Contacts of the helix formed by residues 426 - 444 (chain L) in PDB entry 6PSU
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 426 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110L LEU* 5.1 1.4 - - - +
111L LEU 4.8 3.6 + - - -
113L ARG* 3.5 45.5 - - + +
116L GLU* 3.9 22.7 + - - +
419L PHE* 4.0 5.9 - - - -
425L TYR* 1.3 73.2 - - - +
427L PHE* 1.3 65.8 + - - +
428L SER* 3.5 18.2 - - - +
429L THR* 3.1 18.9 - - + +
430L TYR* 3.6 2.8 + - - +
51O T 4.2 0.2 + - - -
52O A 2.3 49.1 + - - +
53O T 3.8 7.9 - - - -
54O T 3.2 32.1 + - - +
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Residues in contact with PHE 427 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116L GLU* 4.2 16.5 + - + +
379L MET* 4.8 17.9 - - + -
383L ASN* 3.3 42.4 - - + -
412L LEU* 3.3 27.8 - - + -
415L ALA* 4.0 18.6 - - + -
416L VAL* 4.6 8.3 - - + -
419L PHE* 3.3 60.2 - + + -
426L LYS* 1.3 72.7 - - - +
428L SER* 1.3 55.3 + - - +
429L THR 3.3 0.2 - - - -
430L TYR* 3.0 3.3 + + - -
431L ALA* 2.7 48.6 + - + +
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Residues in contact with SER 428 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116L GLU* 5.1 1.0 + - - -
386L LEU* 3.4 20.3 - - - +
426L LYS* 3.1 9.2 - - - +
427L PHE* 1.3 82.2 - - - +
429L THR* 1.3 63.8 + - - +
431L ALA 3.5 1.0 + - - -
432L THR* 3.3 19.2 + - - -
52O A 3.8 2.3 - - - +
53O T 2.8 46.1 + - - +
54O T 3.0 24.3 + - - +
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Residues in contact with THR 429 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426L LYS 3.1 18.8 + - - +
428L SER* 1.3 80.5 + - - +
430L TYR* 1.3 62.4 + - - +
431L ALA 3.5 0.2 + - - -
432L THR* 3.9 3.3 + - - -
433L TRP* 3.8 17.0 + - - -
50O A 3.8 28.7 + - + +
51O T 3.6 25.9 + - - +
52O A 3.7 34.9 + - - +
53O T 3.2 20.8 - - - +
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Residues in contact with TYR 430 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415L ALA* 4.0 4.9 - - + -
418L LYS* 3.4 17.9 + - - +
419L PHE* 3.3 58.6 - + + -
426L LYS 4.1 3.8 - - - +
427L PHE* 3.0 13.5 + + - +
429L THR* 1.3 82.5 - - - +
431L ALA* 1.3 64.8 - - - +
432L THR 3.4 0.2 + - - -
433L TRP* 3.4 19.6 + + + +
434L TRP* 2.8 39.8 + + - -
49O C 4.9 19.8 + + - -
50O A 3.4 46.7 - + - +
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Residues in contact with ALA 431 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386L LEU* 3.4 24.5 - - + -
412L LEU* 4.7 0.2 - - + -
415L ALA* 5.0 4.7 - - + -
427L PHE* 2.7 47.1 + - + +
429L THR 3.4 0.6 - - - -
430L TYR* 1.3 75.4 - - - +
432L THR* 1.3 57.5 + - - +
434L TRP* 2.9 9.5 + - - +
435L ILE* 2.8 39.1 + - + +
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Residues in contact with THR 432 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386L LEU* 3.3 23.6 - - - +
390L ILE* 3.3 37.8 - - + +
428L SER 3.3 7.4 + - - -
429L THR 3.9 0.6 + - - -
430L TYR 3.4 1.2 - - - -
431L ALA* 1.3 74.5 - - - +
433L TRP* 1.3 54.7 + - - +
436L ARG* 2.7 48.5 + - + +
53O T 3.7 28.0 - - + +
35P A 5.0 5.6 - - - +
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Residues in contact with TRP 433 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429L THR* 3.8 18.9 + - - -
430L TYR* 3.4 13.3 + + + +
431L ALA 3.0 0.6 + - - -
432L THR* 1.3 77.9 - - - +
434L TRP* 1.3 64.8 + - + +
436L ARG* 3.8 23.2 - - - +
437L GLN* 3.2 18.0 + - - +
49O C 3.1 60.5 + + + +
50O A 2.9 48.3 + - - -
37P G 3.8 23.6 - + - +
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Residues in contact with TRP 434 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411L GLY* 3.9 21.2 - - - +
414L LYS* 4.4 23.1 - - + -
415L ALA* 3.3 28.6 - - + +
418L LYS* 3.3 35.6 - - + +
430L TYR* 2.8 38.9 + + - -
431L ALA 2.9 9.2 + - - +
433L TRP* 1.3 78.9 - - + +
435L ILE* 1.3 58.1 + - - +
437L GLN* 3.1 33.9 + - + +
438L ALA* 2.8 28.3 + - - +
48O G 4.1 38.8 - + - -
49O C 4.4 14.4 + + - +
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Residues in contact with ILE 435 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383L ASN* 4.4 1.3 - - - +
386L LEU* 4.4 4.3 - - + -
387L VAL* 3.6 27.8 - - + -
390L ILE* 3.3 39.7 - - + -
391L ALA* 6.6 0.2 - - + -
408L GLY* 3.7 18.6 - - - +
411L GLY 4.2 0.7 - - - -
412L LEU* 3.8 32.1 - - + +
431L ALA* 2.8 37.2 + - + +
434L TRP* 1.3 75.0 - - - +
436L ARG* 1.3 64.3 + - - +
438L ALA* 3.4 5.9 + - - +
439L ILE* 3.1 24.7 + - + +
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Residues in contact with ARG 436 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390L ILE* 4.5 7.1 - - + +
394L TYR* 3.2 21.8 + - + +
432L THR* 2.7 37.3 + - + +
433L TRP* 3.8 23.6 - - + +
435L ILE* 1.3 73.4 - - - +
437L GLN* 1.3 60.9 + - - +
438L ALA 3.2 0.2 + - - -
439L ILE* 3.3 3.3 + - - +
440L THR* 3.0 28.1 + - - -
35P A 3.2 35.7 + - - +
37P G 2.9 58.5 + - + +
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Residues in contact with GLN 437 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411L GLY* 5.9 1.6 - - - -
414L LYS* 5.2 9.3 - - - +
433L TRP 3.2 6.7 + - - +
434L TRP* 3.1 41.9 + - + +
436L ARG* 1.3 79.7 - - - +
438L ALA* 1.3 65.0 + - - +
440L THR* 4.8 0.9 - - - -
441L ARG* 2.8 69.2 + - + +
48O G 4.2 13.3 - - - +
49O C 4.1 4.5 - - - +
37P G 2.9 35.3 + - + +
38P C 5.6 0.7 - - - +
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Residues in contact with ALA 438 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407L GLU* 3.1 32.1 - - + +
408L GLY* 4.4 0.7 - - - -
410L ILE* 5.5 0.9 - - + -
411L GLY* 4.1 11.7 - - - +
434L TRP 2.8 18.1 + - - +
435L ILE* 3.4 11.7 - - - +
436L ARG 3.1 0.4 - - - -
437L GLN* 1.3 84.6 - - - +
439L ILE* 1.3 64.9 + - - +
441L ARG* 4.4 0.6 - - - +
442L SER* 3.1 26.0 + - - -
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Residues in contact with ILE 439 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387L VAL* 5.4 0.2 - - + -
390L ILE* 4.9 3.8 - - + -
391L ALA* 4.8 9.0 - - + -
394L TYR* 3.3 27.8 - - + -
404L LEU* 3.0 45.5 - - + +
407L GLU* 3.8 1.6 - - + -
408L GLY* 3.1 26.2 - - - +
435L ILE* 3.1 19.6 + - + +
438L ALA* 1.3 74.4 - - - +
440L THR* 1.3 53.4 + - - +
442L SER* 2.9 7.3 + - - +
443L ILE* 2.6 63.5 + - + +
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Residues in contact with THR 440 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394L TYR* 3.9 21.1 + - - -
436L ARG 3.0 17.2 + - - -
437L GLN* 4.6 2.7 - - - -
439L ILE* 1.3 74.8 - - - +
441L ARG* 1.3 65.3 + - - +
442L SER 3.1 1.3 - - - -
443L ILE* 3.9 10.3 - - + +
444L ALA* 3.2 25.9 + - + +
454L VAL* 5.8 0.5 - - - +
37P G 2.9 37.0 + - + +
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Residues in contact with ARG 441 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437L GLN* 2.8 50.1 + - + +
438L ALA* 4.4 1.1 - - - +
440L THR* 1.3 75.3 - - - +
442L SER* 1.3 59.4 + - - +
444L ALA 4.1 1.0 + - - -
445L ASP* 3.4 22.1 + - - +
454L VAL* 4.6 25.4 - - - +
46O G 4.4 28.9 + - - +
47O G 3.4 34.8 + - - -
48O G 4.5 9.9 + - - -
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Residues in contact with SER 442 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399L LEU* 4.6 6.6 - - - +
407L GLU* 3.5 32.9 - - - +
438L ALA 3.1 15.8 + - - -
439L ILE* 2.9 11.1 + - - +
440L THR 3.1 0.4 - - - -
441L ARG* 1.3 76.2 - - - +
443L ILE* 1.3 62.4 + - - +
444L ALA 3.1 2.5 - - - -
445L ASP* 2.6 26.3 + - - -
446L GLN* 2.9 29.1 + - - +
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Residues in contact with ILE 443 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394L TYR* 3.7 17.5 - - + +
397L ARG* 3.8 33.2 - - + +
399L LEU* 3.8 24.0 - - + -
404L LEU* 3.5 12.3 - - + -
439L ILE* 2.6 51.9 + - + +
440L THR* 3.3 9.8 + - + +
442L SER* 1.3 72.9 + - - +
444L ALA* 1.3 60.0 + - + +
447L ALA* 2.9 35.4 - - + +
448L ARG* 5.7 0.9 - - - +
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Residues in contact with ALA 444 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440L THR* 3.2 17.3 + - + +
441L ARG 4.7 0.2 - - - +
442L SER 3.1 0.6 - - - -
443L ILE* 1.3 78.2 - - + +
445L ASP* 1.3 61.4 + - - +
447L ALA 5.0 0.7 - - - -
448L ARG* 5.9 3.1 - - - +
451L ARG* 4.7 1.2 + - - +
452L ILE* 3.6 9.4 + - - +
454L VAL* 3.9 21.1 - - + +
457L ILE* 3.1 52.6 - - + +
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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