Contacts of the helix formed by residues 409 - 428 (chain I) in PDB entry 6LTJ
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 LEU 409 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405I LYS 2.9 17.6 + - - +
406I ALA* 3.0 6.7 + - - +
408I ARG* 1.3 78.8 - - + +
410I LEU* 1.3 59.7 + - - +
411I ASN 3.3 2.2 - - - -
412I PHE* 3.2 19.1 + - + -
413I GLN* 2.9 28.8 + - - +
610O LEU* 4.0 14.1 - - + +
613O LEU* 3.5 36.8 - - + +
614O GLU* 4.0 30.7 - - + +
617O LYS* 6.1 4.7 - - + -
639O PHE* 3.9 12.9 - - + -
644O ILE* 4.4 0.7 - - - -
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Residues in contact with LEU 410 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378I ILE* 3.6 33.2 - - + -
406I ALA 2.9 5.4 + - - -
407I LEU* 3.6 15.9 - - + +
408I ARG 3.2 2.0 - - - -
409I LEU* 1.3 77.8 - - - +
411I ASN* 1.3 59.1 + - - +
413I GLN* 3.3 15.7 + - - +
414I ARG* 2.9 46.2 + - + +
417I ARG* 5.7 1.6 - - - +
644O ILE* 3.6 29.2 - - + -
645O GLU* 3.7 36.1 - - + +
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Residues in contact with ASN 411 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408I ARG 4.2 7.5 + - - +
409I LEU 3.3 0.4 - - - -
410I LEU* 1.3 78.9 - - - +
412I PHE* 1.3 59.4 + - - +
414I ARG* 3.0 29.8 + - - +
415I GLN* 3.6 22.9 + - - +
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Residues in contact with PHE 412 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409I LEU* 3.2 26.7 + - + +
410I LEU 3.1 0.4 - - - -
411I ASN* 1.3 78.6 - - - +
413I GLN* 1.3 64.0 + - - +
415I GLN* 3.2 10.4 + - + +
416I LEU* 3.0 46.0 + - + +
613O LEU* 3.6 17.5 - - + -
617O LYS* 3.3 60.6 - - + -
618O ASP* 4.3 13.0 - - + -
620O TRP* 4.7 2.0 - + - -
639O PHE* 3.3 36.8 - + - -
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Residues in contact with GLN 413 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409I LEU 2.9 16.5 + - - +
410I LEU* 3.6 11.9 - - - +
412I PHE* 1.3 77.4 - - - +
414I ARG* 1.3 56.5 + - - +
416I LEU* 3.4 2.0 + - - +
417I ARG* 2.9 57.6 + - + +
639O PHE* 2.9 49.2 + - + +
640O LEU* 3.0 16.8 + - + -
642O LEU* 2.9 23.3 + - - +
644O ILE* 3.2 28.8 + - + +
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Residues in contact with ARG 414 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374I LEU* 5.9 1.4 - - - +
375I GLN* 5.9 4.8 - - - +
378I ILE* 5.3 4.4 - - - +
410I LEU* 2.9 37.0 + - + +
411I ASN* 3.0 33.5 + - - +
412I PHE 3.2 0.2 - - - -
413I GLN* 1.3 77.1 - - - +
415I GLN* 1.3 56.9 + - - +
417I ARG* 3.8 9.7 - - - +
418I GLN* 2.9 32.8 + - - +
645O GLU* 3.0 34.4 + - - +
477P ARG* 3.7 27.6 - - + +
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Residues in contact with GLN 415 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411I ASN 3.6 12.7 + - - +
412I PHE* 3.2 13.6 + - + +
414I ARG* 1.3 76.7 - - - +
416I LEU* 1.3 69.1 + - + +
418I GLN* 3.3 19.4 - - - +
419I GLU* 2.9 31.9 + - + +
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Residues in contact with LEU 416 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412I PHE* 3.0 56.4 + - + +
413I GLN* 3.7 6.3 - - - +
415I GLN* 1.3 82.0 - - + +
417I ARG* 1.3 64.0 + - - +
419I GLU* 3.7 9.0 - - - +
420I VAL* 2.9 33.6 + - + +
618O ASP* 4.6 6.3 - - - +
620O TRP* 4.0 15.3 - - + -
636O ILE* 5.0 2.0 - - + -
639O PHE* 4.5 3.6 - - + -
640O LEU* 3.7 16.6 - - + -
494P TYR* 3.4 37.7 - - + +
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Residues in contact with ARG 417 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410I LEU* 5.7 0.8 - - - +
413I GLN* 2.9 56.9 + - + +
414I ARG* 3.8 9.2 - - - +
416I LEU* 1.3 72.8 - - - +
418I GLN* 1.3 59.0 + - - +
420I VAL* 3.8 1.9 - - - +
421I VAL* 2.9 36.2 + - - +
640O LEU* 2.6 44.5 + - + -
642O LEU 3.9 3.4 + - - -
644O ILE 5.9 0.6 - - - +
645O GLU* 4.5 9.1 + - - +
646O ASP* 5.1 1.6 + - - -
476P GLU 4.5 3.8 + - - +
477P ARG* 3.2 25.8 + - - +
478P ARG 4.6 0.2 - - - -
479P ALA* 3.3 34.6 - - - +
482P TYR* 3.1 39.4 - - + +
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Residues in contact with GLN 418 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414I ARG 2.9 17.1 + - - +
415I GLN* 3.3 25.0 + - - +
417I ARG* 1.3 76.7 - - - +
419I GLU* 1.3 66.6 + - - +
421I VAL* 4.5 3.8 - - - -
422I VAL* 2.9 50.3 + - + +
476P GLU* 6.0 3.6 - - - +
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Residues in contact with GLU 419 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415I GLN* 2.9 23.3 + - + +
416I LEU* 3.7 11.9 - - - +
418I GLN* 1.3 83.2 - - - +
420I VAL* 1.3 69.1 + - - +
422I VAL* 3.1 8.3 - - - +
423I CYS* 3.0 38.7 + - - -
494P TYR* 3.6 33.4 + - + -
497P SER* 5.5 1.2 + - - -
498P LYS* 4.2 15.3 + - - -
501P GLN* 4.6 10.7 + - - +
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Residues in contact with VAL 420 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416I LEU* 2.9 25.0 + - + +
417I ARG 4.0 2.2 - - - +
419I GLU* 1.3 74.3 - - - +
421I VAL* 1.3 59.3 + - + +
423I CYS* 3.5 4.8 + - - +
424I MET* 2.9 27.7 + - - +
636O ILE* 5.6 0.4 - - + -
640O LEU* 4.4 24.7 - - + -
482P TYR* 6.0 1.6 - - + -
486P TRP* 5.0 5.4 - - + -
490P ALA* 4.0 33.4 - - + -
491P VAL* 4.6 3.1 - - + +
494P TYR* 3.9 37.7 - - + -
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Residues in contact with VAL 421 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417I ARG 2.9 22.3 + - - +
418I GLN* 4.0 4.7 - - - +
420I VAL* 1.3 76.4 - - + +
422I VAL* 1.3 60.4 + - + +
424I MET* 4.7 3.1 - - - -
425I ARG* 2.8 54.3 + - - +
1859L PHE* 4.1 15.1 - - + -
476P GLU* 4.0 12.1 - - + +
481P PHE* 3.9 15.3 - - + -
482P TYR* 3.5 33.2 - - + +
486P TRP* 4.3 7.2 - - + -
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Residues in contact with VAL 422 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418I GLN* 2.9 35.4 + - + +
419I GLU* 3.1 21.5 - - - +
421I VAL* 1.3 76.2 - - - +
423I CYS* 1.3 64.3 + - - +
425I ARG* 3.9 24.6 + - - +
426I ARG* 2.9 30.7 + - - +
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Residues in contact with CYS 423 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419I GLU* 3.0 39.0 + - - +
420I VAL* 3.9 5.2 - - - +
422I VAL* 1.3 84.9 - - - +
424I MET* 1.3 56.7 + - - +
426I ARG* 3.7 25.2 + - - +
427I ASP* 3.0 37.6 + - - +
493P ARG* 6.6 0.2 - - + -
494P TYR* 6.2 7.4 - - - -
497P SER* 5.7 4.5 - - - -
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Residues in contact with MET 424 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420I VAL 2.9 18.1 + - - +
421I VAL 4.1 0.7 - - - +
423I CYS* 1.3 77.6 - - - +
425I ARG* 1.3 51.0 - - - +
427I ASP* 4.3 1.3 - - - -
428I THR* 2.2 61.3 + - + +
1682L ALA* 3.9 4.7 - - + +
1859L PHE* 3.6 22.7 - - + -
486P TRP* 3.7 32.3 - - + +
489P GLU* 3.4 39.3 - - + +
490P ALA* 3.9 13.9 - - + +
493P ARG* 3.8 21.5 - - - -
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Residues in contact with ARG 425 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421I VAL* 2.8 36.0 + - - +
422I VAL* 3.9 24.5 + - - +
424I MET* 1.3 75.5 - - - +
426I ARG* 1.3 66.0 + - - +
428I THR* 3.5 8.3 + - - -
429I ALA* 3.4 22.5 + - + +
1859L PHE* 3.7 26.4 - - + -
1860L GLU* 5.5 5.2 - - - +
470P VAL* 3.7 46.3 + - - +
471P GLY* 4.0 9.9 - - - +
476P GLU* 2.7 33.7 + - - -
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Residues in contact with ARG 426 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422I VAL 2.9 16.8 + - - +
423I CYS* 3.7 24.2 + - - +
425I ARG* 1.3 78.4 - - - +
427I ASP* 1.3 88.3 + - - +
428I THR 3.6 0.2 + - - -
429I ALA* 3.9 13.6 + - - +
543O PRO* 4.3 21.9 - - + +
545O GLN* 3.0 42.7 - - - +
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Residues in contact with ASP 427 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423I CYS* 3.0 24.9 + - - +
424I MET* 4.0 6.0 - - - +
425I ARG 3.2 0.2 - - - -
426I ARG* 1.3 103.4 + - - +
428I THR* 1.3 58.4 + - - +
429I ALA 3.3 1.8 + - - +
1682L ALA* 4.2 13.7 - - + +
1685L THR* 3.3 21.8 - - - +
1686L TRP* 5.0 0.5 + - - +
540O GLY* 4.5 5.1 - - - +
543O PRO* 4.4 12.3 - - - +
545O GLN* 5.4 1.0 - - - +
493P ARG* 3.0 43.7 + - - +
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Residues in contact with THR 428 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424I MET* 2.2 58.8 + - + +
425I ARG* 3.6 4.6 - - - -
426I ARG 3.4 0.4 - - - -
427I ASP* 1.3 76.3 - - - +
429I ALA* 1.3 57.8 + - - +
1681L LEU* 3.5 36.6 - - + +
1682L ALA* 3.8 7.2 - - - +
1685L THR* 3.9 10.1 - - - -
1859L PHE* 3.2 24.2 + - + +
1980L ARG* 3.6 15.1 + - - -
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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