Contacts of the helix formed by residues 336 - 349 (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 ASP 336 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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334B GLY 4.2 1.4 + - - -
335B ILE* 1.3 70.3 - - - +
337B GLY* 1.3 62.8 + - - +
338B GLU* 2.9 23.3 + - - +
339B SER* 3.5 22.8 + - - -
340B VAL* 3.1 29.3 + - - +
392B HIS* 4.4 5.6 + - - +
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Residues in contact with GLY 337 (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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331B ILE* 4.2 14.2 - - - +
335B ILE* 3.5 14.7 + - - -
336B ASP* 1.3 73.5 + - - +
338B GLU* 1.3 63.4 + - - +
339B SER 3.3 0.2 - - - -
340B VAL 3.5 0.4 + - - -
341B ARG* 2.9 19.6 + - - +
361B GLY* 6.3 0.6 - - - -
364B TRP* 2.9 34.3 + - - -
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Residues in contact with GLU 338 (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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331B ILE* 5.7 2.1 - - - +
336B ASP* 2.9 13.3 + - - +
337B GLY* 1.3 76.3 - - - +
339B SER* 1.3 60.7 + - - +
341B ARG* 3.2 19.6 + - - +
342B ASP* 2.9 43.4 + - - +
354B SER* 2.6 36.9 + - - -
355B SER 5.2 0.9 - - - +
356B PHE* 3.7 15.7 - - + -
361B GLY* 5.3 7.8 + - - -
364B TRP* 5.8 0.2 - - - -
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Residues in contact with SER 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B ASP* 3.3 28.2 + - - -
337B GLY 3.3 0.4 - - - -
338B GLU* 1.3 76.6 - - - +
340B VAL* 1.3 60.2 + - - +
342B ASP* 3.9 6.4 - - - +
343B MET* 3.0 33.3 + - - +
392B HIS* 2.7 27.3 - - - -
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Residues in contact with VAL 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B ILE* 3.9 8.5 - - + -
336B ASP 3.1 17.4 + - - +
337B GLY 3.6 7.9 - - - +
339B SER* 1.3 75.1 - - - +
341B ARG* 1.3 64.2 + - - +
344B LEU* 3.1 28.0 + - + +
364B TRP* 3.8 20.0 - - + +
385B LEU* 4.0 20.6 - - + -
388B VAL* 3.5 19.4 - - + +
389B LEU* 3.7 23.8 - - + -
392B HIS* 3.8 23.6 - - + +
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Residues in contact with ARG 341 (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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40A PHE* 5.0 21.8 + - - +
337B GLY 2.9 17.9 + - - +
338B GLU* 3.2 21.6 + - - +
339B SER 3.4 0.2 - - - -
340B VAL* 1.3 78.8 - - - +
342B ASP* 1.3 67.8 + - - +
344B LEU* 3.5 9.6 + - - +
345B LEU* 3.1 32.7 + - + +
350B ILE 4.6 0.7 - - - +
351B GLU* 5.1 9.2 + - + +
352B ILE* 2.9 38.7 + - + +
353B ALA* 4.0 1.8 - - - +
354B SER* 2.6 35.9 + - - +
356B PHE* 3.5 22.2 - - - -
364B TRP* 4.6 3.6 - - + +
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Residues in contact with ASP 342 (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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338B GLU* 2.9 32.1 + - - +
339B SER* 4.0 6.0 - - - +
340B VAL 3.2 0.2 - - - -
341B ARG* 1.3 91.0 + - - +
343B MET* 1.3 60.8 + - - +
345B LEU* 3.4 5.4 + - - +
346B ALA* 2.8 32.1 + - - +
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Residues in contact with MET 343 (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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339B SER* 3.0 19.3 + - - +
342B ASP* 1.3 74.1 - - - +
344B LEU* 1.3 59.8 + - - +
346B ALA* 4.3 5.4 - - - +
347B GLN* 2.8 55.9 + - + +
348B PHE* 4.3 0.3 - - - -
388B VAL* 3.9 25.6 - - + -
391B ARG* 3.8 39.0 - - + +
392B HIS* 3.8 23.6 - - + +
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Residues in contact with LEU 344 (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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340B VAL* 3.1 23.1 + - + +
341B ARG* 3.6 6.1 - - - +
343B MET* 1.3 75.9 - - - +
345B LEU* 1.3 57.8 - - - +
348B PHE* 2.9 31.1 + - + +
349B GLY 3.1 5.4 + - - -
350B ILE* 3.3 35.8 + - + +
352B ILE* 3.7 31.9 - - + -
381B VAL* 5.7 0.7 - - + +
384B GLY* 3.3 40.2 - - - +
385B LEU* 3.5 21.5 - - + +
388B VAL* 3.9 9.8 - - + +
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Residues in contact with LEU 345 (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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40A PHE 5.0 1.8 - - - +
41A ASP* 3.9 16.2 - - + +
42A PRO* 3.7 31.6 - - + -
14B ARG* 3.6 38.8 + - - +
341B ARG* 3.1 20.9 + - + +
342B ASP* 3.9 4.9 - - - +
344B LEU* 1.3 79.8 - - - +
346B ALA* 1.3 59.7 + - - +
349B GLY* 2.9 32.8 + - - -
350B ILE 3.2 19.7 + - - +
351B GLU* 4.1 18.6 - - + +
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Residues in contact with ALA 346 (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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14B ARG* 5.7 1.9 + - - +
342B ASP* 2.8 21.9 + - + +
343B MET* 4.3 2.5 - - - +
345B LEU* 1.3 74.8 - - - +
347B GLN* 1.3 76.9 + - - +
349B GLY 4.9 0.3 + - - -
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Residues in contact with GLN 347 (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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343B MET* 2.8 38.2 + - + +
346B ALA* 1.3 92.5 + - - +
348B PHE* 1.3 75.5 + - + +
349B GLY 3.7 0.4 - - - -
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Residues in contact with PHE 348 (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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13B LEU 5.6 0.3 - - - +
15B THR* 4.8 0.5 + - - -
344B LEU* 2.9 22.4 + - + +
347B GLN* 1.3 88.7 - - + +
349B GLY* 1.3 60.3 + - - +
350B ILE* 2.9 21.4 + - + -
380B PHE* 3.6 43.3 - + + -
383B ALA* 5.0 2.5 - - + -
384B GLY* 4.0 14.4 - - - -
387B ALA* 3.6 24.2 - - + -
388B VAL* 3.6 30.5 - - + -
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Residues in contact with GLY 349 (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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13B LEU 4.9 4.0 - - - -
14B ARG* 3.4 29.2 - - - +
15B THR 2.8 30.6 + - - +
345B LEU* 2.9 24.2 + - - -
346B ALA 4.9 0.2 + - - -
347B GLN 3.7 1.2 - - - -
348B PHE* 1.3 77.5 - - - +
350B ILE* 1.3 56.5 + - - +
351B GLU 3.7 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
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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