Contacts of the helix formed by residues 348 - 355 (chain A) in PDB entry 1LT8
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 ARG 348 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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331A TRP 4.6 0.9 - - - -
333A SER* 5.3 1.6 - - - -
336A ASP* 3.9 17.0 + - - -
344A ARG 5.0 3.2 + - - -
345A ALA 4.4 11.9 - - - +
346A ARG 3.2 2.0 - - - -
347A ALA* 1.3 111.8 + - - +
349A LYS* 1.3 65.5 + - - +
350A GLU* 3.6 25.1 - - + +
351A TYR* 3.0 27.9 + - + +
352A TRP* 3.6 9.8 + - - -
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Residues in contact with LYS 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A TRP* 5.0 8.5 - - + -
282A GLN* 3.6 17.9 - - - +
313A GLU* 3.9 6.7 + - - -
331A TRP* 3.2 60.0 + - + +
347A ALA 4.1 0.2 + - - -
348A ARG* 1.3 71.9 - - - +
350A GLU* 1.3 65.7 + - - +
352A TRP* 3.5 8.0 + - - +
353A GLU* 2.6 59.4 + - + +
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Residues in contact with GLU 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348A ARG* 3.6 26.1 - - + +
349A LYS* 1.3 78.9 + - - +
351A TYR* 1.3 65.9 + - - +
353A GLU* 3.8 9.6 - - - +
354A ASN* 2.7 42.9 + - - +
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Residues in contact with TYR 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345A ALA 4.8 4.3 - - - +
346A ARG* 3.5 37.9 + - + +
348A ARG* 3.0 24.3 + - + +
350A GLU* 1.3 83.9 - - - +
352A TRP* 1.3 93.0 + + - +
354A ASN* 3.9 2.2 - - - +
355A LEU* 3.1 40.5 + - + +
265B PRO* 2.7 42.6 + - - +
371B ASP 5.1 0.9 + - - -
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Residues in contact with TRP 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A TRP* 3.3 67.6 - + + +
332A GLY* 4.4 7.0 - - - -
335A LEU* 4.1 1.5 - - + +
346A ARG* 2.6 32.9 + - + -
348A ARG 3.7 10.1 - - - -
349A LYS* 3.5 6.1 + - - +
350A GLU 3.4 0.2 - - - -
351A TYR* 1.3 91.6 - + - +
353A GLU* 1.3 58.9 + - - +
354A ASN 3.5 0.3 + - - -
355A LEU* 3.7 26.8 + - + +
357A ILE* 5.6 1.6 - - + +
265B PRO 3.6 7.6 - - - -
266B GLU* 3.2 37.5 - - - -
267B PHE 3.3 21.1 - - - -
268B PRO* 4.1 2.0 - - + -
269B PHE* 3.5 24.5 - + + -
270B GLY* 3.4 13.0 - - - -
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Residues in contact with GLU 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A TRP* 4.5 20.7 - - + +
282A GLN* 4.2 15.2 + - - +
283A LYS* 5.5 1.0 + - - +
313A GLU* 4.3 3.1 - - - +
349A LYS* 2.6 54.4 + - + +
350A GLU* 3.6 7.1 + - - +
351A TYR 3.2 0.6 - - - -
352A TRP* 1.3 78.7 - - - +
354A ASN* 1.3 63.7 + - - +
355A LEU 3.6 0.9 - - - -
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Residues in contact with ASN 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350A GLU* 2.7 36.9 + - - +
351A TYR* 4.1 2.7 - - - +
353A GLU* 1.3 83.3 - - - +
355A LEU* 1.3 64.8 + - - +
356A ARG* 3.4 9.0 + - - +
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Residues in contact with LEU 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351A TYR* 3.1 35.0 + - + +
352A TRP* 3.7 31.3 + - + +
353A GLU 3.6 1.3 - - - -
354A ASN* 1.3 77.3 - - - +
356A ARG* 1.3 72.5 + - - +
357A ILE* 3.3 25.4 + - + +
265B PRO* 3.5 39.5 - - + +
266B GLU* 4.1 8.3 - - + +
364B ASN* 5.1 0.3 + - - -
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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