Contacts of the helix formed by residues 378 - 391 (chain A) in PDB entry 3DCT
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
---------------------------
Residue Dist Surf HB Arom Phob DC
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376A LYS 4.5 5.2 - - - +
377A MET* 1.3 76.7 - - - +
379A GLN* 1.3 56.0 + - - +
380A GLU* 2.9 17.7 + - - +
381A GLU* 2.6 55.9 + - - +
382A TYR* 3.1 10.8 + - - -
418A LEU* 6.0 0.2 - - - +
422A HIS* 6.5 1.3 - - + -
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Residues in contact with GLN 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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257A MET* 3.7 12.9 - - + +
260A TYR* 4.2 11.4 - - + -
261A ASN* 2.3 38.8 + - - +
334A GLU* 4.1 22.3 - - - +
377A MET 4.1 0.4 + - - -
378A THR* 1.3 72.3 - - - +
380A GLU* 1.3 58.4 + - + +
382A TYR* 3.4 5.6 + - - +
383A ALA* 2.9 27.9 + - - +
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Residues in contact with GLU 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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253A LEU* 4.3 28.4 - - + +
257A MET* 3.6 30.5 - - + +
378A THR* 2.8 13.6 + - - +
379A GLN* 1.3 80.4 - - + +
381A GLU* 1.3 61.1 + - - +
383A ALA* 3.9 0.3 - - - +
384A LEU* 3.0 36.5 + - - +
418A LEU* 4.4 17.2 - - + +
422A HIS* 5.4 7.8 + - - -
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Residues in contact with GLU 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A LYS 4.0 2.6 - - - +
377A MET* 2.9 43.7 - - + +
378A THR* 2.6 38.5 + - - +
380A GLU* 1.3 71.3 - - + +
382A TYR* 1.3 64.1 + - - +
384A LEU* 3.9 0.5 - - - +
385A LEU* 2.9 28.8 + - - +
415A LEU* 4.4 13.0 - - + +
418A LEU* 5.9 6.7 - - + +
419A CYS* 4.7 4.3 - - - -
423A GLN* 5.4 1.7 - - - +
429A HIS* 3.1 30.6 + - - -
433A LEU* 4.0 16.3 - - + +
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Residues in contact with TYR 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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260A TYR* 3.8 3.6 - - - +
330A LEU* 4.0 20.0 - - + +
334A GLU* 3.7 59.7 - - + +
337A ASN* 2.8 34.6 + - + +
338A LYS* 6.1 1.8 - - + -
372A ILE* 4.4 15.0 + - + -
373A GLY* 5.0 0.3 - - - -
377A MET* 3.4 46.4 + - + +
378A THR 3.1 22.4 + - - -
379A GLN* 3.6 6.5 - - - +
381A GLU* 1.3 78.8 - - - +
383A ALA* 1.3 62.2 + - - +
385A LEU* 3.8 4.1 - - - +
386A THR* 2.9 30.9 + - - +
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Residues in contact with ALA 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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256A ILE* 4.2 6.9 - - + +
257A MET* 3.5 21.8 - - - -
260A TYR* 3.5 39.4 - - + -
301A PHE* 4.2 5.5 - - - -
379A GLN 2.9 18.7 + - - +
380A GLU 4.0 0.4 - - - +
381A GLU 3.3 0.2 - - - -
382A TYR* 1.3 76.9 - - - +
384A LEU* 1.3 59.0 + - + +
386A THR* 3.7 1.9 - - - -
387A ALA* 3.2 25.5 + - - +
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Residues in contact with LEU 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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253A LEU* 4.4 13.9 - - + -
256A ILE* 4.2 24.0 - - + -
257A MET* 5.8 0.2 - - - -
380A GLU* 3.0 22.5 + - - +
381A GLU 4.1 2.0 - - - +
383A ALA* 1.3 74.3 - - + +
385A LEU* 1.3 62.3 + - - +
386A THR 3.2 1.1 - - - -
387A ALA* 3.9 2.0 - - + +
388A ILE* 2.8 39.2 + - + +
411A LEU* 4.2 26.0 - - + +
414A VAL* 4.3 11.7 - - + -
415A LEU* 3.9 43.3 - - + +
418A LEU* 4.0 17.7 - - + -
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Residues in contact with LEU 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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330A LEU* 3.8 24.7 - - + -
377A MET* 4.4 17.7 - - + -
381A GLU 2.9 17.9 + - - +
382A TYR* 3.8 3.8 - - - +
384A LEU* 1.3 77.5 - - - +
386A THR* 1.3 53.6 + - - +
388A ILE* 3.6 5.6 - - + +
389A VAL* 2.8 39.3 + - + +
415A LEU* 4.4 19.7 - - + +
433A LEU* 3.7 32.8 - - + +
434A LEU* 5.0 1.3 - - + -
436A ARG* 4.1 15.9 - - + -
437A LEU* 4.5 23.6 - - + -
440A LEU* 5.6 2.0 - - + -
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Residues in contact with THR 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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260A TYR* 3.9 17.2 + - + -
298A LEU* 4.8 3.6 - - + -
301A PHE* 4.0 10.5 - - + -
327A ALA* 4.5 17.8 + - + +
330A LEU* 3.6 21.0 - - - +
331A ARG 5.7 0.2 + - - -
382A TYR* 2.9 22.0 + - - +
383A ALA 3.7 6.3 - - - -
385A LEU* 1.3 74.2 - - - +
387A ALA* 1.3 61.3 + - - +
389A VAL* 3.0 3.7 + - - +
390A ILE* 2.8 53.0 + - + +
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Residues in contact with ALA 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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256A ILE* 4.3 8.3 - - + -
301A PHE* 4.3 4.0 - - + -
305A LEU* 3.7 34.3 - - + -
383A ALA 3.2 14.5 + - - +
384A LEU* 3.9 4.0 - - - +
385A LEU 3.5 0.2 - - - -
386A THR* 1.3 79.6 - - - +
388A ILE* 1.3 58.6 + - - +
390A ILE* 3.2 5.6 + - - +
391A LEU* 2.9 32.7 + - - +
411A LEU* 3.8 17.7 - - + -
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Residues in contact with ILE 388 (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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384A LEU 2.8 28.0 + - - +
385A LEU* 3.6 8.5 - - + +
387A ALA* 1.3 72.5 - - - +
389A VAL* 1.3 68.0 + - - +
391A LEU* 3.5 4.6 + - - -
392A SER* 3.4 2.1 + - - -
408A GLN* 2.8 47.6 + - + +
411A LEU* 4.0 21.3 - - + +
412A LEU* 3.5 37.0 - - + +
415A LEU* 3.8 23.8 - - + -
437A LEU* 3.6 27.1 - - + -
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Residues in contact with VAL 389 (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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323A SER* 3.7 13.0 - - - +
326A GLU* 3.6 15.9 - - + +
327A ALA* 4.3 6.3 - - - +
330A LEU* 4.2 4.7 - - + -
385A LEU* 2.8 27.1 + - + +
386A THR* 3.0 7.2 + - - +
388A ILE* 1.3 73.0 - - - +
390A ILE* 1.3 65.1 + - + +
392A SER* 2.9 22.7 + - - -
395A ARG* 3.0 29.0 + - - +
437A LEU* 3.4 23.8 - - + -
440A LEU* 3.7 25.8 - - + -
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Residues in contact with ILE 390 (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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298A LEU* 4.1 13.0 - - + -
301A PHE* 3.7 28.0 - - + -
302A THR* 3.3 43.7 - - + +
305A LEU* 4.0 8.5 - - + -
308A PHE* 4.9 3.4 - - + -
319A LEU* 3.7 26.7 - - + +
320A LEU* 5.1 2.7 - - + -
323A SER* 3.7 22.8 - - - +
327A ALA* 4.9 1.6 - - + -
386A THR* 2.8 32.9 + - + +
387A ALA 3.2 4.7 + - - +
389A VAL* 1.3 79.4 - - + +
391A LEU* 1.3 56.6 + - - +
392A SER* 3.3 4.3 + - - -
395A ARG* 5.2 0.5 + - - -
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Residues in contact with LEU 391 (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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305A LEU* 4.0 20.0 - - + -
306A PRO* 5.5 3.4 - - + +
308A PHE* 4.0 25.1 - - + +
319A LEU* 4.5 8.5 - - + -
387A ALA 2.9 13.9 + - - +
388A ILE 3.5 4.9 - - - +
389A VAL 3.3 0.2 - - - -
390A ILE* 1.3 75.0 - - - +
392A SER* 1.3 57.7 + - - +
393A PRO* 3.3 4.0 - - - +
404A VAL* 3.4 10.6 - - + +
407A LEU* 3.9 41.5 - - + +
408A GLN* 2.9 34.6 + - + +
411A LEU* 3.6 30.5 - - + -
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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