Contacts of the helix formed by residues 386 - 404 (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 ALA 386 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383A ALA* 3.9 13.7 - - + +
384A ARG 2.4 10.3 + - - -
385A PRO* 1.3 71.9 - - - +
387A TYR* 1.3 64.9 + - + +
389A ALA* 2.9 28.4 + - - +
390A VAL* 3.3 6.1 + - - +
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Residues in contact with TYR 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A LYS* 3.8 31.9 - - + +
372A LEU* 5.9 7.6 - - + -
373A LEU* 5.3 0.7 - - - -
379A HIS* 2.8 44.9 - + + -
381A GLY* 4.8 12.3 - - - -
382A LYS 5.5 1.8 - - - -
383A ALA 5.2 6.3 - - - -
384A ARG* 2.8 10.1 + - - +
386A ALA* 1.3 74.7 - - + +
388A LEU* 1.3 57.4 + - - +
389A ALA 2.8 11.3 + - - -
390A VAL* 4.4 15.0 - - + +
391A THR* 3.1 33.6 + - + +
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Residues in contact with LEU 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A LEU* 4.5 8.3 - - + +
379A HIS* 5.3 0.2 - - - -
384A ARG* 3.1 62.2 + - + +
385A PRO* 4.6 6.7 - - + +
387A TYR* 1.3 76.0 - - - +
389A ALA* 1.3 51.7 + - - +
391A THR* 4.1 4.4 + - - +
392A THR* 2.7 32.3 + - - +
425B ALA* 4.7 4.9 - - + -
428B TYR* 3.3 35.4 - - + +
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Residues in contact with ALA 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A PRO 3.8 11.1 + - - +
386A ALA* 2.9 16.5 + - - +
387A TYR 2.8 1.0 - - - -
388A LEU* 1.3 78.0 - - - +
390A VAL* 1.3 55.9 + - - +
391A THR 3.0 1.8 - - - -
392A THR* 2.5 31.4 + - - -
393A ILE* 3.1 12.9 + - + +
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Residues in contact with VAL 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A GLY* 3.8 13.6 - - - +
58A MET* 3.8 39.9 - - + -
59A VAL* 4.4 9.6 - - + +
372A LEU* 5.6 0.7 - - + -
386A ALA 3.3 4.3 + - - +
387A TYR* 3.3 25.1 + - + +
389A ALA* 1.3 77.8 - - - +
391A THR* 1.3 73.0 + - + +
393A ILE* 3.3 21.1 - - + +
394A ALA* 3.1 20.3 + - - +
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Residues in contact with THR 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A VAL* 3.6 14.8 - - + -
369A CYS* 4.9 2.2 - - - -
372A LEU* 3.4 38.4 - - + +
373A LEU* 3.0 32.7 - - + +
387A TYR* 3.1 19.8 + - + +
388A LEU* 4.1 5.7 + - - -
389A ALA 3.0 1.4 - - - -
390A VAL* 1.3 81.0 - - + +
392A THR* 1.3 60.5 + - - +
394A ALA* 3.3 3.5 + - - +
395A PHE* 2.7 38.5 + - - -
428B TYR* 4.3 1.0 + - - -
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Residues in contact with THR 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A LEU* 2.7 28.6 + - - +
389A ALA* 2.5 19.1 + - - -
391A THR* 1.3 72.1 + - - +
393A ILE* 1.3 67.8 + - - +
395A PHE* 3.2 13.7 + - + +
396A LEU* 3.0 31.1 + - + +
425B ALA* 5.5 3.6 - - - +
428B TYR* 5.4 1.6 + - - -
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Residues in contact with ILE 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ILE* 4.1 24.7 - - + +
52A GLY* 3.8 33.7 - - - +
55A GLY* 4.8 2.7 - - - -
389A ALA* 3.1 9.3 + - + +
390A VAL* 3.3 26.0 - - + +
392A THR* 1.3 74.9 - - - +
394A ALA* 1.3 55.9 + - - +
396A LEU* 2.5 37.6 + - + +
397A TYR* 2.8 10.8 + - + -
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Residues in contact with ALA 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A GLY 4.8 0.2 - - - -
56A LEU* 4.0 19.3 - - + +
59A VAL* 3.6 19.1 - - + -
369A CYS* 3.4 22.9 - - - -
390A VAL 3.1 4.9 + - - +
391A THR 3.3 10.3 - - - +
393A ILE* 1.3 82.9 - - - +
395A PHE* 1.3 63.9 + - - +
397A TYR* 3.2 8.3 + - - +
398A CYS* 2.9 27.0 + - - -
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Residues in contact with PHE 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A LEU* 3.8 23.3 - - + -
369A CYS* 3.6 27.8 - - + -
370A ALA* 3.8 15.0 - - - -
373A LEU* 4.2 18.8 - - + -
391A THR* 2.7 39.3 + - - -
392A THR* 3.4 14.4 - - + +
393A ILE 3.1 0.2 - - - -
394A ALA* 1.3 73.0 - - - +
396A LEU* 1.3 58.9 + - + +
398A CYS* 3.5 4.7 + - - +
399A ILE* 2.9 37.4 + - + +
421B THR* 4.5 5.8 - - + -
422B ALA* 3.1 50.7 - - + -
424B TYR 5.9 0.7 - - - -
425B ALA* 5.5 2.7 - - + -
428B TYR* 4.4 7.4 - + - -
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Residues in contact with LEU 396 (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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392A THR* 3.0 31.4 + - + +
393A ILE* 2.5 22.0 + - + +
395A PHE* 1.3 70.6 - - + +
397A TYR* 1.3 55.1 + - - +
399A ILE* 4.5 5.4 - - + -
400A TRP* 2.7 49.5 + - + +
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Residues in contact with TYR 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A THR* 3.6 6.4 + - - -
52A GLY* 3.2 31.2 - - - +
53A ALA* 3.2 25.1 - - + +
56A LEU* 4.5 20.0 - - + -
201A LEU* 3.6 46.0 + - + +
204A PHE* 3.4 29.6 - - - +
362A LEU* 5.4 5.8 - - + -
393A ILE* 2.8 9.6 + - + +
394A ALA* 3.4 13.0 - - - +
396A LEU* 1.3 79.8 - - - +
398A CYS* 1.3 70.0 + - - +
400A TRP* 3.9 3.4 - - - +
401A ALA* 3.0 29.6 + - + +
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Residues in contact with CYS 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A LEU* 4.3 15.5 - - - -
362A LEU* 4.0 14.8 - - + +
365A TYR* 3.3 45.3 - - - -
366A LEU* 3.8 21.3 - - + +
369A CYS* 4.5 1.6 - - - -
394A ALA 2.9 20.9 + - - +
395A PHE 3.7 3.8 - - - +
397A TYR* 1.3 79.6 - - - +
399A ILE* 1.3 60.3 + - - +
401A ALA* 3.8 2.8 - - - +
402A VAL* 3.5 15.1 + - - +
418B MET* 3.4 12.3 - - + +
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Residues in contact with ILE 399 (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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366A LEU* 4.5 3.6 - - + -
395A PHE* 2.9 24.4 + - + +
396A LEU* 3.8 5.6 - - + +
398A CYS* 1.3 75.7 - - - +
400A TRP* 1.3 63.1 + - + +
402A VAL* 3.0 8.1 + - - +
403A VAL* 3.0 25.2 + - + +
415B VAL* 3.8 24.2 - - + +
418B MET* 3.6 27.4 - - + +
419B VAL* 3.6 42.4 - - + +
422B ALA* 4.0 11.4 - - + -
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Residues in contact with TRP 400 (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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194A GLN* 3.3 43.1 + - + +
197A LEU* 4.0 24.9 - - + +
201A LEU* 4.2 17.6 - - + +
396A LEU* 2.7 32.3 + - + +
397A TYR* 4.0 3.1 - - - +
399A ILE* 1.3 72.7 - - + +
401A ALA* 1.3 65.4 + - - +
403A VAL* 3.2 30.9 - - + +
404A GLY* 3.1 21.5 + - - -
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Residues in contact with ALA 401 (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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201A LEU* 3.8 27.2 - - + +
202A TRP* 6.4 0.9 - - - -
362A LEU* 4.5 20.6 - - + -
397A TYR* 3.0 23.3 + - + +
398A CYS 3.8 6.3 - - - +
400A TRP* 1.3 75.9 - - - +
402A VAL* 1.3 63.5 + - - +
404A GLY 2.9 20.3 - - - +
405A SER* 3.9 3.1 - - - -
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Residues in contact with VAL 402 (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* 4.8 6.5 - - + -
362A LEU* 4.1 21.1 - - + -
398A CYS 3.5 11.2 + - - +
399A ILE 3.0 9.6 + - - +
401A ALA* 1.3 76.9 - - - +
403A VAL* 1.3 64.8 + - - +
405A SER* 3.1 23.1 - - - -
410A VAL* 3.9 13.0 - - + -
411B MET* 3.7 5.1 - - + +
414B PHE* 3.7 33.2 - - + -
415B VAL* 3.9 14.4 - - + -
418B MET* 3.4 26.7 - - + -
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Residues in contact with VAL 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A GLN* 5.5 1.6 - - - +
399A ILE* 3.0 14.1 + - + +
400A TRP* 3.2 50.2 + - + +
402A VAL* 1.3 78.0 - - - +
404A GLY* 1.3 62.4 + - - +
405A SER 3.3 5.4 + - - -
411B MET* 3.4 20.6 - - - +
412B TRP* 3.3 40.6 - - + -
415B VAL* 4.0 13.0 - - + -
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Residues in contact with GLY 404 (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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194A GLN* 4.3 17.9 - - - -
198A ASN* 3.9 17.0 - - - +
400A TRP 3.1 7.2 + - - +
401A ALA 2.9 14.6 - - - +
402A VAL 3.6 0.2 - - - -
403A VAL* 1.3 84.3 - - - +
405A SER* 1.3 59.9 + - - -
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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