Contacts of the helix formed by residues 373 - 390 (chain B) in PDB entry 3TVX
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 373 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365B TYR* 3.6 11.7 - - + -
366B HIS 3.4 24.2 - - - +
367B ALA* 4.8 6.4 + - - +
369B VAL 2.6 23.7 + - - +
370B ALA* 3.0 21.8 + - - +
371B TYR 2.7 12.2 + - - +
372B HIS* 1.3 74.1 - - - +
374B SER* 1.3 59.1 + - - +
375B LEU* 3.1 30.8 + - - +
376B HIS* 3.0 23.9 + - - +
377B ALA 3.4 2.8 + - - -
547B ARG* 4.1 10.1 + - - +
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Residues in contact with SER 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B GLY 4.1 4.3 + - - -
329B SER* 4.0 4.2 + - - -
330B LEU* 3.8 8.0 - - - +
362B GLU* 2.6 43.2 + - - +
365B TYR* 3.5 28.8 - - - +
373B ASN* 1.3 75.5 - - - +
375B LEU* 1.3 53.3 + - - +
376B HIS 3.3 0.2 - - - -
377B ALA* 3.3 5.5 - - - +
378B ALA* 2.7 35.2 + - - +
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Residues in contact with LEU 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B ILE* 3.5 38.6 - - + +
319B PHE* 3.8 21.1 - - + -
322B SER* 3.7 15.7 - - - +
329B SER* 3.4 23.3 - - - +
373B ASN* 3.1 15.1 + - - +
374B SER* 1.3 77.4 + - - +
376B HIS* 1.3 57.6 + - - +
378B ALA* 3.4 2.2 + - - +
379B ASP* 2.9 30.1 + - - +
544B TRP* 3.8 13.6 - - + -
547B ARG* 3.7 28.0 - - - +
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Residues in contact with HIS 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B TYR* 3.2 59.7 + + + +
372B HIS* 3.9 8.3 - + - -
373B ASN* 3.0 8.8 + - - +
375B LEU* 1.3 79.2 - - - +
377B ALA* 1.3 62.1 + - - +
379B ASP* 3.3 5.7 + - - +
380B VAL* 3.0 43.5 + - + +
412B HIS* 3.1 14.9 + + - -
413B ASP* 2.9 21.5 - - + -
530B ASP* 3.4 8.3 - - - -
533B ASN* 4.9 1.7 + - - -
544B TRP* 4.3 12.3 - - + -
900B ZN 2.2 28.2 - - - -
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Residues in contact with ALA 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B LEU* 3.9 12.8 - - + -
365B TYR* 3.5 37.5 - - + +
373B ASN 3.4 2.0 + - - -
374B SER 3.2 10.4 + - - +
376B HIS* 1.3 81.6 - - - +
378B ALA* 1.3 64.1 + - - +
380B VAL* 3.8 1.0 - - - +
381B LEU* 2.9 25.8 + - - +
409B ALA 4.2 8.0 - - - +
410B ALA 3.7 10.3 - - - +
412B HIS* 4.5 6.3 - - - -
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Residues in contact with ALA 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B ILE* 3.8 18.8 - - + -
329B SER* 3.6 32.3 - - - +
330B LEU* 3.8 12.4 - - - +
333B ILE* 3.9 8.2 - - + +
374B SER 2.7 19.7 + - - +
375B LEU 3.7 4.7 - - - +
377B ALA* 1.3 72.5 - - - +
379B ASP* 1.3 57.6 + - - +
381B LEU* 3.5 2.1 + - - +
382B GLN* 3.0 30.3 + - - +
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Residues in contact with ASP 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B ILE* 4.2 13.0 - - + +
375B LEU 2.9 18.3 + - - +
376B HIS* 3.6 5.6 + - - +
378B ALA* 1.3 73.9 - - - +
380B VAL* 1.3 62.7 + - - +
382B GLN* 3.2 8.0 + - - +
383B SER* 2.7 37.5 + - - -
532B SER* 4.1 3.3 + - - -
533B ASN* 3.1 28.2 + - - -
536B LYS* 3.0 27.0 + - - -
544B TRP* 3.4 27.4 + - + -
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Residues in contact with VAL 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B HIS* 3.0 51.8 + - + +
377B ALA 3.9 1.3 - - - +
379B ASP* 1.3 78.1 - - - +
381B LEU* 1.3 52.9 + - - +
383B SER* 4.3 0.7 - - - -
384B THR* 2.8 37.4 + - - +
409B ALA* 4.3 11.2 - - + -
412B HIS* 3.8 21.8 - - + +
526B VAL* 4.3 6.7 - - + +
529B ALA* 3.5 39.5 - - + +
530B ASP* 3.8 9.0 - - + +
533B ASN* 5.9 0.4 - - - +
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Residues in contact with LEU 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B LEU* 3.9 16.6 - - + -
333B ILE* 3.9 9.6 - - + -
334B MET* 3.7 42.4 - - + -
337B ILE* 3.9 10.5 - - + -
338B PHE* 5.5 0.2 - - + -
377B ALA 2.9 17.5 + - - +
378B ALA 3.7 1.1 - - - +
380B VAL* 1.3 78.2 - - - +
382B GLN* 1.3 57.9 + - - +
384B THR* 3.2 4.9 + - - -
385B HIS* 2.9 26.5 + - - +
406B LEU* 3.2 49.1 - - + +
409B ALA* 3.7 13.8 - - + +
410B ALA* 4.2 6.5 - - + +
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Residues in contact with GLN 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B LEU* 3.1 27.5 + - + +
313B LYS 3.1 23.0 + - - +
314B TRP* 4.9 3.3 - - - +
316B LEU* 3.6 36.8 - - + +
318B ILE* 4.9 0.8 - - + +
333B ILE* 4.3 14.8 - - + -
337B ILE* 3.9 17.3 - - + -
378B ALA 3.0 18.7 + - - +
379B ASP* 3.2 6.8 + - - +
381B LEU* 1.3 72.1 - - - +
383B SER* 1.3 70.4 + - - +
385B HIS* 3.2 3.9 - - + +
386B VAL* 3.1 35.1 + - - +
536B LYS* 4.7 6.2 + - - -
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Residues in contact with SER 383 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B TRP* 3.5 30.6 - - - -
379B ASP* 2.7 23.5 + - - -
380B VAL* 3.8 4.5 - - - -
382B GLN* 1.3 77.4 + - - +
384B THR* 1.3 59.1 + - - +
386B VAL* 3.3 1.4 + - - -
387B LEU* 2.9 34.5 + - - +
529B ALA* 4.1 10.8 - - - -
532B SER* 3.7 6.9 + - - -
536B LYS* 2.7 24.5 + - - -
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Residues in contact with THR 384 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B VAL* 2.8 19.6 + - - +
381B LEU 3.2 10.3 + - - -
383B SER* 1.3 75.8 - - - +
385B HIS* 1.3 52.9 + - - +
387B LEU* 3.0 7.8 + - - +
388B LEU* 2.8 51.0 + - + +
405B ALA* 3.9 28.5 - - + +
406B LEU* 4.2 4.0 - - + -
409B ALA* 3.6 12.0 - - - +
525B MET* 4.5 8.3 - - + -
526B VAL* 4.4 10.3 - - + -
529B ALA* 3.4 17.3 - - - +
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Residues in contact with HIS 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B LEU* 3.3 23.9 + - + +
312B ASN* 2.9 33.0 + - + +
337B ILE* 3.9 32.5 - - + +
340B GLU* 4.3 8.5 - - + -
341B ARG* 2.7 73.0 + - + +
381B LEU 2.9 13.0 + - - +
382B GLN* 3.2 12.3 - - - +
384B THR* 1.3 76.6 - - - +
386B VAL* 1.3 63.9 + - + +
388B LEU* 3.3 1.0 + - - -
389B ALA* 3.2 8.0 + - + +
406B LEU* 3.9 12.7 - - + +
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Residues in contact with VAL 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B ASN* 3.7 30.5 - - - +
313B LYS* 3.9 5.2 - - - +
314B TRP* 3.7 30.1 - - + +
382B GLN* 3.1 36.2 + - - +
383B SER 3.6 6.7 - - - +
385B HIS* 1.3 76.8 - - + +
387B LEU* 1.3 60.1 + - + +
389B ALA* 2.9 27.6 + - + +
390B THR* 3.2 8.0 + - - -
607B ILE* 5.8 2.2 - - + -
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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
----------------------------------------------------------
314B TRP* 3.9 14.4 - - + -
383B SER 2.9 19.3 + - - +
384B THR 3.0 4.5 + - - +
386B VAL* 1.3 78.0 - - + +
388B LEU* 1.3 61.5 + - - +
390B THR* 3.3 29.9 + - - +
393B LEU* 4.1 7.8 - - - +
525B MET* 3.8 39.0 - - + +
528B CYS* 4.4 2.9 - - + -
529B ALA* 4.3 9.9 - - + +
593B TRP* 3.7 31.2 - - + -
596B TRP* 3.8 24.9 - - + +
604B ALA* 6.3 0.4 - - + -
607B ILE* 4.6 9.0 - - + -
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Residues in contact with LEU 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B ARG* 3.6 13.6 + - - +
384B THR* 2.8 15.4 + - + +
385B HIS* 3.4 7.9 - - - +
387B LEU* 1.3 76.6 - - - +
389B ALA* 1.3 61.0 + - - +
390B THR 3.5 4.2 + - - +
393B LEU* 4.7 12.7 - - - +
394B ASP* 5.7 0.7 - - - -
397B PHE* 4.2 14.8 - - + -
402B ILE* 4.0 31.2 - - + -
405B ALA* 4.2 13.5 - - + -
406B LEU* 4.0 29.4 - - + -
522B LEU* 4.0 16.8 - - + -
525B MET* 3.6 28.4 - - + -
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Residues in contact with ALA 389 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B ASN* 5.5 8.5 - - + +
341B ARG* 3.7 11.9 - - - +
385B HIS* 3.2 14.3 + - + +
386B VAL* 2.9 16.6 + - + +
388B LEU* 1.3 76.1 - - - +
390B THR* 1.3 66.0 + - - +
391B PRO* 3.5 4.9 - - - +
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Residues in contact with THR 390 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B VAL 3.2 6.3 + - - -
387B LEU* 3.4 25.7 - - - +
388B LEU 3.3 2.8 - - - +
389B ALA* 1.3 78.5 - - - +
391B PRO* 1.4 75.4 - - - +
392B ALA 4.1 3.6 - - - +
393B LEU* 3.1 36.7 + - + +
394B ASP* 3.7 7.1 + - - +
596B TRP* 5.3 2.7 - - + +
600B VAL* 4.3 14.1 - - + +
603B ASP* 3.4 21.8 + - - +
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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) + - + + + + + -
------------------------------------------------------------
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