Contacts of the helix formed by residues 378 - 387 (chain A) in PDB entry 1TE6
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 THR 378 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119A LYS* 5.0 3.1 + - - +
376A GLU 3.6 6.0 + - - +
377A ASP* 1.3 79.6 + - - +
379A PHE* 1.3 66.0 + - - +
380A ILE* 3.2 2.9 - - - -
381A ALA* 2.9 20.3 + - - +
382A ASP* 3.9 4.4 + - - +
404A ALA* 3.3 43.5 - - + +
405A LYS* 4.2 9.2 - - - +
408A GLN* 4.0 24.8 + - + +
411A ARG* 5.5 2.7 - - - +
376B GLU* 6.3 0.2 - - + -
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Residues in contact with PHE 379 (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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115A LEU* 3.6 36.6 - - + -
118A CYS* 3.8 27.6 - - + -
119A LYS* 3.9 18.4 - - + +
129A LEU* 3.7 31.0 - - + -
133A ILE* 3.7 22.4 - - + -
343A VAL* 4.8 4.3 - - + -
349A VAL* 4.0 10.5 - - + -
377A ASP* 2.8 21.0 + - - +
378A THR* 1.3 77.1 + - - +
380A ILE* 1.3 68.7 + - + +
381A ALA 3.1 0.7 + - - -
382A ASP* 3.2 5.9 + - - +
383A LEU* 3.0 49.5 + - + -
405A LYS* 5.6 0.2 - - - +
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Residues in contact with ILE 380 (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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343A VAL* 4.8 14.8 - - + -
368A VAL* 3.9 13.1 - - + +
369A SER 4.1 12.8 - - - +
370A HIS* 3.9 23.1 - - + +
374A GLU* 4.8 2.7 - - - +
377A ASP* 4.6 0.8 + - - +
379A PHE* 1.3 77.4 - - + +
381A ALA* 1.3 67.3 + - - +
383A LEU* 3.6 15.4 - - + +
384A VAL* 2.9 26.2 + - - +
392A ILE* 3.8 11.0 - - + +
394A THR* 3.5 32.8 - - - +
405A LYS* 3.6 23.8 - - + -
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Residues in contact with ALA 381 (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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378A THR 2.9 13.1 + - - +
380A ILE* 1.3 81.2 - - - +
382A ASP* 1.3 63.3 + - - +
384A VAL* 3.1 20.9 - - - +
385A VAL* 3.4 11.3 + - - +
392A ILE* 4.7 2.5 - - - -
405A LYS* 3.7 23.3 - - + +
408A GLN* 3.5 25.4 - - + -
409A LEU* 3.5 17.0 - - + +
412A ILE* 3.9 2.5 - - - -
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Residues in contact with ASP 382 (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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129A LEU* 3.5 38.3 + - + +
130A TYR* 3.1 51.3 + - - +
133A ILE* 4.5 2.5 - - + +
378A THR* 4.1 5.5 + - - +
379A PHE 3.2 2.1 + - - +
381A ALA* 1.3 76.0 - - - +
383A LEU* 1.3 56.4 + - - +
385A VAL 3.4 0.3 + - - -
386A GLY* 2.9 26.0 + - - -
408A GLN* 2.9 34.7 + - - +
412A ILE* 4.0 5.3 - - - +
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Residues in contact with LEU 383 (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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133A ILE* 3.9 17.6 - - + +
341A LEU* 4.4 12.6 - - + +
343A VAL* 3.8 28.0 - - + -
353A ILE* 3.8 20.0 - - + -
368A VAL* 4.3 17.3 - - + -
379A PHE* 3.0 36.5 + - + +
380A ILE* 3.6 9.9 - - + +
382A ASP* 1.3 77.9 - - - +
384A VAL* 1.3 58.0 + - - +
386A GLY* 3.2 1.4 + - - -
387A LEU* 2.9 60.9 + - + +
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Residues in contact with VAL 384 (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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143A ILE 4.6 2.1 - - - +
145A PRO* 3.7 33.9 - - + -
368A VAL* 3.5 23.3 - - + +
380A ILE 2.9 14.3 + - - +
381A ALA 3.1 13.9 - - - +
383A LEU* 1.3 76.2 - - - +
385A VAL* 1.3 65.7 + - - +
388A CYS* 3.2 16.8 + - - -
389A THR* 3.2 30.3 + - - +
390A GLY 4.6 0.4 + - - +
391A GLN 3.5 14.4 - - - +
392A ILE* 3.9 10.1 - - + -
409A LEU* 3.9 9.0 - - + -
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Residues in contact with VAL 385 (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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130A TYR* 4.1 14.8 - - + -
142A LEU* 4.0 22.9 - - + +
143A ILE 4.0 12.8 - - - +
144A LEU* 4.3 4.0 - - + -
145A PRO* 4.2 9.9 - - + -
381A ALA 3.4 13.7 + - - +
382A ASP 3.8 5.8 - - - +
383A LEU 3.2 0.6 - - - -
384A VAL* 1.3 78.3 - - + +
386A GLY* 1.3 66.7 + - - +
388A CYS* 3.0 21.0 + - - -
409A LEU* 3.7 20.4 - - + -
412A ILE* 4.0 28.7 - - + -
416A LEU* 4.3 5.8 - - + -
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Residues in contact with GLY 386 (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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130A TYR 3.3 25.0 + - - -
133A ILE* 4.0 4.9 - - - -
134A ALA* 3.4 27.2 - - - +
139A ASN* 3.1 16.5 - - - +
142A LEU* 4.5 1.3 - - - -
382A ASP 2.9 15.5 + - - -
383A LEU 3.7 0.9 - - - -
385A VAL* 1.3 77.1 - - - +
387A LEU* 1.3 59.9 + - - +
388A CYS* 3.2 1.4 + - - -
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Residues in contact with LEU 387 (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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133A ILE* 4.2 5.2 - - + -
137A ALA* 3.5 28.0 - - + -
139A ASN* 3.6 9.9 - - - +
341A LEU* 3.5 31.6 - - + -
353A ILE* 4.1 24.2 - - + -
356A CYS* 3.9 19.1 - - + -
357A LYS* 5.9 1.1 - - + -
360A GLN* 3.2 17.4 + - - +
368A VAL* 4.9 0.4 - - + -
383A LEU* 2.9 38.2 + - + +
386A GLY* 1.3 75.2 - - - +
388A CYS* 1.3 69.6 + - - +
389A THR* 3.0 14.6 + - + -
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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