Contacts of the helix formed by residues 355 - 375 (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 SER 355 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A TRP* 3.9 26.0 - - - -
350A PHE* 4.0 17.5 - - - -
351A GLY 4.2 0.8 - - - +
352A LEU* 4.0 9.7 + - - -
353A VAL 3.3 0.2 - - - -
354A SER* 1.3 78.3 - - - +
356A VAL* 1.3 56.6 + - - +
357A SER 3.1 2.0 - - - -
358A VAL* 2.6 35.4 + - - +
359A ILE* 3.0 12.0 + - - +
409A GLU* 3.8 26.2 - - - +
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Residues in contact with VAL 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A LEU* 3.1 34.3 - - - +
353A VAL* 3.9 8.3 - - + +
354A SER 3.6 0.2 - - - -
355A SER* 1.3 73.7 - - - +
357A SER* 1.3 57.9 + - - +
358A VAL 2.9 4.7 - - - -
359A ILE* 4.4 5.4 - - - +
360A PHE* 2.9 54.1 + - + -
409A GLU* 4.0 15.0 - - - +
412A TRP* 4.2 12.8 - - + -
413A SER* 3.6 29.4 - - - +
416A THR* 4.7 0.2 - - - +
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Residues in contact with SER 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A ALA* 3.0 35.6 + - - +
99A ILE* 3.2 41.9 - - - +
100A GLY* 4.0 11.4 + - - -
353A VAL 3.9 3.2 + - - -
354A SER 3.1 18.2 + - - -
356A VAL* 1.3 77.0 - - - +
358A VAL* 1.3 59.8 + - - +
360A PHE* 3.5 13.2 - - - -
361A THR* 3.0 10.4 - - - +
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Residues in contact with VAL 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A TRP* 4.4 31.4 - - + +
205A ILE* 3.3 27.6 - - + -
354A SER 4.0 12.1 - - - +
355A SER* 2.6 17.7 + - - +
357A SER* 1.3 83.6 + - - +
359A ILE* 1.3 68.7 - - + +
360A PHE 3.0 0.7 - - - -
361A THR* 2.9 24.7 + - + -
362A LEU* 3.8 7.3 + - + +
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Residues in contact with ILE 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A SER* 3.0 12.9 + - - +
356A VAL* 4.0 3.6 - - - +
358A VAL* 1.3 79.5 - - + +
360A PHE* 1.3 65.4 + - - +
362A LEU* 2.9 33.4 + - + +
363A VAL* 4.0 2.9 + - - +
402A VAL* 4.8 4.5 - - + -
405A SER* 3.9 15.5 - - - +
409A GLU* 3.1 41.3 - - + +
410A VAL* 3.6 22.0 - - + -
413A SER* 2.9 29.4 - - - +
414B PHE* 4.3 13.7 - - + -
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Residues in contact with PHE 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A LEU* 2.9 59.1 - - + +
95A LEU* 3.9 31.6 - - + -
96A ALA* 3.8 7.9 - - + -
99A ILE* 5.0 4.9 - - + -
356A VAL* 2.9 38.4 + - + +
357A SER* 3.5 12.6 - - - +
359A ILE* 1.3 76.2 - - - +
361A THR* 1.3 57.8 + - - +
362A LEU 2.9 5.9 + - - -
363A VAL* 3.1 5.3 + - - +
364A PRO* 2.9 3.8 - - - +
413A SER* 4.1 14.1 - - - -
416A THR* 3.1 48.9 - - + -
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Residues in contact with THR 361 (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 - - - -
93A TYR* 4.4 21.1 - - + -
96A ALA* 4.1 14.4 - - + +
205A ILE* 3.6 21.1 - - + +
208A GLU* 4.6 1.1 - - - +
293A TRP* 5.1 3.6 - - + -
357A SER 3.0 24.5 - - - +
358A VAL* 2.9 14.6 + - + +
360A PHE* 1.3 74.7 - - - +
362A LEU* 1.3 57.8 + - - +
364A PRO* 3.1 22.5 - - - +
365A TYR* 2.9 37.4 + - - -
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Residues in contact with LEU 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A LEU* 5.9 0.2 - - + -
205A ILE* 5.7 5.4 - - + -
358A VAL* 3.8 9.0 - - + +
359A ILE* 2.9 36.5 + - + +
361A THR* 1.3 79.3 + - - +
363A VAL* 1.3 52.9 - - + +
365A TYR* 2.6 44.0 + - + +
366A LEU* 2.6 19.4 + - - +
397A TYR* 5.4 7.2 - - + -
398A CYS* 4.0 31.8 - - + +
401A ALA* 4.5 15.5 - - + -
402A VAL* 4.1 21.3 - - + +
414B PHE* 6.2 0.7 - - + -
418B MET* 5.3 3.6 - - + -
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Residues in contact with VAL 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A GLN* 4.3 8.5 - - - +
89A THR* 5.1 2.7 - - - -
92A LEU* 3.4 27.4 - - + -
359A ILE 4.8 2.7 - - - +
360A PHE* 3.1 3.8 + - - +
362A LEU* 1.3 75.2 - - + +
364A PRO* 1.3 69.0 - - + +
366A LEU* 3.4 8.8 + - + +
367A TYR* 3.0 52.8 + - + +
417A LEU* 4.4 10.1 - - + -
414B PHE* 4.0 27.8 - - + -
418B MET* 6.4 1.6 - - + -
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Residues in contact with PRO 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A TYR* 3.9 3.1 - - - +
73A SER* 3.2 20.8 + - - +
89A THR* 3.6 36.3 - - - +
92A LEU* 3.4 9.0 - - + -
93A TYR* 4.0 19.7 - - + -
208A GLU* 4.9 2.2 - - - +
360A PHE 2.9 16.6 - - - +
361A THR* 3.1 13.9 - - - +
363A VAL* 1.3 86.2 - - - +
365A TYR* 1.3 63.5 + - - +
367A TYR* 3.4 1.4 + - + +
368A THR* 2.9 27.0 + - - -
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Residues in contact with TYR 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A LEU* 3.2 21.2 - - + +
60A TYR* 3.4 24.7 - + - -
205A ILE* 4.2 8.5 - - + -
206A GLY* 2.7 32.8 + - - -
207A VAL* 3.4 23.5 + - + -
208A GLU* 3.3 25.5 + - - +
361A THR* 2.9 42.1 + - - -
362A LEU* 2.6 26.0 + - + +
364A PRO* 1.3 73.4 - - - +
366A LEU* 1.3 62.1 + - - +
368A THR* 3.1 4.9 + - - -
369A CYS* 3.1 26.2 + - - -
398A CYS* 3.3 20.0 - - - -
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Residues in contact with LEU 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A LEU 2.6 14.1 + - - +
363A VAL* 3.6 13.7 - - + +
365A TYR* 1.3 72.9 - - - +
367A TYR* 1.3 62.8 + - + +
369A CYS* 3.4 7.1 + - + +
370A ALA* 3.1 22.3 + - - +
395A PHE* 3.8 24.7 - - + +
398A CYS* 3.8 24.3 - - + -
399A ILE* 4.5 4.9 - - + -
418B MET* 3.7 39.7 - - + +
421B THR* 3.4 39.0 - - + +
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Residues in contact with TYR 367 (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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73A SER 5.4 0.9 - - - +
76A TYR* 4.9 0.6 - - - +
77A ALA* 4.2 20.7 + - + -
80A CYS* 4.7 14.6 - - + +
85A LEU* 3.2 32.1 - - + +
88A GLN* 3.2 22.7 + - - -
89A THR* 4.0 18.4 - - - +
363A VAL* 3.0 41.5 + - + +
364A PRO 4.0 3.1 - - - +
366A LEU* 1.3 79.8 - - + +
368A THR* 1.3 65.7 + - - +
369A CYS 3.1 1.1 - - - -
370A ALA* 3.5 4.2 - - + +
371A ALA* 2.9 25.8 + - - +
84B PHE* 4.1 27.1 - + - -
85B LEU* 5.6 0.2 - - - +
88B GLN* 5.4 1.2 + - - -
421B THR* 4.6 11.2 - - + -
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Residues in contact with THR 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A VAL* 3.7 14.4 - - + -
60A TYR* 2.5 62.9 + - + -
63A MET* 4.6 5.0 - - + +
73A SER* 3.6 11.5 + - - -
76A TYR* 4.3 16.6 - - + -
364A PRO 2.9 12.4 + - - -
365A TYR 3.1 9.6 + - - +
367A TYR* 1.3 77.1 - - - +
369A CYS* 1.3 58.9 + - - +
371A ALA* 3.4 2.6 + - - +
372A LEU* 2.9 26.5 + - - +
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Residues in contact with CYS 369 (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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56A LEU* 4.0 13.2 - - - -
59A VAL* 3.9 14.8 - - + -
365A TYR 3.1 17.9 + - - -
366A LEU 3.5 8.5 - - - +
368A THR* 1.3 74.4 - - - +
370A ALA* 1.3 66.7 + - - +
372A LEU* 3.1 10.7 + - - +
373A LEU* 3.6 16.6 - - - +
391A THR* 4.7 2.0 - - - +
394A ALA* 3.4 40.4 - - - -
395A PHE* 3.6 23.8 - - + -
398A CYS* 4.5 4.0 - - - -
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Residues in contact with ALA 370 (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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80A CYS* 4.0 24.0 - - - -
366A LEU 3.1 13.3 + - - +
367A TYR* 3.5 10.8 - - - +
369A CYS* 1.3 75.1 - - - +
371A ALA* 1.3 64.1 + - - +
373A LEU* 3.0 9.7 + - - +
374A LEU* 2.9 30.4 - - + +
395A PHE* 3.8 11.1 - - + -
84B PHE* 6.1 0.2 - - + -
421B THR* 4.6 15.9 - - + +
424B TYR* 6.0 1.8 - - + -
428B TYR* 6.0 0.7 - - - -
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Residues in contact with ALA 371 (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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63A MET* 3.7 8.1 - - + -
76A TYR* 3.4 46.2 - - + +
80A CYS* 4.6 8.7 - - + +
367A TYR 2.9 13.4 + - - +
368A THR 3.7 1.8 - - - +
370A ALA* 1.3 72.0 - - - +
372A LEU* 1.3 53.3 + - - +
373A LEU 2.4 17.6 + - - -
374A LEU* 4.5 3.4 - - - +
375A LEU* 3.1 31.7 + - + +
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Residues in contact with LEU 372 (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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58A MET 4.8 1.3 - - - +
59A VAL* 3.4 43.1 - - + +
62A LYS* 4.0 21.5 - - + +
63A MET* 3.7 27.6 - - + +
66A LEU* 4.5 9.0 - - + -
368A THR 2.9 18.3 + - - +
369A CYS* 3.1 7.7 + - - +
371A ALA* 1.3 72.8 - - - +
373A LEU* 1.3 64.6 + - - +
376A GLY 4.5 3.4 - - - -
379A HIS* 3.5 21.6 + - + +
387A TYR* 5.9 7.6 - - + -
390A VAL* 5.6 1.8 - - + -
391A THR* 3.4 20.8 - - + +
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Residues in contact with LEU 373 (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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369A CYS 3.6 16.6 - - - +
370A ALA 3.0 4.0 + - - +
371A ALA 2.4 7.3 + - - -
372A LEU* 1.3 81.8 - - - +
374A LEU* 1.3 53.7 + - - +
375A LEU 2.4 17.2 + - - -
376A GLY 2.6 23.5 + - - +
377A HIS* 3.2 2.1 + - - +
379A HIS* 3.8 18.3 - - + +
388A LEU* 4.5 13.5 - - + +
391A THR* 3.0 30.5 - - + +
395A PHE* 4.2 6.3 - - + -
428B TYR* 2.9 61.2 - - + +
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Residues in contact with LEU 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ARG 4.7 9.6 - - - +
80A CYS* 5.5 8.1 - - + -
370A ALA* 2.9 40.0 + - + +
371A ALA* 4.8 1.6 - - - +
373A LEU* 1.3 70.2 - - - +
375A LEU* 1.3 74.1 + - - +
377A HIS* 3.3 23.8 + - - +
424B TYR* 4.1 23.1 - - + +
427B ASN 5.1 1.8 - - - +
428B TYR* 4.2 18.6 - - + -
429B ASN* 4.9 3.4 - - - +
430B ARG* 3.0 61.0 - - + +
431B LEU* 4.4 2.5 - - - +
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Residues in contact with LEU 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A MET* 3.4 30.5 - - + -
66A LEU* 5.0 6.8 - - + +
76A TYR* 4.4 1.8 - - - +
79A ARG* 3.3 58.8 - - + +
371A ALA* 3.1 18.6 + - + +
373A LEU 2.4 12.7 + - - -
374A LEU* 1.3 89.2 - - - +
376A GLY* 1.3 55.8 + - - +
377A HIS* 2.8 12.5 + - - +
378A GLY 5.0 0.2 - - - +
380A PHE* 4.1 18.9 - - - -
431B LEU 4.1 8.5 - - - +
434B ASN* 4.2 4.9 - - + -
435B PRO* 4.0 31.9 - - + +
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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