Contacts of the helix formed by residues 376 - 394 (chain B) in PDB entry 6TXA
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 HIS 376 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B VAL* 3.5 31.5 - - + +
157B PHE* 4.6 6.7 - + + -
371B ARG 4.5 4.0 + - - -
372B ARG 3.7 21.1 - - - +
373B ALA* 3.0 21.1 + - - +
374B TYR 3.3 1.4 - - - -
375B GLN* 1.3 76.0 - - - +
377B LYS* 1.3 84.2 + - + +
378B VAL* 3.3 38.4 + - + -
379B GLY* 3.0 11.4 + - - +
380B ASN* 2.9 22.2 + - - +
551B ARG* 5.0 0.4 - - - +
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Residues in contact with LYS 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B GLN 3.3 2.6 + - - -
376B HIS* 1.3 92.5 + - + +
378B VAL* 1.3 72.6 + - + +
381B ILE 3.3 12.5 + - - -
456B TYR* 3.6 59.2 - - + -
551B ARG* 4.1 13.9 - - - +
553B TYR* 2.8 31.9 + - - +
352C ARG* 5.7 6.6 - - - +
354C LYS* 5.2 13.5 - - - +
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Residues in contact with VAL 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B VAL* 3.9 8.7 - - + -
376B HIS* 3.2 22.0 + - + +
377B LYS* 1.3 93.6 - - + +
379B GLY* 1.3 67.1 + - - +
380B ASN 3.2 1.1 - - - -
381B ILE* 3.4 7.4 - - + +
382B ILE* 2.9 30.7 + - + +
451B ARG* 4.1 8.5 - - - +
453B LEU* 3.6 29.2 - - + -
456B TYR* 5.9 2.7 - - + -
553B TYR* 6.3 0.2 - - + -
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Residues in contact with GLY 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B GLY 4.5 13.4 - - - -
153B GLY* 4.9 4.3 - - - -
156B VAL* 3.5 20.6 - - - +
373B ALA 5.6 1.3 - - - -
374B TYR 5.5 0.9 - - - -
376B HIS* 3.0 13.0 + - - -
378B VAL* 1.3 79.3 - - - +
380B ASN* 1.3 59.8 + - - +
382B ILE* 3.4 3.0 + - - +
383B ASP* 3.0 33.1 + - - +
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Residues in contact with ASN 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B ARG* 3.6 14.3 + - - +
374B TYR 3.2 25.5 + - - -
375B GLN* 2.9 26.8 + - - +
376B HIS 2.9 15.7 + - - +
377B LYS 3.9 4.5 - - - +
379B GLY* 1.3 74.7 - - - +
381B ILE* 1.3 58.8 + - - +
383B ASP* 3.3 11.6 + - - +
384B THR* 2.9 33.4 + - - +
501B ASP* 3.6 14.3 - - - +
503B ILE* 3.3 18.0 - - - +
551B ARG* 3.3 5.7 + - - -
553B TYR* 4.0 5.4 - - - +
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Residues in contact with ILE 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B LYS 3.3 5.2 + - - +
378B VAL* 3.3 27.3 + - + +
380B ASN* 1.3 78.6 - - - +
382B ILE* 1.3 61.9 + - + +
384B THR* 2.9 30.2 + - + +
385B MET* 2.9 21.0 + - - +
453B LEU* 4.4 13.2 - - + -
454B PHE* 3.9 37.9 - - + +
499B ILE* 4.2 8.3 - - + -
553B TYR* 3.3 55.1 + - + -
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Residues in contact with ILE 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B GLY* 4.3 6.7 - - - +
155B TYR* 3.5 43.1 - - + +
156B VAL* 4.7 1.6 - - + -
378B VAL* 2.9 26.9 + - + +
379B GLY 3.8 4.0 - - - +
381B ILE* 1.3 73.3 - - - +
383B ASP* 1.3 60.5 + - - +
385B MET* 3.3 6.4 + - - +
386B ILE* 2.9 47.4 + - + +
448B ILE* 4.3 13.9 - - + -
451B ARG* 4.1 11.0 - - - +
453B LEU* 3.8 35.9 - - + -
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Residues in contact with ASP 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B LEU 5.2 1.7 - - - +
151B GLY* 5.5 0.5 - - - -
152B GLY* 3.0 33.4 + - - -
216B MET* 3.7 30.6 + - + +
220B ARG* 3.7 21.2 + - - +
374B TYR 5.4 1.2 - - - +
379B GLY 3.0 17.6 + - - +
380B ASN* 3.3 16.9 + - - +
382B ILE* 1.3 75.5 - - - +
384B THR* 1.3 56.3 - - - +
386B ILE* 3.3 2.9 + - - +
387B THR* 2.8 34.0 + - - -
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Residues in contact with THR 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B ARG* 3.0 33.2 - - - +
380B ASN 2.9 18.8 + - - +
381B ILE* 2.9 37.1 + - + +
383B ASP* 1.3 71.0 - - - +
385B MET* 1.3 58.7 + - - +
387B THR* 3.4 8.0 + - - -
388B ASP* 2.8 29.9 + - - +
454B PHE* 4.8 1.7 - - - -
499B ILE* 4.7 18.3 - - + +
501B ASP* 4.6 8.1 - - + +
553B TYR* 6.3 0.2 - - + -
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Residues in contact with MET 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B ILE* 2.9 24.1 + - - +
382B ILE* 3.7 4.5 - - - +
383B ASP 3.3 0.2 - - - -
384B THR* 1.3 76.0 + - - +
386B ILE* 1.3 59.6 + - - +
388B ASP* 3.4 5.7 + - - +
389B ALA* 3.0 21.8 + - - +
444B ILE* 3.2 34.0 - - + +
447B GLN* 4.3 6.3 - - + -
448B ILE* 3.7 28.3 - - + -
452B ASN 3.9 19.3 - - - +
453B LEU* 3.9 28.9 - - + -
454B PHE* 3.4 42.6 - - + -
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Residues in contact with ILE 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B GLY* 4.9 4.0 - - - -
155B TYR* 4.7 6.3 - - + -
213B PHE* 4.2 22.0 - - + -
216B MET* 3.6 19.7 - - + -
382B ILE* 2.9 36.0 + - + +
383B ASP* 3.8 3.6 - - - +
385B MET* 1.3 73.6 - - - +
387B THR* 1.3 66.1 + - - +
389B ALA* 3.2 2.4 + - - +
390B PHE* 2.9 48.7 + - + -
427B PHE* 3.8 29.4 - - + -
445B LEU* 4.3 5.8 - - + -
448B ILE* 3.7 15.0 - - + -
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Residues in contact with THR 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B MET* 3.2 25.2 - - - +
220B ARG* 3.5 16.1 - - + +
221B PHE* 3.7 29.9 + - + +
224B LEU* 4.1 18.4 - - + -
383B ASP 2.8 19.1 + - - -
384B THR* 3.6 8.7 - - - +
386B ILE* 1.3 76.2 - - - +
388B ASP* 1.3 55.7 + - - +
390B PHE* 3.1 9.1 + - - +
391B LEU* 2.9 33.3 + - + +
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Residues in contact with ASP 388 (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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384B THR 2.8 18.8 + - - +
385B MET* 3.5 9.2 - - - +
386B ILE 3.2 0.2 - - - -
387B THR* 1.3 76.0 - - - +
389B ALA* 1.3 62.4 + - - +
391B LEU* 3.2 17.1 + - - +
392B LYS* 3.1 49.3 + - - +
444B ILE* 4.0 12.2 - - + +
454B PHE* 4.7 10.7 - - - -
555B LYS* 3.9 19.9 + - - -
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Residues in contact with ALA 389 (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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385B MET 3.0 11.1 + - - +
386B ILE 3.2 4.5 + - - +
388B ASP* 1.3 76.2 - - - +
390B PHE* 1.3 60.2 + - + +
392B LYS* 3.5 0.8 + - - +
393B ALA* 3.0 24.4 + - - +
430B ILE* 4.4 0.8 - - + +
441B ALA* 3.2 31.5 - - + +
444B ILE* 3.9 12.2 - - + +
445B LEU* 3.5 34.5 - - + -
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Residues in contact with PHE 390 (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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212B PRO* 4.0 14.1 - - + -
213B PHE* 4.1 12.1 - + - -
216B MET* 3.6 26.5 - - + -
217B PHE* 4.9 1.8 - + - -
221B PHE* 3.5 26.0 - + + -
386B ILE* 2.9 34.9 + - + +
387B THR 3.4 8.3 - - - +
389B ALA* 1.3 76.8 - - + +
391B LEU* 1.3 60.5 + - - +
393B ALA* 3.2 4.9 + - - -
394B ASP* 2.9 30.8 + - - +
409B ILE* 4.5 16.4 - - + +
426B ILE* 3.1 34.8 - - + -
427B PHE* 4.4 9.6 - + - -
430B ILE* 3.9 18.4 - - + -
445B LEU* 5.5 1.3 - - + -
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Residues in contact with LEU 391 (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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221B PHE* 3.7 11.4 - - + -
224B LEU* 3.9 30.7 - - + +
225B ALA* 3.7 42.6 - - + +
387B THR* 2.9 21.9 + - + +
388B ASP* 3.2 18.1 + - - +
390B PHE* 1.3 78.3 - - - +
392B LYS* 1.3 61.2 + - + +
394B ASP* 3.4 16.3 + - + +
395B ASP* 4.7 4.5 + - - +
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Residues in contact with LYS 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B ASP* 3.1 40.7 + - - +
389B ALA 3.9 4.0 - - - +
391B LEU* 1.3 77.5 - - + +
393B ALA* 1.3 59.4 + - - +
394B ASP 3.7 0.2 + - - -
395B ASP* 4.8 1.4 + - - +
396B TYR* 3.5 22.2 - - - -
437B LYS 4.9 1.7 - - - +
440B ASP* 3.7 33.3 - - + +
441B ALA* 4.2 14.8 + - + +
444B ILE* 4.1 16.0 - - + +
555B LYS* 5.9 1.2 - - - +
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Residues in contact with ALA 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B ALA 3.0 17.6 + - - +
390B PHE* 3.2 3.8 + - - +
392B LYS* 1.3 75.3 - - - +
394B ASP* 1.3 66.2 + - - +
395B ASP 3.3 2.0 - - - -
396B TYR* 3.2 12.4 + - - -
397B ILE* 3.3 19.1 + - + +
409B ILE* 4.9 0.9 - - + -
430B ILE* 3.7 23.1 - - + -
438B LEU* 3.6 26.3 - - + +
441B ALA* 3.7 5.4 - - + +
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Residues in contact with ASP 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B PHE* 4.3 8.6 - - - -
225B ALA* 4.3 5.9 - - - +
390B PHE 2.9 11.9 + - - +
391B LEU* 3.5 17.3 - - - +
392B LYS 3.4 2.2 - - - -
393B ALA* 1.3 77.8 - - - +
395B ASP* 1.3 69.8 + - - +
396B TYR 3.2 0.5 + - - -
397B ILE* 3.4 11.1 + - - +
408B ARG* 3.4 18.6 - - - +
409B ILE* 3.2 29.7 + - - +
410B SER* 2.7 34.9 + - - -
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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
------------------------------------------------------------
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