Contacts of the helix formed by residues 368 - 382 (chain A) in PDB entry 1T0R
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 368 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326A GLU* 4.8 0.7 + - - -
364A GLY 3.1 15.8 + - - +
365A TRP* 2.9 2.5 + - - -
367A ASP* 1.3 84.4 - - - +
369A TRP* 1.3 81.5 + - - +
370A GLY 3.1 0.4 - - - -
371A GLN* 2.8 31.0 + - - +
372A CYS 3.9 0.9 + - - -
407A THR* 3.8 14.7 - - + +
408A PRO* 3.7 20.3 - - - +
409A GLY* 3.7 9.5 + - - -
411A LYS* 3.6 36.1 - - + +
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Residues in contact with TRP 369 (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 TYR* 5.4 0.2 - - - +
325A ASP 4.2 0.6 + - - -
326A GLU* 2.7 45.6 + - - -
329A HIS* 3.5 22.0 - + + +
330A GLY* 3.3 33.7 - - - -
333A LEU* 4.2 12.3 - - + -
365A TRP* 2.9 44.5 + + + +
368A THR* 1.3 97.4 + - - +
370A GLY* 1.3 63.0 + - - +
371A GLN 3.1 0.9 + - - -
372A CYS* 3.2 13.0 + - - +
373A TRP* 3.1 22.0 + - + +
406A HIS* 2.8 38.1 - - - -
407A THR 3.9 0.2 - - - -
408A PRO* 3.5 21.1 - - + -
14C PHE* 3.5 16.2 - + + -
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Residues in contact with GLY 370 (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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355A ARG* 3.3 25.2 + - - -
365A TRP* 2.9 24.9 + - - -
366A ASN* 3.6 9.0 - - - -
369A TRP* 1.3 77.4 - - - +
371A GLN* 1.3 51.6 + - - +
373A TRP* 3.0 3.5 + - - -
374A ASP* 2.7 39.7 + - - +
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Residues in contact with GLN 371 (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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366A ASN 3.4 13.0 + - - +
367A ASP* 2.9 22.7 - - - +
368A THR 2.8 17.1 + - - +
370A GLY* 1.3 75.1 - - - +
372A CYS* 1.3 61.5 + - - +
374A ASP* 3.0 29.1 + - - +
375A VAL* 3.4 12.0 + - - +
409A GLY* 3.9 20.0 - - - +
410A ASN* 3.1 16.7 + - - +
12C ARG* 4.1 14.9 - - + +
42C ARG 4.8 1.1 - - - +
44C HIS* 4.0 26.7 + - - +
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Residues in contact with CYS 372 (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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333A LEU* 3.8 26.2 - - + -
368A THR 4.8 0.4 - - - -
369A TRP 3.2 7.2 + - - +
371A GLN* 1.3 78.1 - - - +
373A TRP* 1.3 63.0 + - - +
375A VAL* 3.2 6.9 + - - +
376A ILE* 3.1 26.8 + - - +
408A PRO* 3.8 35.0 - - - -
12C ARG 4.2 5.6 - - - -
14C PHE 4.5 4.7 - - - -
42C ARG* 3.5 38.9 - - + +
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Residues in contact with TRP 373 (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 TYR* 5.1 1.4 + - - -
329A HIS 5.5 1.6 + - - -
332A HIS* 3.6 28.0 - + - -
333A LEU* 3.6 32.0 - - + +
336A TRP* 3.9 46.0 - + + -
348A ALA* 4.1 14.1 - - + -
350A VAL* 3.5 35.7 - - + -
355A ARG* 4.2 12.1 - - - +
365A TRP* 3.7 26.2 - + - -
369A TRP* 3.1 25.5 + - + +
370A GLY* 3.0 8.1 + - - +
372A CYS* 1.3 76.7 - - - +
374A ASP* 1.3 61.3 + - - +
376A ILE* 3.8 17.1 - - + +
377A THR* 2.9 35.2 + - - -
487A TRP* 5.0 2.5 - + - -
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Residues in contact with ASP 374 (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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355A ARG* 2.8 33.8 + - - +
366A ASN 5.0 1.7 - - - +
370A GLY 2.7 16.9 + - - +
371A GLN* 3.0 26.2 + - - +
373A TRP* 1.3 76.3 - - - +
375A VAL* 1.3 62.7 + - - +
377A THR* 3.2 5.8 + - - -
378A ASP* 2.9 33.5 + - - +
44C HIS* 4.3 12.1 - - + +
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Residues in contact with VAL 375 (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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371A GLN 3.6 13.5 - - - +
372A CYS 3.2 5.8 + - - +
374A ASP* 1.3 76.5 - - - +
376A ILE* 1.3 62.2 + - - +
378A ASP* 3.5 9.7 + - + +
379A ASN* 3.3 23.2 + - - +
40C ASN* 3.5 37.9 - - - +
41C ARG 3.6 7.2 - - - +
42C ARG* 3.7 7.0 - - - +
43C VAL* 3.7 18.2 - - - +
44C HIS* 3.7 31.9 - - + +
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Residues in contact with ILE 376 (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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333A LEU* 3.8 29.2 - - + -
336A TRP* 3.6 37.5 - - + -
337A TYR* 4.2 12.1 - - + -
372A CYS 3.1 18.5 + - - +
373A TRP* 3.8 21.5 - - + +
375A VAL* 1.3 76.8 - - - +
377A THR* 1.3 63.1 + - - +
379A ASN* 3.3 5.7 + - - +
380A LEU* 3.2 26.9 + - + +
388A THR* 3.7 15.0 - - + +
487A TRP* 5.2 1.1 - - + -
41C ARG 3.7 16.6 - - - +
42C ARG* 4.3 4.0 - - + -
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Residues in contact with THR 377 (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 VAL* 4.8 4.3 + - - +
355A ARG* 4.9 6.5 + - - -
373A TRP 2.9 23.0 + - - -
374A ASP* 3.6 5.2 - - - -
376A ILE* 1.3 75.1 - - - +
378A ASP* 1.3 69.4 + - - +
380A LEU* 3.2 11.5 + - - +
381A VAL* 3.0 26.0 + - + +
487A TRP* 3.6 20.9 - - + -
488A VAL* 5.4 1.6 - - + -
491A TYR* 3.7 47.0 - - + -
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Residues in contact with ASP 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A ASP* 2.9 28.9 + - - +
375A VAL* 3.8 9.1 - - + +
377A THR* 1.3 79.6 - - - +
379A ASN* 1.3 53.3 + - - +
381A VAL* 3.1 6.1 + - - +
382A ASN* 2.7 56.1 + - - +
44C HIS* 4.5 10.2 + - - -
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Residues in contact with ASN 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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375A VAL* 3.3 11.6 + - - +
376A ILE* 3.7 8.4 - - - +
377A THR 3.3 0.6 - - - -
378A ASP* 1.3 81.7 - - - +
380A LEU* 1.3 58.9 + - - +
382A ASN* 4.4 5.1 - - - +
383A GLY 3.2 3.3 + - - -
384A LYS* 2.6 72.6 + - - +
387A LEU* 3.4 20.7 - - - +
388A THR* 4.1 7.6 - - + -
40C ASN* 2.7 28.1 + - - +
41C ARG* 4.7 0.5 - - - +
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Residues in contact with LEU 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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336A TRP* 4.4 2.0 - - + -
376A ILE* 3.2 23.1 + - + +
377A THR* 3.2 7.2 + - - +
379A ASN* 1.3 76.4 - - - +
381A VAL* 1.3 63.2 + - - +
383A GLY* 3.6 8.0 + - - -
384A LYS 4.8 0.7 - - - +
385A PRO* 3.9 19.9 - - + +
388A THR* 3.8 23.6 - - + +
485A TYR* 3.9 29.2 - - + -
487A TRP* 3.7 35.2 - - + -
488A VAL* 4.0 20.0 - - + +
492A GLN* 5.1 2.4 + - - -
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Residues in contact with VAL 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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377A THR* 3.0 18.7 + - + +
378A ASP* 3.5 9.0 - - - +
380A LEU* 1.3 78.7 - - - +
382A ASN* 1.3 64.8 + - - +
383A GLY 3.1 5.9 + - - -
488A VAL* 3.6 22.9 - - + +
491A TYR* 3.9 32.5 - - + +
492A GLN* 4.1 27.8 + - + +
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Residues in contact with ASN 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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378A ASP* 2.7 42.6 + - - +
379A ASN* 4.2 7.1 - - - +
381A VAL* 1.3 79.8 - - - +
383A GLY* 1.3 62.3 + - - +
384A LYS* 3.3 20.7 + - + +
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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