Contacts of the helix formed by residues 406 - 423 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350B PHE* 5.6 3.8 - - - -
405B SER* 1.3 77.8 + - - +
407B ALA* 1.3 66.5 + - - +
408B LYS* 3.2 11.0 - - - -
409B GLU* 2.9 30.8 + - - -
410B VAL* 2.8 24.8 + - - +
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Residues in contact with ALA 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A ALA* 3.3 32.1 - - + +
408A LYS* 4.0 20.6 - - + +
411A MET* 4.1 11.6 - - - +
405B SER 2.9 8.4 + - - +
406B GLY* 1.3 72.3 - - - +
408B LYS* 1.3 74.1 + - - +
410B VAL* 3.6 0.5 + - - -
411B MET* 3.2 15.4 + - - +
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Residues in contact with LYS 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A ALA* 4.1 13.2 - - + +
352B LEU* 4.0 19.3 - - + -
406B GLY* 4.0 12.1 - - - -
407B ALA* 1.3 83.2 - - - +
409B GLU* 1.3 87.5 + - + +
411B MET* 3.0 32.4 + - + +
412B TRP* 3.1 14.6 + - - +
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Residues in contact with GLU 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B PHE* 3.9 29.5 - - - +
352B LEU* 3.6 29.3 - - + +
355B SER* 3.8 23.7 + - - +
356B VAL* 4.0 11.9 - - + +
359B ILE* 3.1 23.1 - - + +
405B SER* 4.7 1.1 + - - +
406B GLY* 2.9 30.7 + - - +
408B LYS* 1.3 94.7 + - + +
410B VAL* 1.3 56.8 + - - +
412B TRP* 4.0 6.6 - - - +
413B SER* 3.3 12.3 + - - -
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Residues in contact with VAL 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A MET* 3.2 46.0 - - + +
414A PHE* 4.0 14.5 - - + -
359B ILE* 3.7 24.7 - - + -
402B VAL* 3.8 32.3 - - + +
405B SER* 4.2 8.5 - - - +
406B GLY 2.8 12.5 + - - +
409B GLU* 1.3 74.4 - - - +
411B MET* 1.3 65.7 + - - +
412B TRP 2.9 2.2 - - - -
413B SER* 3.0 14.5 + - - -
414B PHE* 3.0 10.4 + - - +
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Residues in contact with MET 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A VAL 3.7 15.5 - - - +
403A VAL* 3.4 26.0 - - + +
405A SER 4.4 14.8 - - - +
407A ALA* 4.1 11.0 - - - +
410A VAL* 3.2 32.3 - - + +
407B ALA 3.2 13.2 + - - +
408B LYS* 3.0 21.6 + - - +
410B VAL* 1.3 77.6 - - - +
412B TRP* 1.3 78.7 + - + +
414B PHE* 3.1 6.9 - - - +
415B VAL* 3.0 49.4 + - + +
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Residues in contact with TRP 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A VAL* 3.3 36.1 - - + -
352B LEU* 4.1 26.3 - - + +
356B VAL* 4.2 12.1 - - + -
408B LYS* 3.1 28.6 + - - +
409B GLU* 4.0 7.4 - - - +
410B VAL 2.9 0.4 - - - -
411B MET* 1.3 95.1 - - + +
413B SER* 1.3 53.8 + - - +
414B PHE 3.1 1.3 - - - -
415B VAL* 3.0 19.8 + - + +
416B THR* 2.7 39.6 + - - -
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Residues in contact with SER 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A PHE* 4.3 13.0 - - - -
92B LEU* 5.1 0.4 - - - +
356B VAL* 3.6 8.7 + - - +
359B ILE* 3.0 41.0 - - - +
360B PHE* 4.1 12.8 - - - -
409B GLU 3.3 10.4 + - - -
410B VAL* 3.0 9.1 + - - -
412B TRP* 1.3 76.2 - - - +
414B PHE* 1.3 64.2 + - - +
416B THR* 3.2 20.8 - - - -
417B LEU* 3.3 11.8 + - - +
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Residues in contact with PHE 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A ILE* 4.3 12.1 - - + -
362A LEU* 6.2 0.7 - - + -
363A VAL* 4.0 24.2 - - + -
402A VAL* 3.7 31.0 - - + -
410A VAL* 4.0 14.4 - - + -
413A SER* 4.3 11.4 - - - -
414A PHE* 3.3 38.4 - + + -
417A LEU* 3.5 27.4 - - + -
410B VAL 3.0 10.3 + - - +
411B MET 3.1 11.0 - - - +
413B SER* 1.3 76.1 - - - +
415B VAL* 1.3 64.3 + - - +
417B LEU* 2.9 21.1 + - + +
418B MET* 3.2 33.5 + - + +
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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
----------------------------------------------------------
399A ILE* 3.8 28.7 - - + +
402A VAL* 3.9 12.3 - - + -
403A VAL* 4.0 18.4 - - + -
411B MET* 3.0 31.9 + - + +
412B TRP* 3.0 26.6 + - + +
414B PHE* 1.3 73.3 - - - +
416B THR* 1.3 66.5 + - - +
418B MET* 3.4 10.5 + - - +
419B VAL* 3.1 20.4 + - + +
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Residues in contact with THR 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B LEU* 4.6 1.3 - - + -
95B LEU* 5.7 5.8 - - + -
356B VAL* 4.7 0.9 - - - +
360B PHE* 3.1 42.6 - - + -
412B TRP 2.7 21.4 + - - -
413B SER 3.2 8.1 - - - -
415B VAL* 1.3 75.2 - - - +
417B LEU* 1.3 56.2 + - - +
419B VAL* 2.8 15.8 + - + +
420B ILE* 2.7 53.4 + - + +
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Residues in contact with LEU 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A PHE* 3.4 31.2 - - + -
417A LEU* 4.7 14.8 - - + -
88B GLN* 4.1 31.5 + - + +
92B LEU* 3.3 31.4 - - + -
363B VAL* 4.3 11.0 - - + -
413B SER 3.6 9.9 - - - +
414B PHE* 2.9 12.5 + - + +
416B THR* 1.3 76.6 - - - +
418B MET* 1.3 58.9 + - + +
420B ILE* 3.2 9.5 + - + +
421B THR* 2.9 33.2 + - - -
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Residues in contact with MET 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A LEU* 5.3 4.3 - - + -
363A VAL* 6.4 1.3 - - + -
366A LEU* 3.7 32.8 - - + +
398A CYS* 3.4 28.7 - - + +
399A ILE* 3.6 24.1 - - + +
402A VAL* 3.4 36.8 - - + -
414B PHE* 3.3 31.4 - - + +
415B VAL* 3.8 9.0 - - - +
416B THR 3.0 0.4 + - - -
417B LEU* 1.3 76.5 - - + +
419B VAL* 1.3 59.6 + - - +
421B THR* 3.3 2.8 + - - -
422B ALA* 2.9 26.3 + - - +
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Residues in contact with VAL 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A ILE* 3.6 22.1 - - + +
415B VAL* 3.1 12.7 + - + +
416B THR* 2.8 21.1 + - + +
418B MET* 1.3 73.4 - - - +
420B ILE* 1.3 71.6 + - + +
421B THR 3.0 2.0 - - - -
422B ALA* 3.2 5.2 + - + +
423B MET* 2.8 32.9 + - + +
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Residues in contact with ILE 420 (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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88B GLN* 3.9 32.3 - - + +
91B VAL* 3.6 32.5 - - + -
92B LEU* 3.7 29.2 - - + -
95B LEU* 5.5 1.3 - - + -
416B THR* 2.7 41.3 + - + +
417B LEU* 3.4 11.2 - - - +
419B VAL* 1.3 75.2 - - + +
421B THR* 1.3 57.7 + - - +
423B MET* 3.4 17.5 - - + +
424B TYR* 3.0 27.9 - - + -
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Residues in contact with THR 421 (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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366A LEU* 3.4 23.9 - - + +
367A TYR* 4.6 6.0 - - + -
370A ALA* 4.6 19.8 - - + +
395A PHE* 4.6 2.6 - - + -
84B PHE* 2.7 43.4 - - + -
88B GLN* 3.8 2.8 + - - -
417B LEU 2.9 15.1 + - - -
418B MET 3.4 7.9 - - - -
419B VAL 3.0 0.2 - - - -
420B ILE* 1.3 73.6 - - - +
422B ALA* 1.3 58.1 + - - +
423B MET 2.7 3.6 - - - -
424B TYR* 2.5 33.7 + - + +
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Residues in contact with ALA 422 (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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395A PHE* 3.1 43.9 - - + -
399A ILE* 4.0 9.4 - - + -
418B MET 2.9 13.7 + - - +
419B VAL* 3.4 17.0 - - + +
421B THR* 1.3 75.9 - - - +
423B MET* 1.3 50.1 + - - +
424B TYR 3.6 0.3 - - - -
425B ALA* 2.7 35.5 + - - +
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Residues in contact with MET 423 (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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91B VAL* 5.2 16.8 - - + -
95B LEU* 6.3 1.6 - - + -
419B VAL* 2.8 21.5 + - + +
420B ILE* 3.4 22.2 - - + +
421B THR 2.6 4.9 + - - -
422B ALA* 1.3 70.8 - - - +
424B TYR* 1.3 70.1 + - + -
425B ALA* 3.2 5.8 - - - +
426B LEU* 3.6 39.5 - - + +
427B ASN* 4.2 1.6 + - - -
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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
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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