Contacts of the helix formed by residues 374 - 392 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B GLU* 3.0 27.7 + - - -
296B ARG* 5.6 0.2 - - - +
300B HIS* 3.8 13.6 - - - +
371B TYR* 2.8 54.3 + - - +
372B SER 3.1 2.4 + - - -
373B CYS* 1.3 73.9 - - - +
375B LYS* 1.3 66.9 + - - +
376B GLU* 3.7 26.2 + - - +
377B ASN* 3.1 44.6 + - + +
378B VAL* 3.2 14.8 + - - +
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Residues in contact with LYS 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B HIS* 6.0 1.3 - - - -
300B HIS* 3.4 10.8 - - + -
374B ARG* 1.3 73.5 - - - +
376B GLU* 1.3 75.8 + - + +
378B VAL* 3.4 1.7 + - - +
379B LEU* 3.1 35.9 + - + +
406B LEU* 6.4 0.2 - - + -
409B TYR* 3.6 64.5 + - + +
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Residues in contact with GLU 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B ARG* 3.3 30.2 - - - +
375B LYS* 1.3 86.8 + - + +
377B ASN* 1.3 61.1 + - - +
379B LEU* 3.7 7.3 + - + +
380B PHE* 3.0 30.3 + - - +
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Residues in contact with ASN 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B THR* 3.6 20.4 - - - +
17B MET* 3.5 18.8 - - - +
23B GLU* 2.9 22.1 + - - +
372B SER* 3.3 25.9 - - - +
374B ARG* 3.1 42.5 + - + +
376B GLU* 1.3 79.0 + - - +
378B VAL* 1.3 54.5 + - - +
380B PHE* 3.3 4.2 + - - +
381B VAL* 2.7 37.2 + - - +
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Residues in contact with VAL 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B MET* 4.2 12.3 - - + -
300B HIS* 4.1 20.6 - - + +
303B ALA 4.2 1.3 - - - -
304B LEU* 3.8 30.7 - - + +
368B THR* 4.4 7.6 - - + -
374B ARG 3.2 14.0 + - - +
375B LYS 3.4 1.5 + - - +
377B ASN* 1.3 72.4 - - - +
379B LEU* 1.3 67.4 + - - +
381B VAL* 3.4 9.3 - - - +
382B LEU* 3.1 34.0 + - + +
405B ALA* 4.7 0.4 - - + -
409B TYR* 3.4 35.0 - - + +
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Residues in contact with LEU 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B LYS* 3.1 38.4 + - + +
376B GLU* 3.9 6.7 - - + +
378B VAL* 1.3 78.8 - - - +
380B PHE* 1.4 56.5 + - - +
382B LEU* 3.3 1.6 + - - -
383B ALA* 3.0 27.0 + - - +
402B LEU* 3.5 31.2 - - + +
405B ALA* 3.9 22.2 - - + -
406B LEU* 4.1 28.5 - - + -
409B TYR* 4.0 12.3 - - + -
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Residues in contact with PHE 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B THR* 3.2 34.3 - - + -
348B PHE* 3.6 49.1 - + + -
350B ILE* 3.3 11.0 - - + +
376B GLU 3.0 20.0 + - - +
377B ASN* 3.9 5.4 - - - +
379B LEU* 1.4 73.3 - - - +
381B VAL* 1.3 58.6 + - - +
383B ALA* 3.3 7.5 + - + +
384B GLY 2.8 28.4 + - - -
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Residues in contact with VAL 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B THR* 5.4 0.4 - - - +
17B MET* 4.0 22.0 - - + -
304B LEU* 3.8 23.6 - - + -
344B LEU* 5.7 0.9 - - + -
350B ILE* 3.7 28.0 - - + +
352B ILE* 3.9 21.5 - - + -
366B ILE* 4.3 11.9 - - + -
377B ASN 2.7 20.5 + - - +
378B VAL* 3.4 15.0 - - - +
380B PHE* 1.3 75.2 - - - +
382B LEU* 1.3 58.4 + - - +
385B LEU* 3.0 31.4 + - + +
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Residues in contact with LEU 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B ALA 4.5 2.2 - - - +
304B LEU* 4.0 12.3 - - + +
307B GLY* 3.7 11.7 - - - -
308B ILE* 3.6 46.7 - - + +
311B MET* 3.5 13.6 - - + +
378B VAL* 3.1 28.6 + - + +
379B LEU 3.7 2.9 - - - +
381B VAL* 1.3 74.3 - - - +
383B ALA* 1.3 62.6 + - - +
385B LEU* 4.6 1.1 - - - -
386B GLU* 2.8 30.8 + - - +
401B ALA* 4.5 3.7 - - + +
402B LEU* 4.1 14.8 - - + -
405B ALA* 3.6 30.7 - - + -
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Residues in contact with ALA 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B PHE* 5.1 2.5 - - + -
379B LEU 3.0 13.6 + - - +
380B PHE* 3.8 11.0 - - + +
382B LEU* 1.3 77.3 - - - +
384B GLY* 1.3 63.2 + - - +
386B GLU* 3.3 6.7 + - - +
387B ALA* 3.0 25.9 + - - +
402B LEU* 3.6 27.9 - - + +
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Residues in contact with GLY 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B LEU* 3.3 22.4 - - - +
348B PHE* 4.0 16.2 - - - -
350B ILE* 3.8 9.0 - - - -
380B PHE* 2.8 17.0 + - - -
383B ALA* 1.3 76.0 - - - +
385B LEU* 1.3 55.7 + - - +
387B ALA* 3.3 3.8 + - - +
388B VAL* 3.0 27.2 + - - +
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Residues in contact with LEU 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B ILE* 4.0 27.6 - - + -
311B MET* 4.4 4.5 - - + -
313B LEU* 4.3 15.0 - - + -
329B VAL* 5.1 4.9 - - + -
340B VAL* 4.0 23.6 - - + -
344B LEU* 3.5 18.9 - - + +
352B ILE* 4.5 9.2 - - + -
364B TRP* 4.8 9.9 - - + -
366B ILE* 4.2 15.0 - - + -
381B VAL* 3.0 20.6 + - + +
382B LEU* 4.1 2.7 - - - +
384B GLY* 1.3 70.3 - - - +
386B GLU* 1.3 67.7 + - - +
388B VAL* 3.4 0.8 + - - -
389B LEU* 2.9 44.8 + - + +
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Residues in contact with GLU 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B MET* 3.9 19.8 - - + +
382B LEU 2.8 23.9 + - - +
383B ALA* 3.6 7.3 - - - +
385B LEU* 1.3 74.5 - - - +
387B ALA* 1.3 64.2 + - - +
389B LEU* 3.7 0.9 - - - -
390B LEU* 2.9 39.2 + - + +
396B ILE* 3.8 13.3 - - + +
397B GLU 3.8 4.3 - - - +
398B ALA* 3.5 10.0 - - - +
399B GLY* 2.9 34.2 + - - -
400B LYS 4.2 0.2 + - - -
401B ALA* 4.1 16.0 + - + +
402B LEU* 5.6 6.0 - - - +
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Residues in contact with ALA 387 (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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348B PHE* 3.6 22.9 - - + -
383B ALA 3.0 17.0 + - - +
384B GLY 3.6 4.0 - - - +
386B GLU* 1.3 77.8 + - - +
388B VAL* 1.3 58.6 + - - +
390B LEU* 3.5 10.6 + - - +
391B ARG* 3.1 28.6 + - - +
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Residues in contact with VAL 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B VAL* 3.5 45.3 - - + +
343B MET* 3.9 24.9 - - + -
344B LEU* 3.9 14.8 - - + +
348B PHE* 3.6 23.8 - - + -
384B GLY 3.0 19.5 + - - +
385B LEU 4.1 2.5 - - - +
387B ALA* 1.3 73.3 - - - +
389B LEU* 1.3 56.9 + - - +
391B ARG* 3.4 6.5 + - - +
392B HIS* 2.6 46.0 + - + +
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Residues in contact with LEU 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B MET* 4.3 4.9 - - - -
313B LEU* 3.7 35.0 - - + -
332B PRO* 5.3 1.6 - - + -
335B ILE* 4.6 9.4 - - + -
340B VAL* 3.7 26.2 - - + -
364B TRP* 3.9 18.6 - - + -
385B LEU* 2.9 37.0 + - + +
388B VAL* 1.3 75.2 - - - +
390B LEU* 1.3 54.3 + - - +
392B HIS* 3.1 11.3 + - + +
393B ASN 3.2 0.2 + - - -
394B ALA* 2.8 45.4 + - + +
396B ILE* 3.6 16.2 - - + -
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Residues in contact with LEU 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B GLU* 2.9 39.5 + - + +
387B ALA* 3.8 8.5 - - - +
389B LEU* 1.3 74.0 - - - +
391B ARG* 1.3 58.7 + - - +
393B ASN* 3.1 21.8 + - - +
394B ALA 4.6 8.7 - - - +
396B ILE* 3.8 31.4 - - + +
398B ALA* 3.9 23.6 - - + -
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Residues in contact with ARG 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B MET* 3.8 34.1 - - + +
387B ALA 3.1 18.2 + - - +
388B VAL 3.5 7.4 - - - +
389B LEU 3.3 0.2 - - - -
390B LEU* 1.3 77.0 - - - +
392B HIS* 1.3 58.9 + - - +
393B ASN* 3.3 6.4 + - - +
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Residues in contact with HIS 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B GLY 5.5 1.0 - - - +
335B ILE* 4.4 18.9 - - + +
336B ASP* 4.4 7.3 + - - +
339B SER* 2.7 44.8 + - - -
340B VAL* 3.7 15.9 - - + +
343B MET* 3.8 21.2 - - + +
388B VAL* 2.6 48.8 + - + +
389B LEU* 3.1 7.5 + - - +
391B ARG* 1.3 77.5 - - - +
393B ASN* 1.3 69.2 + - - +
394B ALA* 3.2 1.9 + - - +
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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