Contacts of the helix formed by residues 406 - 423 (chain A) in PDB entry 3LRB
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 GLY 406 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350A PHE* 5.6 3.6 - - - -
405A SER* 1.3 76.8 + - - +
407A ALA* 1.3 66.8 + - - +
408A LYS* 3.2 10.8 - - - -
409A GLU* 2.9 32.1 + - - -
410A VAL* 2.9 24.8 + - - +
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Residues in contact with ALA 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A SER 2.9 7.6 + - - +
406A GLY* 1.3 72.1 - - - +
408A LYS* 1.3 74.6 + - - +
411A MET* 3.2 15.4 + - - +
407B ALA* 3.3 37.8 - - + +
408B LYS* 4.1 13.5 - - + +
411B MET* 4.1 13.0 - - - +
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Residues in contact with LYS 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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352A LEU* 4.0 19.5 - - + -
406A GLY* 4.1 5.1 - - - -
407A ALA* 1.3 91.6 - - - +
409A GLU* 1.3 86.7 + - + +
411A MET* 3.0 32.8 + - + +
412A TRP* 3.1 14.7 + - - +
407B ALA* 4.0 13.0 - - + +
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Residues in contact with GLU 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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350A PHE* 3.9 29.3 - - - +
352A LEU* 3.6 29.9 - - + +
355A SER* 3.8 23.3 + - - +
356A VAL* 4.0 12.5 - - + +
359A ILE* 3.1 21.3 - - + +
405A SER* 4.8 1.1 + - - +
406A GLY* 2.9 31.8 + - - +
408A LYS* 1.3 93.0 + - + +
410A VAL* 1.3 56.2 + - - +
412A TRP* 4.0 6.4 - - - +
413A SER* 3.3 12.5 + - - -
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Residues in contact with VAL 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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359A ILE* 3.6 25.6 - - + -
402A VAL* 3.9 31.9 - - + +
405A SER* 4.1 8.7 - - - +
406A GLY 2.9 10.6 + - - +
409A GLU* 1.3 74.3 - - - +
411A MET* 1.3 69.9 + - - +
412A TRP 2.9 2.0 - - - -
413A SER* 2.9 14.1 + - - -
414A PHE* 3.0 10.6 + - - +
411B MET* 3.2 44.4 - - + +
414B PHE* 4.0 14.3 - - + -
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Residues in contact with MET 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A ALA 3.2 11.2 + - - +
408A LYS* 3.0 21.4 + - - +
410A VAL* 1.3 78.1 - - - +
412A TRP* 1.3 79.9 + - + +
414A PHE* 3.1 6.8 - - - +
415A VAL* 3.0 48.8 + - + +
402B VAL 3.6 16.2 - - - +
403B VAL* 3.5 25.4 - - - +
405B SER 4.3 13.0 - - - +
407B ALA* 4.1 10.8 - - - +
410B VAL* 3.2 35.5 - - + +
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Residues in contact with TRP 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A LEU* 4.1 26.7 - - + +
356A VAL* 4.2 12.6 - - + -
408A LYS* 3.1 28.7 + - - +
409A GLU* 4.0 7.4 - - - +
410A VAL 2.9 0.4 - - - -
411A MET* 1.3 91.8 - - + +
413A SER* 1.3 53.1 + - - +
414A PHE 3.1 1.6 - - - -
415A VAL* 3.0 19.4 + - + +
416A THR* 2.7 39.9 + - - -
403B VAL* 3.2 40.4 - - + -
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Residues in contact with SER 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A LEU* 5.1 0.2 - - - +
356A VAL* 3.6 8.7 + - - +
359A ILE* 2.9 41.4 - - - +
360A PHE* 4.1 12.6 + - - -
409A GLU 3.3 10.3 + - - -
410A VAL* 2.9 9.1 + - - -
412A TRP* 1.3 75.8 - - - +
414A PHE* 1.3 64.5 + - - +
416A THR* 3.1 23.1 - - - -
417A LEU* 3.3 10.9 + - - +
414B PHE* 4.3 13.2 - - - -
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Residues in contact with PHE 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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410A VAL 3.0 10.5 + - - +
411A MET 3.1 11.2 - - - +
412A TRP 3.1 0.2 - - - -
413A SER* 1.3 76.3 - - - +
415A VAL* 1.3 64.0 + - - +
417A LEU* 2.9 20.5 + - + +
418A MET* 3.2 33.3 + - + +
359B ILE* 4.3 13.0 - - + -
362B LEU* 6.2 0.4 - - + -
363B VAL* 4.0 24.0 - - + -
402B VAL* 3.7 29.4 - - + -
410B VAL* 4.0 15.3 - - + -
413B SER* 4.3 11.2 - - - -
414B PHE* 3.3 38.6 - + + -
417B LEU* 3.4 27.1 - - + -
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Residues in contact with VAL 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 MET* 3.0 24.6 + - + +
412A TRP* 3.0 27.0 + - + +
414A PHE* 1.3 73.1 - - - +
416A THR* 1.3 67.3 + - - +
418A MET* 3.4 10.0 + - - +
419A VAL* 3.1 19.7 + - + +
399B ILE* 3.7 29.8 - - + +
402B VAL* 3.9 18.4 - - + -
403B VAL* 4.0 18.2 - - + -
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Residues in contact with THR 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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92A LEU* 4.6 1.3 - - + -
95A LEU* 5.7 6.5 - - + -
356A VAL* 4.7 0.7 - - - +
360A PHE* 3.1 42.4 - - + -
412A TRP 2.7 21.3 + - - -
413A SER 3.1 8.5 - - - -
415A VAL* 1.3 75.0 - - - +
417A LEU* 1.3 53.7 + - - +
419A VAL* 2.8 15.7 + - + +
420A ILE* 2.7 53.6 + - + +
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Residues in contact with LEU 417 (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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88A GLN* 4.1 30.2 + - + +
92A LEU* 3.3 31.9 - - + -
363A VAL* 4.4 11.9 - - + -
413A SER 3.6 9.9 - - - +
414A PHE* 2.9 12.7 + - + +
416A THR* 1.3 76.2 - - - +
418A MET* 1.3 59.0 + - + +
420A ILE* 3.2 9.2 + - - +
421A THR* 2.9 34.0 + - - -
414B PHE* 3.5 30.7 - - + -
417B LEU* 4.7 14.1 - - + -
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Residues in contact with MET 418 (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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414A PHE* 3.3 31.6 - - + +
415A VAL* 3.7 9.0 - - - +
416A THR 3.0 0.4 + - - -
417A LEU* 1.3 76.5 - - + +
419A VAL* 1.3 58.0 + - - +
421A THR* 3.4 4.2 + - - -
422A ALA* 2.9 25.1 + - - +
362B LEU* 5.1 5.6 - - + -
363B VAL* 5.9 2.0 - - + +
366B LEU* 3.5 35.5 - - + +
398B CYS* 3.4 28.7 - - + +
399B ILE* 3.8 20.9 - - + +
402B VAL* 3.3 37.5 - - + -
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Residues in contact with VAL 419 (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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415A VAL* 3.1 12.3 + - + +
416A THR* 2.8 21.1 + - + +
418A MET* 1.3 73.6 - - - +
420A ILE* 1.3 71.2 + - + +
421A THR 3.0 1.8 - - - -
422A ALA* 3.2 6.5 + - + +
423A MET* 2.8 34.1 + - + +
399B ILE* 3.5 24.2 - - + +
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Residues in contact with ILE 420 (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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88A GLN* 3.9 30.3 - - + +
91A VAL* 3.7 34.3 - - + -
92A LEU* 3.8 24.9 - - + -
95A LEU* 5.7 0.7 - - + -
416A THR* 2.7 44.8 + - + +
417A LEU* 3.4 10.5 - - - +
419A VAL* 1.3 74.9 - - + +
421A THR* 1.3 58.7 + - - +
423A MET* 3.3 18.6 - - + +
424A TYR* 3.0 35.6 - - + -
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Residues in contact with THR 421 (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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84A PHE* 2.6 42.8 - - + -
88A GLN* 3.7 3.3 + - - -
417A LEU 2.9 14.7 + - - -
418A MET 3.4 7.9 - - - -
420A ILE* 1.3 73.6 - - - +
422A ALA* 1.3 57.4 + - - +
423A MET 2.7 3.6 - - - -
424A TYR* 2.5 35.4 + - + +
366B LEU* 3.4 23.2 - - + +
367B TYR* 4.5 6.3 - - + -
370B ALA* 4.5 21.3 - - + +
395B PHE* 4.5 2.4 - - + -
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Residues in contact with ALA 422 (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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418A MET 2.9 13.7 + - - +
419A VAL* 3.4 17.3 - - + +
421A THR* 1.3 76.0 - - - +
423A MET* 1.3 51.5 + - - +
424A TYR 3.6 0.2 - - - -
425A ALA* 2.7 35.5 + - - +
395B PHE* 3.0 44.7 - - + -
399B ILE* 4.0 9.6 - - + -
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Residues in contact with MET 423 (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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91A VAL* 5.1 16.4 - - + -
95A LEU* 6.3 1.3 - - + -
419A VAL* 2.8 18.1 + - + +
420A ILE* 3.3 26.0 - - + +
421A THR 2.6 5.3 + - - -
422A ALA* 1.3 70.0 - - - +
424A TYR* 1.3 68.5 + - + -
425A ALA* 3.2 5.8 - - - +
426A LEU* 3.6 37.5 - - + +
427A ASN* 4.1 2.4 + - - -
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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