Contacts of the helix formed by residues 386 - 404 (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 ALA 386 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B ALA* 3.9 14.8 + - + +
384B ARG 2.4 10.5 + - - -
385B PRO* 1.3 71.1 - - - +
387B TYR* 1.3 66.1 + - + +
389B ALA* 2.9 28.3 - - - +
390B VAL* 3.3 6.2 + - - +
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Residues in contact with TYR 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B LYS* 3.8 32.2 - - + +
372B LEU* 5.9 7.2 - - + -
373B LEU* 5.3 0.4 - - - -
379B HIS* 2.8 45.3 - + + -
381B GLY* 4.8 12.6 - - - -
382B LYS 5.5 2.2 - - - -
383B ALA 5.3 5.4 - - - -
384B ARG* 2.8 10.1 + - - +
386B ALA* 1.3 75.1 - - + +
388B LEU* 1.3 57.3 + - - +
389B ALA 2.8 11.6 + - - -
390B VAL* 3.3 15.0 + - + +
391B THR* 3.1 34.2 + - + +
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Residues in contact with LEU 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A ALA* 4.6 6.3 - - + +
428A TYR* 3.2 36.3 - - + +
373B LEU* 4.5 6.7 - - + +
384B ARG* 3.1 61.1 + - + +
385B PRO* 4.6 6.7 - - + +
387B TYR* 1.3 75.5 - - - +
389B ALA* 1.3 51.6 + - - +
391B THR* 4.1 4.4 + - - +
392B THR* 2.7 31.4 + - - +
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Residues in contact with ALA 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B PRO 3.8 11.3 + - - +
386B ALA* 2.9 16.0 + - - +
387B TYR 2.8 0.8 - - - -
388B LEU* 1.3 78.0 - - - +
390B VAL* 1.3 55.7 + - - +
391B THR 3.0 1.8 - - - -
392B THR* 2.5 31.7 + - - -
393B ILE* 3.1 12.3 + - + +
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Residues in contact with VAL 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B GLY* 3.8 13.0 - - - +
58B MET* 3.8 40.6 - - + -
59B VAL* 4.4 9.0 - - + +
372B LEU* 5.6 0.9 - - + -
386B ALA 3.3 4.9 + - - +
387B TYR* 3.3 25.1 + - + +
389B ALA* 1.3 79.6 - - - +
391B THR* 1.3 73.0 + - + +
393B ILE* 3.3 21.1 - - + +
394B ALA* 3.1 20.3 + - - +
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Residues in contact with THR 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A TYR* 4.0 2.8 + - - -
59B VAL* 3.6 15.5 - - + -
369B CYS* 4.9 2.7 - - - -
372B LEU* 3.4 37.7 - - + -
373B LEU* 3.0 32.5 - - + +
387B TYR* 3.1 20.3 + - + +
388B LEU 4.1 4.7 + - - -
389B ALA 2.8 1.0 + - - -
390B VAL* 1.3 81.2 - - + +
392B THR* 1.3 59.0 + - - +
394B ALA* 3.3 3.0 - - - +
395B PHE* 2.7 37.4 + - - -
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Residues in contact with THR 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A TYR* 5.3 1.4 + - - -
388B LEU* 2.7 28.9 + - - +
389B ALA* 2.5 19.4 + - - -
391B THR* 1.3 71.9 + - - +
393B ILE* 1.3 67.5 + - - +
395B PHE* 3.2 14.4 + - + +
396B LEU* 3.0 30.8 + - + +
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Residues in contact with ILE 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B ILE* 4.1 24.2 - - + +
52B GLY* 3.8 33.2 - - - +
55B GLY* 4.7 3.1 - - - -
389B ALA* 3.1 9.5 + - + +
390B VAL* 3.3 25.8 - - + +
392B THR* 1.3 74.9 - - - +
394B ALA* 1.3 55.5 + - - +
396B LEU* 2.6 37.9 + - + +
397B TYR* 2.8 11.4 + - + +
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Residues in contact with ALA 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B GLY 4.8 0.2 - - - -
56B LEU* 4.1 19.5 - - + +
59B VAL* 3.6 20.2 - - + -
369B CYS* 3.4 22.9 - - - -
390B VAL 3.1 4.9 + - - +
391B THR 3.3 8.7 - - - +
393B ILE* 1.3 84.5 - - - +
395B PHE* 1.3 62.7 + - - +
397B TYR* 3.3 7.6 + - - +
398B CYS* 2.9 27.9 + - - -
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Residues in contact with PHE 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A THR* 4.4 5.4 - - + -
422A ALA* 3.0 55.2 - - + -
424A TYR 5.6 0.7 - - - -
425A ALA* 5.2 3.1 - - + -
428A TYR* 4.2 7.9 - + - -
366B LEU* 3.8 21.8 - - + -
369B CYS* 3.7 27.1 - - + -
370B ALA* 3.8 14.4 - - - -
373B LEU* 4.1 20.9 - - + -
391B THR* 2.7 36.4 + - - -
392B THR* 3.4 15.7 - - + +
393B ILE 3.0 0.2 + - - -
394B ALA* 1.3 72.2 - - - +
396B LEU* 1.3 58.3 + - + +
398B CYS* 3.4 5.1 + - - +
399B ILE* 2.9 37.6 + - + +
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Residues in contact with LEU 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B THR* 3.0 31.1 + - + +
393B ILE* 2.6 21.8 + - + +
395B PHE* 1.3 69.1 - - + +
397B TYR* 1.3 54.5 + - - +
399B ILE* 3.2 5.6 + - + -
400B TRP* 2.7 49.7 + - + +
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Residues in contact with TYR 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B THR* 3.6 7.9 + - - -
52B GLY* 3.2 31.0 - - - +
53B ALA* 3.2 22.9 - - + +
56B LEU* 4.5 19.5 - - + -
201B LEU* 3.5 46.4 + - + +
204B PHE* 3.4 29.3 - - - +
362B LEU* 5.5 5.8 - - + -
393B ILE* 2.8 9.0 + - + +
394B ALA* 3.5 13.2 - - - +
396B LEU* 1.3 78.9 - - - +
398B CYS* 1.3 68.8 + - - +
400B TRP* 3.8 3.2 - - - +
401B ALA* 3.0 30.0 + - + +
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Residues in contact with CYS 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A MET* 3.4 13.6 - - + +
56B LEU* 4.3 15.5 - - - -
362B LEU* 4.0 12.0 - - + +
365B TYR* 3.3 38.6 - - - -
366B LEU* 3.7 28.7 - - + +
369B CYS* 4.5 1.3 - - - -
394B ALA 2.9 21.8 + - - +
395B PHE 3.7 4.0 - - - +
397B TYR* 1.3 79.5 - - - +
399B ILE* 1.3 60.5 + - - +
401B ALA* 3.9 2.8 - - - +
402B VAL* 3.5 15.1 + - - +
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Residues in contact with ILE 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A VAL* 3.7 25.1 - - + +
418A MET* 3.8 26.9 - - + +
419A VAL* 3.5 43.5 - - + +
422A ALA* 4.0 11.0 - - + -
366B LEU* 4.5 3.1 - - + -
395B PHE* 2.9 24.5 + - + +
396B LEU* 3.8 5.6 - - + +
398B CYS* 1.3 75.4 - - - +
400B TRP* 1.3 63.0 + - + +
402B VAL* 3.0 7.4 + - - +
403B VAL* 2.9 25.0 + - + +
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Residues in contact with TRP 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B GLN* 3.2 43.1 + - + +
197B LEU* 4.0 25.1 - - + +
201B LEU* 4.2 17.2 - - + +
396B LEU* 2.7 31.8 + - + +
397B TYR* 3.9 3.4 - - - +
399B ILE* 1.3 72.1 - - + +
401B ALA* 1.3 66.5 + - - +
403B VAL* 3.2 28.9 - - + +
404B GLY* 3.1 22.0 + - - -
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Residues in contact with ALA 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B LEU* 3.8 27.6 - - + +
202B TRP* 6.0 0.9 - - - +
362B LEU* 4.6 20.4 - - + -
397B TYR* 3.0 22.3 + - + +
398B CYS 3.9 6.3 - - - +
400B TRP* 1.3 76.4 - - - +
402B VAL* 1.3 62.8 + - - +
404B GLY 3.0 19.6 - - - +
405B SER* 3.9 3.3 - - - -
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Residues in contact with VAL 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A MET* 3.6 5.4 - - + +
414A PHE* 3.7 32.3 - - + -
415A VAL* 3.9 14.4 - - + -
418A MET* 3.3 27.4 - - + -
359B ILE* 4.7 5.8 - - + -
362B LEU* 4.1 22.2 - - + -
398B CYS 3.5 10.1 - - - +
399B ILE 3.0 9.6 + - - +
401B ALA* 1.3 79.5 - - - +
403B VAL* 1.3 65.6 + - - +
405B SER* 3.1 22.2 - - - -
410B VAL* 3.8 13.2 - - + -
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Residues in contact with VAL 403 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A MET* 3.5 19.1 - - - +
412A TRP* 3.2 42.5 - - + -
415A VAL* 4.0 14.1 - - + -
194B GLN* 5.4 1.3 - - - +
399B ILE* 2.9 13.9 + - + +
400B TRP* 3.2 50.4 + - + +
402B VAL* 1.3 77.3 - - - +
404B GLY* 1.3 61.7 + - - +
405B SER 3.3 5.5 + - - -
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Residues in contact with GLY 404 (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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194B GLN* 4.3 18.4 - - - -
198B ASN* 3.8 17.0 - - - +
400B TRP 3.1 7.6 + - - -
401B ALA 3.0 10.4 - - - +
402B VAL 3.6 0.2 - - - -
403B VAL* 1.3 83.3 - - - +
405B SER* 1.3 64.1 + - - -
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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) + - + + + + + -
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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