Contacts of the helix formed by residues 408 - 431 (chain L) in PDB entry 4XLN
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 THR 408 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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402L GLY* 4.9 0.4 - - - -
406L GLY 5.5 0.4 - - - +
407L VAL* 1.3 79.2 - - - +
409L ARG* 1.3 68.1 + - - +
410L GLU 4.2 0.9 - - - -
411L ARG* 3.1 22.0 + - - +
412L ILE* 3.2 9.9 + - - +
2R T 2.5 55.9 + - + +
3R T 3.6 29.8 - - + +
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Residues in contact with ARG 409 (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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398L LEU* 3.6 38.4 + - + +
399L GLU* 3.3 31.5 + - + +
402L GLY* 5.3 0.2 - - - -
407L VAL 4.0 0.4 + - - -
408L THR* 1.3 73.0 - - - +
410L GLU* 1.3 72.8 + - - +
412L ILE* 3.2 5.0 + - - +
413L ARG* 2.9 22.8 + - - +
3R T 6.1 1.3 - - + -
4R G 4.3 6.3 + - - -
5R A 3.1 26.5 - - - +
6R C 4.8 2.2 - - - +
42S T 3.3 26.5 + - - +
43S G 2.7 42.3 + - - -
44S T 3.2 23.5 + - - +
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Residues in contact with GLU 410 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408L THR* 3.2 4.4 - - - +
409L ARG* 1.3 83.7 - - - +
411L ARG* 1.3 63.1 + - - +
413L ARG* 2.4 46.1 + - - +
414L GLN* 3.0 30.0 + - - +
2R T 4.3 15.3 - - + +
3R T 4.2 13.7 - - + +
4R G 4.9 0.2 - - - +
44S T 3.2 16.8 - - - +
45S C 2.7 38.7 + - - +
46S A 3.6 18.0 + - - +
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Residues in contact with ARG 411 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379L ARG* 2.9 27.5 - - - +
407L VAL* 3.8 19.5 - - + -
408L THR* 3.1 21.4 + - - +
410L GLU* 1.3 80.6 - - - +
412L ILE* 1.3 57.0 + - - +
414L GLN* 3.3 13.0 + - - +
415L ILE* 2.9 63.7 + - + +
1R C 3.2 57.2 + - - +
2R T 3.8 6.8 - - + +
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Residues in contact with ILE 412 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383L VAL* 4.0 15.7 - - + -
398L LEU* 3.8 13.5 - - + +
401L VAL* 3.6 40.4 - - + +
402L GLY* 3.6 22.4 - - - +
405L PHE* 4.3 3.6 - - + -
407L VAL* 3.6 24.2 - - + -
408L THR 3.2 3.1 + - - +
409L ARG 3.2 8.1 + - - +
411L ARG* 1.3 76.2 - - - +
413L ARG* 1.3 64.3 - - - +
415L ILE* 3.2 17.2 + - + +
416L GLU* 2.9 39.8 + - - +
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Residues in contact with ARG 413 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398L LEU* 4.1 11.8 - - + +
409L ARG 2.9 12.8 + - - +
410L GLU* 2.4 44.4 + - - +
412L ILE* 1.3 79.4 - - - +
414L GLN* 1.3 87.7 + - - +
416L GLU* 3.2 12.6 - - - +
417L ASN* 2.8 41.8 + - - +
44S T 3.4 51.0 + - - +
45S C 2.7 32.2 + - - +
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Residues in contact with GLN 414 (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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410L GLU* 3.0 23.6 + - - +
411L ARG* 3.8 11.1 + - - +
413L ARG* 1.3 98.1 - - - +
415L ILE* 1.3 56.9 + - - +
417L ASN* 3.4 9.1 + - - +
418L LYS* 2.9 32.4 + - - +
1R C 3.5 33.7 + - - +
2R T 4.2 10.0 - - - +
47S A 4.7 13.7 - - - +
48S G 5.8 0.4 + - - -
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Residues in contact with ILE 415 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379L ARG* 3.6 26.2 - - + +
380L GLU* 3.6 35.2 - - + +
383L VAL* 4.3 11.4 - - + -
407L VAL* 5.1 0.7 - - + -
411L ARG* 2.9 65.6 + - + +
412L ILE* 3.3 23.1 - - + +
414L GLN* 1.3 76.2 - - - +
416L GLU* 1.3 60.3 + - - +
418L LYS* 3.7 4.2 - - - +
419L ALA* 2.9 28.6 + - - +
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Residues in contact with GLU 416 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383L VAL* 4.5 6.7 - - + -
384L LEU* 3.7 27.1 - - + +
387L ARG* 3.1 49.0 + - + +
388L LYS* 5.1 7.3 + - - -
398L LEU* 3.2 21.1 - - - +
412L ILE* 2.9 17.3 + - - +
413L ARG* 3.2 17.5 - - - +
415L ILE* 1.3 74.0 - - - +
417L ASN* 1.3 67.8 + - - +
419L ALA* 4.0 0.2 - - - +
420L LEU* 2.9 29.8 + - - +
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Residues in contact with ASN 417 (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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413L ARG* 2.8 45.2 + - - +
414L GLN* 3.7 8.3 - - - +
416L GLU* 1.3 80.8 - - - +
418L LYS* 1.3 63.8 - - - +
420L LEU* 3.1 9.1 + - - +
421L ARG* 3.0 49.0 + - - +
44S T 5.6 2.6 + - - -
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Residues in contact with LYS 418 (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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380L GLU* 5.2 3.8 - - - +
414L GLN 2.9 18.6 + - - +
415L ILE* 3.7 4.7 - - - +
417L ASN* 1.3 75.4 - - - +
419L ALA* 1.3 58.7 + - - +
421L ARG* 3.2 23.7 + - + +
422L LYS* 2.9 51.5 + - + +
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Residues in contact with ALA 419 (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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376L LEU* 3.8 7.3 - - + +
380L GLU* 3.5 42.3 + - + +
384L LEU* 3.7 18.8 - - + -
415L ILE 2.9 18.1 + - - +
418L LYS* 1.3 74.3 - - - +
420L LEU* 1.3 65.5 + - - +
422L LYS* 3.2 4.6 + - - +
423L LEU* 2.9 28.0 + - - +
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Residues in contact with LEU 420 (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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773I LEU* 4.6 5.6 - - + -
776I SER* 3.2 41.3 - - - +
777I ILE* 3.4 43.1 - - + +
384L LEU* 4.6 5.1 - - + +
416L GLU 2.9 20.3 + - - +
417L ASN* 3.2 8.5 - - - +
419L ALA* 1.3 75.8 - - - +
421L ARG* 1.3 61.3 + - + +
423L LEU* 3.1 14.0 + - + +
424L LYS* 3.0 32.0 + - - +
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Residues in contact with ARG 421 (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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414L GLN 5.3 0.2 + - - -
417L ASN* 3.0 36.0 + - - +
418L LYS* 3.7 37.1 - - + +
420L LEU* 1.3 81.0 - - + +
422L LYS* 1.3 58.2 + - + +
424L LYS* 3.0 31.4 + - + +
425L TYR* 2.9 27.7 + - - +
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Residues in contact with LYS 422 (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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375L LYS* 5.4 3.9 - - - +
376L LEU* 4.1 12.8 - - + +
377L SER* 6.1 1.0 - - - +
380L GLU* 4.0 20.8 + - - +
418L LYS* 2.9 45.3 + - + +
419L ALA 3.2 5.6 + - - +
421L ARG* 1.3 76.2 - - + +
423L LEU* 1.3 61.1 + - - +
425L TYR* 3.7 9.0 + - - +
426L HIS* 3.7 19.9 + - - +
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Residues in contact with LEU 423 (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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773I LEU* 5.5 1.1 - - + -
777I ILE* 3.7 32.3 - - + -
372L ALA* 3.2 33.2 - - + +
373L LEU* 4.6 4.7 - - + -
375L LYS* 4.5 5.6 - - + +
376L LEU* 3.6 22.0 - - + -
384L LEU* 3.6 29.4 - - + -
419L ALA 2.9 14.5 + - - +
420L LEU* 3.2 9.4 - - - +
422L LYS* 1.3 76.0 - - - +
424L LYS* 1.3 58.6 - - - +
425L TYR 3.1 0.2 - - - -
426L HIS* 3.6 4.4 + - - +
427L GLU* 2.9 33.4 + - + +
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Residues in contact with LYS 424 (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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777I ILE* 3.3 33.4 + - + +
778I PHE* 5.1 8.7 + - - +
420L LEU* 3.0 20.0 + - - +
421L ARG* 3.0 30.0 + - + +
423L LEU* 1.3 76.8 - - - +
425L TYR* 1.3 55.0 + - - +
427L GLU* 3.8 6.0 - - - +
428L SER* 2.9 28.3 + - - -
434L ARG* 4.0 11.3 + - - +
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Residues in contact with TYR 425 (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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421L ARG 2.9 13.9 + - - +
422L LYS* 3.9 9.2 - - - +
423L LEU 3.1 0.2 - - - -
424L LYS* 1.3 73.8 - - - +
426L HIS* 1.3 83.4 + + + +
428L SER* 2.9 24.0 + - - -
429L ARG* 3.5 44.9 + - + +
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Residues in contact with HIS 426 (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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375L LYS* 3.8 50.4 + - + +
422L LYS 3.7 7.7 + - - +
423L LEU 3.6 5.3 + - - +
425L TYR* 1.3 89.2 - + - +
427L GLU* 1.3 58.1 + - - +
429L ARG* 3.1 32.7 + - - +
430L THR* 2.9 40.0 + - + +
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Residues in contact with GLU 427 (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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777I ILE* 5.0 7.9 - - + -
778I PHE* 4.5 10.3 - - + -
372L ALA* 5.2 4.2 - - - +
423L LEU* 2.9 22.0 + - + +
424L LYS* 3.8 6.3 - - - +
426L HIS* 1.3 77.0 - - - +
428L SER* 1.3 63.7 + - - +
430L THR* 3.0 24.4 + - - -
431L ARG 3.3 4.0 + - - -
432L LYS* 3.4 4.0 + - - +
433L LEU* 2.9 34.1 + - + +
434L ARG* 2.6 50.4 + - - +
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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
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424L LYS* 2.9 14.9 + - - -
425L TYR* 2.9 17.9 + - - -
427L GLU* 1.3 78.8 - - - +
429L ARG* 1.3 62.5 + - - +
431L ARG* 3.9 16.8 + - - -
434L ARG* 3.4 32.0 + - - +
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Residues in contact with ARG 429 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425L TYR* 3.5 50.4 + - + +
426L HIS* 3.1 39.8 + - - +
428L SER* 1.3 81.2 - - - +
430L THR* 1.3 65.5 + - + +
431L ARG* 5.1 1.8 - - - +
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Residues in contact with THR 430 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668J PRO* 5.0 4.0 - - - +
375L LYS* 4.6 10.3 - - - +
426L HIS* 2.9 33.3 + - + +
427L GLU* 3.0 33.1 + - - -
429L ARG* 1.3 81.4 - - + +
431L ARG* 1.3 66.4 + - - +
432L LYS* 3.0 27.6 + - + +
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Residues in contact with ARG 431 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668J PRO* 4.2 20.7 - - + +
427L GLU* 3.3 12.5 + - - -
428L SER 3.9 16.1 + - - -
429L ARG 3.6 1.9 - - - +
430L THR* 1.3 80.4 + - - +
432L LYS* 1.3 63.8 + - - +
434L ARG* 3.3 48.9 + - - +
435L ASP* 4.3 3.8 + - - +
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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