Contacts of the helix formed by residues 359 - 379 (chain A) in PDB entry 1L2L
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 GLU 359 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358A GLY* 1.3 68.3 - - - -
360A HIS* 1.3 61.7 + - + +
361A VAL 3.1 2.7 - - - -
362A ARG* 2.7 38.9 + - - +
363A ASP* 2.9 33.7 + - - +
416A ILE* 3.9 18.4 - - + -
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Residues in contact with HIS 360 (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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17A LYS* 4.7 13.3 + - - -
357A LYS 5.8 1.1 - - - +
358A GLY* 3.1 4.4 - - - -
359A GLU* 1.3 81.9 - - + +
361A VAL* 1.3 61.9 + - + +
363A ASP* 3.5 20.0 - - - +
364A ALA* 3.1 24.1 + - - +
453A GLU* 4.1 3.8 - - - +
456A LEU* 3.5 51.9 + - + +
457A HIS* 4.1 25.4 + - + -
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Residues in contact with VAL 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A ARG* 5.9 0.7 - - - +
352A ALA* 4.1 11.2 - - + -
354A THR* 3.8 26.7 - - + +
356A GLU* 4.1 11.4 - - + +
357A LYS 4.8 1.6 - - - -
358A GLY 3.7 16.4 - - - +
359A GLU 3.1 0.2 - - - -
360A HIS* 1.3 79.1 - - + +
362A ARG* 1.3 62.2 + - - +
364A ALA* 3.6 2.8 + - - +
365A LEU* 3.2 23.5 + - + +
423A GLN* 4.0 7.6 - - - +
425A THR* 3.3 27.8 - - + -
453A GLU* 3.6 30.7 - - + +
457A HIS* 5.7 1.1 - - + -
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Residues in contact with ARG 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A TRP* 4.3 11.9 - - - -
10A LEU* 4.3 23.1 - - - +
358A GLY 4.4 0.2 + - - -
359A GLU* 2.7 46.8 + - - +
361A VAL* 1.3 78.7 - - - +
363A ASP* 1.3 69.8 + - - +
365A LEU 3.2 0.7 + - - -
366A LEU* 3.0 33.0 + - + +
413A ARG 4.2 0.8 + - - -
414A ASP* 2.9 47.4 + - - +
416A ILE* 3.4 27.7 - - + +
425A THR* 3.9 15.4 + - - +
426A PHE 5.0 0.4 - - - -
427A ILE* 3.3 28.2 - - + +
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Residues in contact with ASP 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU 5.5 0.3 - - - +
13A LYS* 5.4 0.5 - - - +
14A ALA* 3.7 26.2 + - + +
17A LYS* 3.7 23.6 - - + +
18A VAL* 4.4 6.0 - - + +
359A GLU* 2.9 25.8 + - - +
360A HIS* 3.5 28.8 - - - +
361A VAL 3.4 0.2 - - - -
362A ARG* 1.3 83.6 + - - +
364A ALA* 1.3 56.5 + - - +
366A LEU* 3.3 4.0 + - - +
367A PHE* 2.9 30.1 + - - +
456A LEU* 3.8 12.0 - - + +
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Residues in contact with ALA 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A VAL* 5.1 0.7 - - - -
341A ARG* 5.2 0.9 - - - +
360A HIS 3.1 6.5 + - - +
361A VAL 3.8 4.0 - - - +
363A ASP* 1.3 77.8 - - - +
365A LEU* 1.3 65.9 + - + +
367A PHE* 3.3 3.0 + - - +
368A SER* 3.0 24.3 + - - -
449A ALA* 3.2 32.9 - - + +
452A SER* 3.3 15.3 - - - +
453A GLU* 3.4 26.5 - - + +
456A LEU* 4.8 0.8 - - - +
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Residues in contact with LEU 365 (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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341A ARG* 4.9 5.6 - - - +
343A HIS* 3.7 39.9 - - + +
350A TYR* 3.7 17.6 - - + -
352A ALA* 3.9 13.7 - - + +
361A VAL* 3.2 14.1 + - + +
362A ARG 3.7 0.4 - - - +
364A ALA* 1.3 75.9 - - - +
366A LEU* 1.3 58.7 + - - +
368A SER* 2.7 19.6 + - - -
369A ALA* 2.9 17.3 + - - +
425A THR* 3.5 45.8 - - + +
427A ILE* 3.1 22.7 - - + -
449A ALA* 4.4 4.3 - - + -
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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
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7A TRP* 4.3 7.0 - - + -
10A LEU* 3.5 40.4 - - + +
11A TYR* 3.5 45.1 - - + -
14A ALA* 3.7 13.2 - - + -
362A ARG* 3.0 29.4 + - + +
363A ASP* 3.6 5.6 - - - +
365A LEU* 1.3 76.7 - - - +
367A PHE* 1.3 62.2 + - - +
369A ALA* 3.3 2.6 + - - -
370A LEU* 3.1 27.9 + - - +
427A ILE* 3.2 30.1 - - + -
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Residues in contact with PHE 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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14A ALA* 4.6 3.5 - - - +
15A LEU* 3.9 27.8 - - + +
18A VAL* 3.5 46.9 - - + -
19A GLU 5.2 0.2 - - - -
22A ILE* 4.1 14.6 - - + -
128A TYR* 4.0 33.9 - + - -
363A ASP 2.9 17.4 + - - +
364A ALA 3.7 3.6 - - - +
366A LEU* 1.3 77.4 - - - +
368A SER* 1.3 63.8 - - - +
370A LEU* 3.1 12.4 + - - +
371A ALA* 3.0 19.2 + - + +
384A LEU* 4.7 11.4 - - + -
387A ILE* 4.3 16.2 - - + -
448A SER* 3.9 14.4 - - - -
452A SER* 3.8 12.1 - - - +
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Residues in contact with SER 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A HIS* 3.9 0.7 + - - -
350A TYR* 3.2 15.5 + - - -
364A ALA 3.0 15.0 + - - -
365A LEU* 2.7 21.0 + - - -
367A PHE* 1.3 76.3 - - - +
369A ALA* 1.3 61.7 + - - +
371A ALA* 3.2 3.8 + - - +
372A ALA* 3.0 23.4 + - - +
445A ILE* 3.2 32.9 + - - +
448A SER* 4.1 11.2 - - - -
449A ALA* 3.6 13.9 - - - +
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Residues in contact with ALA 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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11A TYR* 3.5 26.7 - - + +
350A TYR* 3.3 29.8 - - + +
365A LEU 2.9 12.2 + - - +
366A LEU* 3.6 4.5 - - - +
367A PHE 3.2 0.2 - - - -
368A SER* 1.3 77.5 + - - +
370A LEU* 1.3 57.2 + - - +
372A ALA* 3.4 1.9 + - - +
373A ALA* 3.0 29.1 + - - +
427A ILE* 4.8 2.5 - - + -
429A THR* 4.3 12.7 + - - +
430A LYS* 5.2 2.8 - - - +
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Residues in contact with LEU 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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11A TYR* 3.5 32.5 - - + +
15A LEU* 3.6 36.6 - - + +
366A LEU 3.1 19.9 + - - +
367A PHE* 3.1 10.7 + - - +
369A ALA* 1.3 75.4 - - - +
371A ALA* 1.3 59.5 + - - +
373A ALA* 3.4 6.1 + - + +
374A THR* 2.8 33.3 + - - -
387A ILE* 3.4 15.2 - - + +
390A GLY* 3.6 31.9 - - - +
391A LEU* 3.7 16.8 - - + -
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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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128A TYR* 4.0 20.9 - - - +
367A PHE* 3.0 13.9 + - + +
368A SER* 3.2 13.0 + - - +
370A LEU* 1.3 78.1 - - - +
372A ALA* 1.3 55.4 + - - +
374A THR* 3.3 1.4 + - - -
375A LYS* 2.9 25.2 + - - +
381A ILE* 3.5 19.2 - - + +
387A ILE* 3.7 17.9 - - + +
444A THR* 4.5 6.1 - - + -
448A SER* 4.3 7.0 - - - +
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Residues in contact with ALA 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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350A TYR* 3.6 24.7 - - - +
368A SER 3.0 7.8 + - - +
369A ALA 3.6 3.4 - - - +
371A ALA* 1.3 76.3 - - - +
373A ALA* 1.3 57.7 + - - +
375A LYS* 3.2 3.6 + - - +
376A ALA* 2.8 30.8 + - - +
430A LYS* 5.3 1.1 - - + -
440A GLY* 4.1 20.6 + - - +
444A THR* 5.2 1.7 - - - +
445A ILE* 3.9 19.1 - - + -
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Residues in contact with ALA 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 ALA 3.0 17.4 + - - +
370A LEU* 3.7 7.6 - - + +
372A ALA* 1.3 76.0 - - - +
374A THR* 1.3 61.2 + - - +
376A ALA* 3.3 3.7 + - - +
377A MET* 3.1 29.9 + - - +
390A GLY* 4.5 14.4 - - - +
393A VAL* 4.7 5.6 - - + -
430A LYS* 3.5 42.0 - - + +
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Residues in contact with THR 374 (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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370A LEU 2.8 23.8 + - - -
371A ALA 3.5 5.4 - - - -
373A ALA* 1.3 73.8 - - - +
375A LYS* 1.3 60.9 + - - +
376A ALA 3.1 1.6 - - - -
377A MET* 4.2 3.7 - - - +
378A LYS* 2.8 51.9 + - + +
381A ILE* 4.3 9.2 - - + -
386A ASP* 3.7 24.4 + - + +
387A ILE* 3.4 31.7 + - + -
389A GLU* 4.6 6.2 - - + +
390A GLY* 3.8 8.1 + - - +
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Residues in contact with LYS 375 (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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119A ILE* 5.3 6.1 - - - +
371A ALA 2.9 16.1 + - - +
372A ALA* 3.9 5.4 - - - +
374A THR* 1.3 77.9 - - - +
376A ALA* 1.3 55.9 + - - +
379A GLY* 2.7 41.1 + - - +
380A ASN* 3.9 22.9 - - - +
381A ILE* 3.8 18.1 - - + +
440A GLY* 4.7 11.0 - - - -
441A ILE* 4.0 25.7 - - + +
444A THR* 3.6 28.6 + - + +
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Residues in contact with ALA 376 (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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372A ALA 2.8 17.6 + - - +
373A ALA* 3.3 11.4 - - - +
374A THR 3.1 0.4 - - - -
375A LYS* 1.3 80.6 - - - +
377A MET* 1.3 63.5 + - + +
379A GLY* 4.1 2.9 + - - -
430A LYS* 4.9 10.8 - - + -
440A GLY 6.0 1.6 - - - +
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Residues in contact with MET 377 (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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373A ALA 3.1 15.7 + - - +
374A THR* 4.2 2.7 - - - +
376A ALA* 1.3 81.1 - - + +
378A LYS* 1.3 62.9 + - - +
379A GLY 3.6 0.2 + - - -
389A GLU* 5.2 7.9 - - - +
393A VAL* 3.5 35.0 - - + -
430A LYS* 5.6 5.2 - - - -
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Residues in contact with LYS 378 (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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374A THR* 2.8 29.5 + - + +
377A MET* 1.3 76.6 - - + +
379A GLY* 1.3 57.4 + - - +
380A ASN* 3.1 29.8 + - + +
381A ILE* 5.0 0.9 - - - -
382A GLU* 4.9 9.0 - - - -
386A ASP* 3.6 25.8 + - + +
389A GLU* 4.2 24.6 + - - +
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Residues in contact with GLY 379 (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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375A LYS* 2.7 37.1 + - - +
376A ALA 4.6 2.7 - - - -
377A MET 3.3 2.4 - - - -
378A LYS* 1.3 72.7 - - - +
380A ASN* 1.3 63.4 + - - +
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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