Contacts of the helix formed by residues 413 - 429 (chain B) in PDB entry 5LGT
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 SER 413 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379B CYS* 3.1 17.4 - - - -
406B SER* 4.5 1.3 - - - -
412B LYS* 1.3 75.8 - - - +
414B VAL* 1.3 60.0 + - - +
415B VAL* 2.9 17.2 - - - +
416B GLN* 2.8 44.0 + - - +
417B VAL* 3.0 24.3 + - - +
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Residues in contact with VAL 414 (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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402B PHE* 3.3 35.4 - - + -
403B GLN* 3.2 26.5 - - + +
406B SER* 4.2 12.1 - - - +
413B SER* 1.3 71.0 - - - +
415B VAL* 1.3 63.8 + - - +
417B VAL* 3.4 8.5 - - - +
418B LYS* 3.1 33.7 + - - +
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Residues in contact with VAL 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B SER* 2.9 27.4 - - - +
414B VAL* 1.3 75.2 - - - +
416B GLN* 1.3 57.9 + - + +
418B LYS* 2.7 37.0 + - + +
419B ASN* 2.6 38.9 + - - +
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Residues in contact with GLN 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379B CYS* 3.9 7.3 - - - +
380B ASN 2.8 33.9 + - - +
381B ALA* 3.6 14.4 + - - +
383B TRP* 3.8 13.0 + - + +
412B LYS* 3.7 17.3 - - + +
413B SER* 2.8 54.2 + - - +
415B VAL* 1.3 74.7 - - + +
417B VAL* 1.3 56.9 + - - +
419B ASN* 3.3 11.9 + - - +
420B PHE* 2.9 29.3 + - - +
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Residues in contact with VAL 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B TRP* 4.7 3.3 - - + -
402B PHE* 4.0 20.0 - - + -
405B ILE* 3.8 23.1 - - + -
406B SER* 3.9 31.0 - - - +
409B ILE* 4.9 4.9 - - + -
412B LYS* 4.2 10.3 - - + +
413B SER 3.0 16.9 + - - +
414B VAL* 3.4 9.9 - - - +
416B GLN* 1.3 76.5 - - - +
418B LYS* 1.3 59.4 + - - +
420B PHE* 3.0 17.1 - - + +
421B PHE* 2.8 38.6 - - + -
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Residues in contact with LYS 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402B PHE* 3.2 43.3 - - + -
414B VAL* 3.1 30.1 + - - +
415B VAL* 2.7 22.9 + - + +
417B VAL* 1.3 68.8 - - - +
419B ASN* 1.3 67.8 + - - +
421B PHE* 3.0 25.9 + - - +
422B VAL* 3.5 7.9 + - - +
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Residues in contact with ASN 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B VAL* 2.6 55.4 + - - +
416B GLN* 3.3 12.8 - - - +
418B LYS* 1.3 71.5 - - - +
420B PHE* 1.3 53.7 + - - +
422B VAL* 2.6 33.7 + - - +
423B ASN* 2.6 32.9 + - - +
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Residues in contact with PHE 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B TRP* 3.4 44.2 - + + -
388B GLN* 4.1 11.0 - - + -
391B ALA* 3.6 25.8 - - + -
392B VAL* 4.6 1.1 - - + -
395B ILE* 4.0 13.2 - - + -
416B GLN 2.9 16.2 + - - +
417B VAL* 3.0 16.4 - - + +
418B LYS 3.1 0.2 - - - -
419B ASN* 1.3 75.3 - - - +
421B PHE* 1.3 67.3 + + - +
423B ASN* 3.1 8.7 - - - +
424B TYR* 2.9 51.7 + + + +
425B ARG 3.9 0.2 + - - -
428B PHE* 3.8 25.8 - + - -
430B ILE* 3.9 20.0 - - + -
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Residues in contact with PHE 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B ILE* 4.1 22.9 - - + -
399B GLY 4.0 12.3 - - - -
400B ARG* 5.3 1.1 - - + -
402B PHE* 3.4 36.1 - + - -
405B ILE* 4.2 3.8 - - + -
417B VAL* 2.8 46.9 - - + -
418B LYS* 3.0 15.1 + - - +
419B ASN 2.9 0.2 + - - -
420B PHE* 1.3 75.5 - + - +
422B VAL* 1.3 54.3 + - + +
425B ARG* 2.6 46.4 + - + +
430B ILE* 3.8 26.2 - - + -
434B LEU* 3.9 22.7 - - + -
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Residues in contact with VAL 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418B LYS 3.7 10.5 - - - +
419B ASN* 2.6 20.7 + - - +
421B PHE* 1.3 76.5 - - + +
423B ASN* 1.3 64.8 + - - +
424B TYR 3.2 0.9 + - - -
425B ARG* 3.7 19.7 + - - +
426B ARG* 4.2 5.2 - - - +
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Residues in contact with ASN 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B TRP* 5.8 1.8 - - - +
419B ASN* 2.6 54.6 + - - +
420B PHE* 3.1 9.5 - - - +
422B VAL* 1.3 74.0 - - - +
424B TYR* 1.3 66.6 + - + +
426B ARG* 2.7 32.0 - - - +
427B ARG* 3.3 8.5 + - - +
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Residues in contact with TYR 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B TRP* 4.5 17.8 - + - +
388B GLN* 3.4 27.2 + - - -
420B PHE* 2.9 50.5 + + + +
423B ASN* 1.3 87.4 - - + +
425B ARG* 1.3 56.0 + - - +
426B ARG* 3.0 5.6 - - - +
427B ARG* 2.5 74.4 + - + +
428B PHE* 3.2 36.1 + + + -
430B ILE* 4.0 2.7 - - + -
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Residues in contact with ARG 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421B PHE* 2.6 31.6 + - - +
422B VAL* 3.7 15.1 + - - +
424B TYR* 1.3 69.6 - - - +
426B ARG* 1.3 66.9 + - - +
429B ASN* 3.1 19.8 + - - -
430B ILE* 3.4 27.5 + - + +
431B ASP* 2.5 56.2 + - - +
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Residues in contact with ARG 426 (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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422B VAL 4.2 3.5 + - - +
423B ASN 2.7 32.3 - - - +
424B TYR* 2.7 10.2 + - - +
425B ARG* 1.3 78.7 - - - +
427B ARG* 1.3 86.7 + - + +
429B ASN* 4.1 7.8 + - - +
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Residues in contact with ARG 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B ASN* 3.3 15.8 + - - +
424B TYR* 2.5 54.0 + - + +
426B ARG* 1.3 103.7 - - + +
428B PHE* 1.3 71.9 + - + +
429B ASN* 3.3 14.7 - - - +
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Residues in contact with PHE 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B GLN* 3.6 33.9 - - + -
389B LEU* 6.3 3.1 - - + -
392B VAL* 3.4 30.8 - - + +
420B PHE* 3.8 27.8 - + - -
424B TYR* 3.2 21.8 + + + +
427B ARG* 1.3 90.9 - - + +
429B ASN* 1.3 69.9 + - - +
430B ILE* 2.8 20.7 + - + -
433B VAL* 3.3 16.5 - - - +
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Residues in contact with ASN 429 (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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425B ARG 3.1 10.2 + - - -
426B ARG 4.1 5.6 + - - +
427B ARG* 3.3 16.9 - - - +
428B PHE* 1.3 74.3 - - - +
430B ILE* 1.3 53.7 + - - +
431B ASP* 2.9 8.5 - - - -
432B GLU* 2.7 59.4 + - + +
433B VAL* 2.8 11.0 + - + +
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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
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Atomic class I II III IV V VI VII VIII
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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