Contacts of the helix formed by residues 378 - 387 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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376A GLU* 5.9 0.9 - - + +
119B LYS* 5.1 2.3 + - - +
376B GLU 3.6 10.8 - - - +
377B ASP* 1.3 77.2 + - - +
379B PHE* 1.3 66.0 + - - +
380B ILE* 3.3 3.8 - - - -
381B ALA* 2.9 19.3 + - - +
382B ASP* 3.8 4.7 + - - +
404B ALA* 3.4 34.5 - - + +
405B LYS* 4.3 7.2 - - - -
408B GLN* 3.9 29.0 + - + +
411B ARG* 5.4 2.9 - - - +
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Residues in contact with PHE 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B LEU* 3.5 39.3 - - + -
118B CYS* 3.9 20.4 - - + -
119B LYS* 3.9 17.5 - - + +
129B LEU* 3.7 31.2 - - + -
133B ILE* 3.8 22.2 - - + -
343B VAL* 5.0 5.2 - - + -
349B VAL* 3.8 15.9 - - + -
377B ASP* 2.8 21.2 + - - +
378B THR* 1.3 77.0 + - - +
380B ILE* 1.3 70.2 + - + +
381B ALA 3.0 1.4 + - - -
382B ASP* 3.0 6.6 + - - +
383B LEU* 3.0 48.0 + - + -
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Residues in contact with ILE 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343B VAL* 4.4 23.3 - - + -
368B VAL* 3.9 18.0 - - + +
369B SER 4.4 6.5 - - - +
370B HIS* 4.2 20.0 - - - +
374B GLU* 4.9 3.1 - - - +
377B ASP* 4.6 0.6 + - - -
379B PHE* 1.3 78.1 - - + +
381B ALA* 1.3 64.4 + - - +
383B LEU* 3.6 13.3 - - + +
384B VAL* 3.0 26.0 + - - +
392B ILE* 3.9 11.6 - - + +
394B THR* 3.5 31.6 - - - +
405B LYS* 3.5 27.1 - - + -
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Residues in contact with ALA 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378B THR 2.9 13.0 + - - +
380B ILE* 1.3 82.6 - - - +
382B ASP* 1.3 62.1 + - - +
384B VAL* 3.1 21.0 - - - +
385B VAL* 3.5 4.9 + - - +
392B ILE* 4.9 1.3 - - - -
405B LYS* 3.6 23.3 - - - +
408B GLN* 3.5 24.7 - - + -
409B LEU* 3.4 25.3 - - + +
412B ILE* 5.6 0.9 - - + -
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Residues in contact with ASP 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B LEU* 3.3 43.0 + - + +
130B TYR* 3.1 47.8 + - - +
133B ILE* 4.6 2.1 - - + +
378B THR* 4.0 6.8 + - - +
379B PHE 3.0 2.1 + - - +
381B ALA* 1.3 75.5 - - - +
383B LEU* 1.3 56.9 - - - +
385B VAL* 3.3 1.8 + - - -
386B GLY* 2.9 26.0 + - - -
408B GLN* 2.9 35.2 + - - +
412B ILE* 3.8 4.1 - - - +
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Residues in contact with LEU 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B ILE* 4.1 14.5 - - + +
341B LEU* 4.5 7.4 - - + +
343B VAL* 3.5 30.7 - - + -
349B VAL* 5.6 1.6 - - + -
352B ALA* 5.5 1.3 - - + -
353B ILE* 3.5 32.5 - - + -
368B VAL* 4.3 19.3 - - + -
379B PHE* 3.0 32.5 + - + +
380B ILE* 3.6 13.7 - - + +
382B ASP* 1.3 76.9 - - - +
384B VAL* 1.3 57.2 + - - +
386B GLY 3.3 0.9 + - - -
387B LEU* 2.9 49.5 + - + +
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Residues in contact with VAL 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B ILE 4.4 2.3 - - - +
145B PRO* 3.7 32.8 - - + -
368B VAL* 3.6 20.4 - - + -
380B ILE 3.0 14.2 + - - +
381B ALA 3.1 16.8 - - - +
383B LEU* 1.3 76.7 - - - +
385B VAL* 1.3 56.3 + - - +
388B CYS* 3.1 19.9 + - - -
389B THR* 3.2 31.5 + - - +
390B GLY 4.6 0.8 + - - +
391B GLN 3.6 13.5 - - - +
392B ILE* 4.0 11.7 - - + -
409B LEU* 3.9 7.9 - - + -
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Residues in contact with VAL 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B TYR* 4.0 15.5 - - + -
142B LEU* 3.2 36.7 - - + +
143B ILE 3.9 12.7 + - - +
144B LEU* 4.2 5.2 - - + -
145B PRO* 4.2 9.4 - - + -
381B ALA 3.5 13.2 - - - +
382B ASP 3.3 7.1 + - - +
383B LEU 3.1 0.4 - - - -
384B VAL* 1.3 77.9 - - + +
386B GLY* 1.3 65.0 + - - +
387B LEU 3.2 0.2 - - - -
388B CYS* 3.1 14.7 + - - -
409B LEU* 3.6 20.6 - - + -
412B ILE* 4.0 24.0 - - + -
416B LEU* 4.7 4.0 - - + -
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Residues in contact with GLY 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B TYR 3.3 23.1 + - - -
133B ILE* 4.0 6.0 - - - +
134B ALA* 3.4 21.4 - - - +
139B ASN* 2.9 21.1 + - - +
142B LEU* 3.7 5.2 - - - -
382B ASP 2.9 14.5 + - - -
383B LEU 3.8 0.9 - - - -
385B VAL* 1.3 77.2 - - - +
387B LEU* 1.3 59.8 + - - +
388B CYS* 3.6 0.7 + - - -
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Residues in contact with LEU 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B ILE* 4.3 3.6 - - + -
137B ALA* 3.8 21.5 - - + -
139B ASN* 3.6 9.8 + - - +
341B LEU* 3.6 29.2 - - + -
353B ILE* 3.1 32.8 - - + -
356B CYS* 3.8 17.0 - - + -
357B LYS* 5.7 1.6 - - + -
360B GLN* 3.3 17.8 + - - +
368B VAL* 4.9 0.2 - - + -
383B LEU* 2.9 40.0 + - + +
386B GLY* 1.3 76.5 - - - +
388B CYS* 1.3 70.8 + - - +
389B THR* 3.2 15.9 + - + -
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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