Contacts of the helix formed by residues 363 - 383 (chain A) in PDB entry 6UIT
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 ASN 363 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A THR* 1.3 91.1 + - - +
364A ASP* 1.3 63.9 + - - +
365A VAL* 3.0 8.8 + - - +
366A LYS* 3.0 26.4 + - - +
367A GLN* 3.3 18.9 + - - +
401A TRP* 3.4 19.9 - - - -
424A LYS 5.9 0.4 - - - +
425A LEU* 4.5 7.7 - - + +
508A ALA 3.2 16.6 + - - -
509A GLN* 2.7 29.7 + - - +
511A ASP* 3.3 20.4 - - + +
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Residues in contact with ASP 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A LYS* 2.6 35.6 + - - +
335A GLY 5.2 3.1 + - - -
337A TRP* 3.8 15.6 - - + -
363A ASN* 1.3 78.0 - - - +
365A VAL* 1.3 57.8 + - - +
367A GLN* 3.9 7.0 + - - +
368A LEU* 2.9 28.4 + - - +
423A VAL* 3.5 23.2 - - + +
424A LYS 4.5 5.9 + - - +
426A TRP* 3.9 7.3 + - - -
511A ASP* 3.1 20.8 + - - +
512A GLN* 3.3 18.2 - - - +
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Residues in contact with VAL 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A ASN* 3.0 7.1 + - - +
364A ASP* 1.3 76.7 - - - +
366A LYS* 1.3 66.2 + - - +
368A LEU* 3.4 6.4 + - + +
369A THR* 3.0 26.6 + - - -
393A ILE* 4.2 15.3 - - + -
397A THR* 4.8 2.7 - - + -
398A TRP* 3.6 21.1 - - + -
401A TRP* 3.4 38.6 - - + -
423A VAL* 4.1 14.1 - - + -
424A LYS 4.5 4.7 - - - +
425A LEU* 3.7 27.4 - - + -
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Residues in contact with LYS 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A HIS 4.1 14.6 + - - -
362A THR* 3.5 28.7 - - - +
363A ASN* 3.0 18.7 + - - +
365A VAL* 1.3 75.5 - - - +
367A GLN* 1.3 58.1 - - - +
369A THR* 3.0 9.5 + - - -
370A GLU* 2.8 40.2 + - + +
401A TRP* 3.8 23.5 - - + +
405A TYR* 3.4 31.5 + - + +
406A TRP* 6.2 0.2 - - - -
508A ALA* 4.0 22.5 - - - +
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Residues in contact with GLN 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A GLY* 3.0 28.4 - - - +
337A TRP* 3.3 18.4 + - + +
354A TYR* 3.8 6.9 - - + -
356A ARG 5.3 4.7 - - - +
357A MET* 4.6 6.3 - - - +
362A THR* 3.6 21.1 - - + +
363A ASN 3.3 14.0 + - - +
364A ASP* 3.8 8.4 + - - +
365A VAL 3.2 0.4 - - - -
366A LYS* 1.3 73.5 - - - +
368A LEU* 1.3 66.4 + - - +
370A GLU* 3.2 20.3 + - - +
371A ALA* 2.9 22.7 + - - +
512A GLN* 2.5 42.6 + - - +
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Residues in contact with LEU 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A ILE* 4.3 22.7 - - + -
337A TRP* 3.4 34.7 - - + -
364A ASP 2.9 18.1 + - - +
365A VAL* 3.7 6.5 - - + +
367A GLN* 1.3 75.8 - - - +
369A THR* 1.3 56.4 + - - +
371A ALA* 3.0 6.9 + - - +
372A VAL* 2.8 36.6 + - + +
391A LEU* 4.1 13.5 - - + -
392A PRO* 4.6 6.7 - - + -
393A ILE* 3.6 43.7 - - + -
411A ILE* 4.4 7.2 - - + -
423A VAL* 4.6 8.1 - - + -
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Residues in contact with THR 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A VAL 3.0 15.1 + - - -
366A LYS* 3.0 11.5 + - - -
368A LEU* 1.3 77.1 - - - +
370A GLU* 1.3 62.8 + - + +
372A VAL* 3.4 8.2 + - - +
373A GLN* 3.0 42.8 + - - +
398A TRP* 3.3 23.7 - - - -
401A TRP* 5.1 1.0 + - - -
409A THR* 3.7 18.5 + - - +
410A TRP 4.2 12.6 - - - +
411A ILE* 3.9 6.1 - - + +
394B GLN* 5.3 1.1 - - - +
397B THR* 4.5 3.8 - - - +
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Residues in contact with GLU 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A TYR* 3.0 33.2 + - - +
356A ARG 4.1 4.0 - - - +
358A ARG* 3.3 35.6 + - - +
362A THR* 4.9 2.4 + - - -
366A LYS* 2.8 31.3 + - + +
367A GLN* 3.5 17.4 - - - +
369A THR* 1.3 77.3 - - + +
371A ALA* 1.3 57.1 + - - +
373A GLN* 3.1 12.4 + - - +
374A LYS* 2.9 28.1 + - - +
394B GLN* 3.6 26.2 + - - +
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Residues in contact with ALA 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A ILE* 4.2 16.2 - - + -
337A TRP* 4.8 11.4 - - + -
339A TYR* 6.2 0.2 - - + -
354A TYR* 3.8 31.1 - - + -
367A GLN 2.9 13.5 + - - +
368A LEU* 3.2 11.9 - - - +
370A GLU* 1.3 72.4 - - - +
372A VAL* 1.3 65.4 + - - +
374A LYS* 3.2 2.0 + - - +
375A ILE* 3.0 33.4 + - + +
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Residues in contact with VAL 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A ILE* 4.3 5.1 - - + +
368A LEU* 2.8 26.6 + - + +
369A THR* 3.6 8.3 - - + +
371A ALA* 1.3 71.3 - - - +
373A GLN* 1.3 52.9 + - - +
375A ILE 3.6 0.2 + - - -
376A THR* 2.6 38.0 + - - +
389A PHE* 3.5 24.7 - - + -
391A LEU* 4.2 24.7 - - + -
410A TRP 5.5 0.2 - - - +
411A ILE* 4.1 22.9 - - + -
412A PRO* 3.4 32.8 - - + -
401B TRP* 4.5 4.0 - - + -
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Residues in contact with GLN 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A THR* 3.0 35.0 + - - +
370A GLU* 3.3 12.9 - - - +
371A ALA 3.1 0.2 - - - -
372A VAL* 1.3 74.3 - - - +
374A LYS* 1.3 68.8 + - - +
376A THR* 3.1 6.8 + - - -
377A THR* 3.0 23.6 + - - -
410A TRP 4.1 0.7 - - - +
394B GLN* 2.6 30.7 + - - -
396B GLU* 3.8 9.5 - - + +
397B THR* 2.7 38.3 + - - +
400B THR* 3.7 20.4 + - - +
401B TRP* 3.7 16.8 - - + -
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Residues in contact with LYS 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A TYR* 3.5 17.0 + - - -
353A LYS 3.9 21.3 - - - -
354A TYR* 3.6 30.3 - - + -
370A GLU 2.9 16.2 + - - +
371A ALA* 3.2 6.9 + - - +
373A GLN* 1.3 74.3 - - - +
375A ILE* 1.3 64.0 + - - +
377A THR* 3.0 7.1 + - - -
378A GLU* 2.8 51.7 + - + +
710T G 5.5 0.6 + - - -
711T C 3.6 24.7 + - - +
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Residues in contact with ILE 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A ALA* 4.1 7.9 - - + -
329A ILE* 3.7 23.3 - - + -
339A TYR* 3.4 50.9 - - + -
341A ILE* 4.0 18.4 - - + -
354A TYR* 6.2 0.2 - - + -
371A ALA* 3.0 18.7 + - + +
372A VAL 3.9 3.1 - - - +
374A LYS* 1.3 75.7 - - + +
376A THR* 1.3 50.5 + - - +
378A GLU* 3.2 8.5 + - - +
379A SER* 2.7 51.6 + - - +
387A PRO* 4.4 0.2 - - + -
389A PHE* 3.8 20.4 - - + -
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Residues in contact with THR 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A VAL 2.6 25.0 + - - -
373A GLN 3.4 4.9 - - - -
375A ILE* 1.3 77.1 - - - +
377A THR* 1.3 63.9 + - - +
379A SER* 3.9 3.5 - - - -
380A ILE* 3.1 35.2 + - + +
385A LYS 4.8 0.2 - - - +
386A THR* 3.6 27.8 - - + +
387A PRO* 4.5 5.8 - - - -
389A PHE* 3.6 16.6 - - - -
400B THR* 3.8 11.4 - - + -
401B TRP* 3.7 27.3 - - + +
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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
----------------------------------------------------------
373A GLN 3.0 11.8 + - - -
374A LYS* 3.4 11.6 - - - -
376A THR* 1.3 76.8 - - - +
378A GLU* 1.3 58.8 + - - +
380A ILE* 3.3 11.6 + - - +
381A VAL* 3.1 29.0 + - + +
25B PRO* 4.0 22.4 - - + +
400B THR* 3.5 19.7 + - - +
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Residues in contact with GLU 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A TYR* 2.6 28.5 + - - -
341A ILE* 4.7 5.4 - - + +
350A LYS* 2.9 36.9 + - - +
374A LYS* 2.8 31.9 + - + +
375A ILE* 3.7 6.6 - - - +
377A THR* 1.3 76.4 - - - +
379A SER* 1.3 64.9 + - - +
380A ILE 3.1 1.8 - - - -
381A VAL* 3.3 7.2 + - + +
382A ILE* 3.0 36.8 + - + +
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Residues in contact with SER 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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325A LEU* 4.7 1.1 - - - -
341A ILE* 4.1 2.6 - - - +
375A ILE* 2.7 31.5 + - - +
376A THR 3.9 1.3 - - - -
378A GLU* 1.3 74.2 - - - +
380A ILE* 1.3 56.1 + - - +
383A TRP* 2.8 57.4 + - - -
384A GLY 3.1 4.0 + - - -
385A LYS 3.3 17.7 - - - +
387A PRO* 3.2 30.1 - - - +
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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
----------------------------------------------------------
376A THR* 3.1 34.9 + - + +
377A THR* 3.5 8.3 - - - +
378A GLU 3.1 0.2 - - - -
379A SER* 1.3 75.1 - - - +
381A VAL* 1.3 64.2 + - - +
384A GLY* 2.9 22.9 - - - -
385A LYS 3.8 22.4 - - - +
386A THR* 4.1 8.1 - - - +
25B PRO* 3.9 20.9 - - + +
26B LEU 3.6 30.4 - - - +
27B THR* 4.3 16.8 - - + +
135B ILE* 4.8 1.0 - - - +
400B THR* 4.8 12.6 - - + +
401B TRP* 6.0 1.1 - - + +
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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
----------------------------------------------------------
94A ILE 5.7 2.0 - - - +
377A THR* 3.1 18.9 + - + +
378A GLU* 3.3 9.2 + - + +
380A ILE* 1.3 81.4 - - - +
382A ILE* 1.3 63.9 + - + +
25B PRO* 3.6 25.1 - - + -
26B LEU 5.6 0.2 - - - -
134B SER 4.7 1.4 - - - +
135B ILE* 3.9 3.1 - - - +
136B ASN* 2.7 33.5 + - - +
137B ASN* 3.7 26.2 - - - +
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Residues in contact with ILE 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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96A HIS* 4.1 16.6 - - + -
98A ALA 4.5 0.4 - - - -
99A GLY* 3.8 18.1 - - - +
350A LYS* 3.8 29.4 - - + -
378A GLU* 3.0 33.7 + - + +
381A VAL* 1.3 86.2 - - + +
383A TRP* 1.3 96.2 + - + +
135B ILE* 3.8 3.3 - - - +
136B ASN* 3.1 35.4 - - - +
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Residues in contact with TRP 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A ALA* 2.8 38.3 + - + -
99A GLY* 3.8 8.3 - - - -
319A TYR* 3.4 48.3 + + + +
325A LEU* 3.4 30.7 - - + -
341A ILE* 3.6 36.3 - - + -
349A LEU* 3.9 20.1 - - + +
350A LYS* 4.1 10.8 - - + -
378A GLU* 5.0 0.4 - - + -
379A SER* 2.8 45.6 + - - +
382A ILE* 1.3 92.9 - - + +
384A GLY* 1.3 64.0 + - - +
385A LYS* 3.3 4.9 + - + +
28B GLU* 3.8 14.7 - - - +
135B ILE* 4.0 8.7 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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