Contacts of the helix formed by residues 394 - 416 (chain A) in PDB entry 4BHT
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 LYS 394 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A LEU* 4.4 4.3 - - + -
392A GLY 4.3 0.4 + - - -
393A TRP* 1.3 75.8 - - - +
395A ALA* 1.3 60.8 + - - +
396A GLU* 3.2 17.9 - - + +
397A LYS* 2.9 27.5 + - + +
398A VAL* 3.0 11.3 + - - +
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Residues in contact with ALA 395 (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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205A LEU* 3.7 25.1 - - + +
206A ILE* 3.5 24.2 - - + +
394A LYS* 1.3 73.1 - - - +
396A GLU* 1.3 69.7 + - + +
398A VAL* 3.2 1.2 + - - +
399A ASP* 2.9 27.9 + - - +
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Residues in contact with GLU 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A LYS* 3.4 22.3 - - + +
395A ALA* 1.3 79.8 + - + +
397A LYS* 1.3 57.7 + - - +
399A ASP* 3.9 4.6 - - - +
400A ALA* 2.8 32.4 + - - +
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Residues in contact with LYS 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A TRP* 3.5 57.6 - - + +
394A LYS* 2.9 17.3 + - + +
396A GLU* 1.3 76.9 - - - +
398A VAL* 1.3 66.3 + - - +
400A ALA* 4.0 4.5 - - + +
401A ARG* 3.2 31.6 + - + +
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Residues in contact with VAL 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A SER* 3.9 13.2 - - - +
205A LEU* 3.4 26.0 - - + +
206A ILE* 3.5 21.1 - - + -
379A THR* 4.2 8.5 - - + +
382A LEU* 3.9 19.6 - - + +
386A GLN* 4.1 5.8 - - - +
393A TRP* 3.9 28.7 - - + +
394A LYS 3.0 14.4 + - - +
395A ALA* 3.2 2.2 + - - +
397A LYS* 1.3 77.5 - - - +
399A ASP* 1.3 58.6 + - - +
401A ARG* 3.4 2.1 + - - +
402A LEU* 2.9 27.0 + - - +
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Residues in contact with ASP 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A ILE* 3.9 13.1 - - + +
213A TYR* 3.4 20.1 - - - -
217A TYR* 2.5 37.6 + - - -
250A LYS* 3.6 11.6 + - - -
395A ALA 2.9 17.4 + - - +
396A GLU* 3.9 5.4 - - - +
398A VAL* 1.3 75.7 - - - +
400A ALA* 1.3 64.9 + - - +
402A LEU* 3.5 6.2 - - - +
403A HIS* 2.9 23.6 + - - +
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Residues in contact with ALA 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A GLU 2.8 23.6 + - - +
397A LYS* 4.0 5.2 - - - +
399A ASP* 1.3 72.6 - - - +
401A ARG* 1.3 63.0 + - - +
403A HIS* 3.5 7.4 + - - +
404A HIS* 3.1 21.7 + - - +
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Residues in contact with ARG 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A LEU* 6.3 2.0 - - - +
382A LEU* 4.0 27.6 - - + +
393A TRP* 4.4 22.5 - - + -
397A LYS* 3.2 23.1 + - + +
398A VAL 3.8 2.2 - - - +
400A ALA* 1.3 76.6 - - - +
402A LEU* 1.3 66.4 + - - +
404A HIS* 3.3 19.7 + - - +
405A ILE* 3.0 33.9 + - + +
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Residues in contact with LEU 402 (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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206A ILE* 4.1 12.1 - - + -
210A ALA* 3.8 23.1 - - - +
213A TYR* 4.0 18.8 - - + -
214A GLY* 4.4 0.9 - - - +
217A TYR* 4.1 11.7 - - + -
375A GLY* 3.6 27.4 - - - +
378A ALA* 4.3 9.2 - - + -
379A THR* 3.5 25.8 - - - +
382A LEU* 4.2 7.1 - - + +
398A VAL 2.9 17.9 + - - +
399A ASP* 3.5 4.7 - - - +
401A ARG* 1.3 74.7 - - - +
403A HIS* 1.3 65.8 + - - +
405A ILE* 3.1 8.6 + - - +
406A MET* 3.1 27.5 + - + +
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Residues in contact with HIS 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A TYR* 3.4 58.0 + + + +
220A GLU* 6.3 1.0 - - - +
254A PHE* 4.5 10.8 - + - -
399A ASP 2.9 17.5 + - - +
400A ALA* 3.5 8.4 - - - +
401A ARG 3.2 0.2 - - - -
402A LEU* 1.3 78.3 - - - +
404A HIS* 1.3 62.4 + - - +
406A MET* 3.2 3.5 + - - +
407A LEU* 3.0 42.5 + - + +
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Residues in contact with HIS 404 (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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400A ALA 3.1 14.2 + - - +
401A ARG* 3.3 23.4 + - - +
403A HIS* 1.3 74.8 - - - +
405A ILE* 1.3 63.2 + - - +
407A LEU* 3.1 16.6 + - + +
408A ASP* 2.9 54.7 + - - +
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Residues in contact with ILE 405 (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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120A THR* 3.4 21.3 - - - +
121A THR* 4.8 4.0 - - - +
122A LEU* 3.9 36.8 - - + -
378A ALA* 4.1 20.0 - - + -
382A LEU* 4.5 16.6 - - + -
401A ARG* 3.0 26.6 + - + +
402A LEU* 3.4 9.4 - - - +
404A HIS* 1.3 83.0 - - - +
406A MET* 1.3 56.5 - - - +
408A ASP* 2.8 26.3 + - - +
409A ILE* 2.8 28.9 + - + +
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Residues in contact with MET 406 (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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214A GLY* 3.5 34.5 - - - +
217A TYR* 4.0 17.0 - - + -
218A PHE* 3.8 24.8 - - + +
371A ALA 3.7 22.9 - - - +
372A ALA 3.8 7.6 - - - +
374A ALA 4.3 0.2 - - - -
375A GLY* 3.7 29.8 - - - +
402A LEU* 3.1 17.1 + - + +
403A HIS 3.2 6.5 + - - +
405A ILE* 1.3 79.1 - - - +
407A LEU* 1.3 58.9 + - - +
409A ILE* 3.3 17.8 + - + +
410A HIS* 2.8 29.7 + - - +
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Residues in contact with LEU 407 (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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217A TYR 4.7 5.8 - - - +
221A ALA* 3.9 26.7 - - + -
403A HIS* 3.0 41.8 + - + +
404A HIS* 3.5 15.9 - - + +
406A MET* 1.3 78.2 - - - +
408A ASP* 1.3 58.0 + - - +
410A HIS* 3.4 5.0 + - + +
411A HIS* 2.9 28.4 + - - +
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Residues in contact with ASP 408 (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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119A LEU 5.2 1.3 - - - -
121A THR* 4.0 29.3 + - + +
404A HIS* 2.9 44.0 + - - +
405A ILE* 2.8 12.6 + - - +
407A LEU* 1.3 76.5 - - - +
409A ILE* 1.3 63.3 + - - +
411A HIS* 3.2 8.7 + - - +
412A ALA* 2.9 25.3 + - - +
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Residues in contact with ILE 409 (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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119A LEU* 3.3 46.9 - - + +
120A THR* 4.0 14.4 - - + +
218A PHE* 4.0 16.2 - - + -
371A ALA* 4.1 10.3 - - + +
374A ALA* 3.8 26.5 - - + +
405A ILE* 2.8 28.7 + - + +
406A MET* 3.6 26.0 - - + +
408A ASP* 1.3 71.8 - - - +
410A HIS* 1.3 65.0 + - - +
412A ALA* 3.2 6.0 + - - +
413A CYS* 3.1 22.3 + - - -
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Residues in contact with HIS 410 (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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218A PHE* 3.6 24.2 - + + -
221A ALA* 3.5 38.7 - - + +
222A MET* 3.3 15.6 + - - -
225A ARG* 4.3 9.0 - - + -
406A MET 2.8 17.2 + - - +
407A LEU* 3.6 5.9 + - - +
409A ILE* 1.3 78.2 - - - +
411A HIS* 1.3 64.5 + - - +
413A CYS* 3.3 4.9 + - - +
414A VAL* 3.1 38.6 + - + +
425A TYR* 3.2 36.8 + + - -
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Residues in contact with HIS 411 (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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407A LEU 2.9 18.5 + - - +
408A ASP* 3.6 10.5 - - - +
410A HIS* 1.3 77.9 + - - +
412A ALA* 1.3 68.6 + - - +
414A VAL* 3.2 10.2 + - + +
415A GLU* 3.1 32.9 + - + +
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Residues in contact with ALA 412 (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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119A LEU* 4.2 10.3 - - + +
408A ASP 2.9 13.6 + - - +
409A ILE* 3.5 9.6 - - - +
411A HIS* 1.3 79.6 - - + +
413A CYS* 1.3 61.9 + - - +
415A GLU* 3.2 24.7 + - - +
416A HIS* 3.5 13.9 + - - -
432A ALA* 3.8 20.8 - - + +
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Residues in contact with CYS 413 (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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119A LEU* 4.9 2.9 - - - -
218A PHE* 4.3 6.7 - - - -
371A ALA* 3.9 17.0 - - - -
409A ILE* 3.1 21.2 + - - -
410A HIS 3.3 7.8 + - - +
412A ALA* 1.3 76.0 - - - +
414A VAL* 1.3 58.5 + - - +
416A HIS 3.4 0.3 + - - -
417A GLY* 2.9 25.6 + - - -
423A THR* 4.0 2.7 - - - +
425A TYR* 3.7 21.5 - - + -
428A GLY* 3.3 17.7 - - - -
429A ALA* 3.7 35.4 - - - +
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Residues in contact with VAL 414 (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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225A ARG* 3.5 56.7 + - - +
410A HIS* 3.1 33.8 + - + +
411A HIS* 3.2 12.7 + - + +
413A CYS* 1.3 74.1 - - - +
415A GLU* 1.3 68.8 + - - +
416A HIS 3.2 0.7 + - - -
417A GLY* 3.3 8.8 + - - -
418A GLY 4.4 7.4 + - - +
419A GLU* 5.7 0.7 - - - +
423A THR* 4.0 15.4 + - + +
425A TYR* 4.3 0.9 - - + +
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Residues in contact with GLU 415 (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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411A HIS* 3.1 25.1 + - + +
412A ALA* 3.2 14.9 + - - +
414A VAL* 1.3 79.2 - - - +
416A HIS* 1.3 85.9 + - + +
417A GLY 3.8 0.2 + - - -
418A GLY 4.8 2.1 + - - -
419A GLU* 5.0 7.1 - - - +
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Residues in contact with HIS 416 (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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38A PHE* 4.3 16.0 - + - -
412A ALA* 3.5 13.7 + - - -
413A CYS 3.4 3.9 + - - -
414A VAL 3.1 0.4 - - - -
415A GLU* 1.3 106.1 + - + +
417A GLY* 1.3 54.2 + - - +
418A GLY 3.3 4.9 - - - -
427A GLN* 3.0 27.0 + - - +
428A GLY* 3.6 10.5 - - - +
431A ILE* 3.6 36.1 - - + +
432A ALA* 4.0 22.1 - - + -
435A VAL* 4.7 10.8 - - + +
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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) + - + + + + + -
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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