Contacts of the helix formed by residues 374 - 392 (chain A) in PDB entry 3ISL
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 ARG 374 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A GLU* 2.7 30.5 + - - -
296A ARG* 5.6 0.2 - - - +
300A HIS* 3.8 13.0 - - - +
371A TYR* 2.9 51.5 + - - +
372A SER 2.9 6.9 + - - -
373A CYS* 1.3 75.1 - - - +
375A LYS* 1.3 65.5 + - - +
376A GLU* 3.5 29.8 + - - +
377A ASN* 3.1 33.1 + - + +
378A VAL* 3.0 21.2 + - - +
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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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300A HIS* 3.2 12.7 - - + -
374A ARG* 1.3 73.1 - - - +
376A GLU* 1.3 78.3 + - + +
378A VAL* 3.3 0.9 + - - +
379A LEU* 2.9 51.8 + - + +
406A LEU* 5.4 2.9 - - - +
409A TYR* 3.2 58.0 + - + -
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Residues in contact with GLU 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A ARG* 3.1 33.1 + - - +
375A LYS* 1.3 92.0 + - + +
377A ASN* 1.3 60.4 + - - +
379A LEU* 3.8 7.8 - - + +
380A PHE* 2.9 30.1 + - - +
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Residues in contact with ASN 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A THR* 3.8 19.6 + - - +
17A MET* 3.5 17.3 - - - +
23A GLU* 2.9 25.3 + - - +
372A SER* 3.4 27.6 - - - +
374A ARG* 3.1 35.7 + - + +
376A GLU* 1.3 76.2 - - - +
378A VAL* 1.3 61.4 + - - +
380A PHE* 4.0 4.5 - - - +
381A VAL* 2.9 34.0 + - - +
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Residues in contact with VAL 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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17A MET* 4.0 15.0 - - + -
300A HIS* 4.0 22.4 - - + +
303A ALA* 4.3 0.9 - - + -
304A LEU* 3.9 29.8 - - + +
368A THR* 4.2 9.0 - - + -
374A ARG 3.0 13.7 + - - +
375A LYS 3.7 2.2 - - - +
377A ASN* 1.3 80.1 - - - +
379A LEU* 1.3 64.5 + - - +
381A VAL* 3.3 18.5 - - - +
382A LEU* 3.3 17.0 + - + +
405A ALA* 4.8 0.7 - - + -
409A TYR* 3.3 33.7 - - + +
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Residues in contact with LEU 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A LYS* 2.9 41.8 + - + +
376A GLU* 3.8 7.2 - - + +
378A VAL* 1.3 77.4 - - - +
380A PHE* 1.3 56.7 + - - +
382A LEU* 3.4 1.8 + - - -
383A ALA* 3.0 28.6 + - - +
402A LEU* 3.7 19.8 - - + +
405A ALA* 3.8 28.0 - - + -
406A LEU* 4.1 28.3 - - + -
409A TYR* 3.9 13.2 - - + -
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Residues in contact with PHE 380 (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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15A THR* 3.4 29.8 - - + -
348A PHE* 3.6 52.7 - + + -
350A ILE* 3.2 16.5 - - + +
376A GLU 2.9 22.1 + - - +
377A ASN* 3.3 5.8 + - - +
379A LEU* 1.3 70.0 - - - +
381A VAL* 1.3 60.8 + - - +
383A ALA* 4.4 10.1 - - + -
384A GLY 2.8 26.7 + - - -
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Residues in contact with VAL 381 (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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15A THR* 5.3 0.8 - - + +
17A MET* 3.9 22.4 - - + -
304A LEU* 3.9 23.8 - - + -
344A LEU* 4.8 2.2 - - + +
350A ILE* 3.8 21.8 - - + +
352A ILE* 3.7 29.4 - - + -
366A ILE* 4.4 11.2 - - + -
377A ASN 2.9 15.6 + - - +
378A VAL* 3.3 14.8 - - - +
380A PHE* 1.3 76.6 - - - +
382A LEU* 1.3 63.0 + - + +
384A GLY 3.9 0.2 - - - -
385A LEU* 2.9 33.7 + - + +
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Residues in contact with LEU 382 (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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303A ALA 4.5 2.0 - - - +
304A LEU* 3.8 15.0 - - + -
307A GLY* 3.8 12.6 - - - +
308A ILE* 3.7 45.1 - - + +
311A MET* 4.7 5.6 - - - +
378A VAL* 3.3 25.9 + - + +
379A LEU* 3.9 3.1 - - - +
380A PHE 3.2 0.6 - - - -
381A VAL* 1.3 79.9 - - + +
383A ALA* 1.3 61.3 + - - +
385A LEU* 4.2 3.3 - - + +
386A GLU* 2.8 31.8 + - - +
401A ALA* 4.5 10.3 - - + +
402A LEU* 4.1 14.1 - - + -
405A ALA* 3.7 31.0 - - + -
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Residues in contact with ALA 383 (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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348A PHE* 5.0 3.1 - - + -
379A LEU 3.0 17.4 + - - +
380A PHE* 3.3 13.0 + - + +
382A LEU* 1.3 78.2 - - - +
384A GLY* 1.3 62.5 + - - +
386A GLU* 3.4 7.0 + - - +
387A ALA* 3.1 23.7 + - - +
402A LEU* 4.1 23.0 - - + +
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Residues in contact with GLY 384 (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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344A LEU* 3.4 16.8 - - - -
348A PHE* 3.9 21.9 - - - -
350A ILE* 3.9 4.7 - - - -
380A PHE 2.8 19.7 + - - -
383A ALA* 1.3 73.1 - - - +
385A LEU* 1.3 57.6 + - - +
387A ALA* 3.3 1.9 + - - +
388A VAL* 2.9 34.8 + - - +
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Residues in contact with LEU 385 (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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308A ILE* 3.9 28.3 - - + -
311A MET* 3.6 11.0 - - + -
313A LEU* 4.2 7.9 - - + -
329A VAL* 5.3 3.1 - - + -
340A VAL* 3.9 24.7 - - + -
344A LEU* 3.7 13.5 - - + +
352A ILE* 4.2 18.4 - - + -
364A TRP* 4.7 9.0 - - + -
366A ILE* 4.3 15.3 - - + -
381A VAL* 2.9 21.2 + - + +
382A LEU* 4.2 2.7 - - - +
384A GLY* 1.3 72.7 - - - +
386A GLU* 1.3 65.5 + - - +
388A VAL* 3.5 1.0 + - - +
389A LEU* 3.0 46.3 + - + +
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Residues in contact with GLU 386 (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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311A MET* 3.4 21.4 - - + +
382A LEU 2.8 20.0 + - - +
383A ALA* 3.6 6.9 - - - +
385A LEU* 1.3 76.5 - - - +
387A ALA* 1.3 58.2 + - - +
389A LEU* 3.2 1.6 + - - -
390A LEU* 2.9 50.3 + - + +
396A ILE* 3.8 10.4 - - + +
397A GLU 4.6 0.3 - - - +
398A ALA 2.0 36.9 - - - +
399A GLY* 3.8 7.7 + - - -
401A ALA* 3.9 16.5 - - + +
402A LEU* 4.8 5.6 + - - +
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Residues in contact with ALA 387 (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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348A PHE* 3.8 23.8 - - + -
383A ALA 3.1 15.3 + - - +
386A GLU* 1.3 77.6 - - - +
388A VAL* 1.3 58.3 + - - +
390A LEU* 3.6 10.6 + - - +
391A ARG* 2.9 27.8 + - - +
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Residues in contact with VAL 388 (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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340A VAL* 3.7 31.4 - - + +
343A MET* 3.8 23.3 - - + -
344A LEU* 3.9 17.0 - - + +
348A PHE* 3.9 21.1 - - + -
384A GLY 2.9 19.6 + - - +
385A LEU 4.1 2.5 - - - +
387A ALA* 1.3 73.2 - - - +
389A LEU* 1.3 65.9 + - - +
391A ARG* 3.1 6.0 + - - +
392A HIS* 2.8 49.9 + - + +
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Residues in contact with LEU 389 (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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311A MET* 3.1 30.5 - - + -
313A LEU* 3.8 20.2 - - + -
332A PRO* 5.1 2.0 - - + -
335A ILE* 4.2 19.7 - - + -
340A VAL* 3.8 25.1 - - + -
364A TRP* 3.8 17.3 - - + -
385A LEU* 3.0 34.1 + - + +
386A GLU 3.8 2.2 - - - +
388A VAL* 1.3 75.7 - - - +
390A LEU* 1.3 57.3 + - - +
392A HIS* 3.0 5.6 + - + +
393A ASN 3.0 9.0 + - - -
394A ALA* 2.5 28.8 + - + +
396A ILE* 4.0 10.8 - - + -
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Residues in contact with LEU 390 (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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386A GLU* 2.9 45.2 + - + +
387A ALA* 3.8 7.6 - - - +
389A LEU* 1.3 75.5 - - - +
391A ARG* 1.4 61.3 + - - +
393A ASN* 3.0 16.5 + - - -
394A ALA* 3.0 23.0 - - + +
396A ILE* 3.8 31.2 - - + +
398A ALA* 5.3 8.3 - - - +
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Residues in contact with ARG 391 (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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343A MET* 3.8 34.8 - - + +
387A ALA 2.9 16.2 + - - +
388A VAL* 3.1 8.9 + - - +
390A LEU* 1.4 74.8 - - - +
392A HIS* 1.3 59.3 + - + +
393A ASN* 3.3 3.5 + - - +
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Residues in contact with HIS 392 (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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334A GLY 5.2 1.9 - - - +
335A ILE* 4.4 19.1 - - + +
336A ASP* 4.5 5.1 + - - +
339A SER* 2.4 46.9 + - - -
340A VAL* 3.7 16.5 - - + +
343A MET* 3.6 25.1 - - + +
388A VAL* 2.8 44.2 + - + +
389A LEU* 3.0 8.0 + - - +
391A ARG* 1.3 77.5 - - - +
393A ASN* 1.3 71.6 + - - +
394A ALA 3.8 0.2 + - - -
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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