Contacts of the helix formed by residues 335 - 355 (chain B) in PDB entry 1SAF
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 335 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334B GLY* 1.3 69.4 - - - -
336B GLU* 1.3 71.2 + - - +
338B PHE* 3.0 18.3 + - + +
339B GLU* 3.3 22.0 + - + +
326D GLU* 4.0 23.0 + - - +
328D PHE* 3.2 30.0 - - + -
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Residues in contact with GLU 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B GLY* 5.0 2.2 - - - -
335B ARG* 1.3 80.4 - - - +
337B ARG* 1.3 76.7 + - + +
338B PHE 3.2 0.7 + - - -
339B GLU* 3.3 23.2 + - - +
340B MET* 3.4 9.4 + - - +
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Residues in contact with ARG 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B ILE* 4.1 5.6 - - - -
333B ARG* 3.6 33.4 + - - +
334B GLY* 3.8 4.2 + - - +
335B ARG 3.2 0.2 - - - -
336B GLU* 1.3 85.7 - - + +
338B PHE* 1.3 65.2 + - - +
340B MET* 3.0 27.3 + - + +
341B PHE* 3.2 29.6 + - + -
345D ASN* 4.9 4.2 - - - +
348D LEU* 3.7 35.0 + - + +
349D GLU* 3.9 25.6 + - - +
352D ASP* 2.8 35.8 + - - +
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Residues in contact with PHE 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B ILE* 3.4 32.1 - - + +
334B GLY 3.1 15.4 + - - +
335B ARG* 3.0 11.8 + - + +
337B ARG* 1.3 76.0 - - - +
339B GLU* 1.3 73.0 + - + +
340B MET 2.9 1.0 + - - -
341B PHE* 3.0 12.6 + - - +
342B ARG* 3.0 32.9 + - + +
328D PHE* 3.4 34.1 - + + -
329D THR 2.7 39.9 - - - -
330D LEU* 3.9 16.2 - - + -
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Residues in contact with GLU 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B ARG* 3.7 29.3 + - + +
336B GLU* 3.3 14.6 + - - +
338B PHE* 1.3 84.4 - - + +
340B MET* 1.3 62.8 + - - +
342B ARG* 3.8 27.8 + - - +
343B GLU* 3.0 23.0 + - - +
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Residues in contact with MET 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B GLU 3.4 5.6 + - - +
337B ARG* 3.0 19.1 + - + +
339B GLU* 1.3 79.7 - - - +
341B PHE* 1.3 82.2 + - + +
343B GLU* 3.1 20.3 + - + +
344B LEU* 3.3 20.4 + - + +
340C MET* 4.6 29.6 - - - +
343C GLU* 6.4 2.0 - - - -
344C LEU* 5.0 11.0 - - + -
348D LEU* 4.0 27.6 - - + -
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Residues in contact with PHE 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B LEU* 4.8 4.7 - - + -
332B ILE* 3.3 39.0 - - + -
337B ARG* 3.2 30.2 + - - -
338B PHE 3.0 2.7 + - - +
340B MET* 1.3 89.9 - - + +
342B ARG* 1.3 66.9 + - - +
344B LEU* 2.9 23.0 + - + +
345B ASN* 3.0 10.6 + - - +
344C LEU* 6.3 0.2 - - + -
330D LEU* 4.4 5.4 - - + -
341D PHE* 4.3 22.4 - + - -
344D LEU* 4.0 14.1 - - + -
345D ASN* 3.6 41.5 - - + -
348D LEU* 3.7 30.1 - - + -
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Residues in contact with ARG 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B ILE* 5.1 0.2 - - - +
338B PHE* 3.0 34.8 + - + +
339B GLU* 3.8 28.2 + - - +
341B PHE* 1.3 79.1 - - - +
343B GLU* 1.3 63.8 + - - +
345B ASN* 3.1 10.7 + - + +
346B GLU* 3.0 36.3 + - - +
330D LEU* 4.1 21.9 - - + +
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Residues in contact with GLU 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A LEU* 3.9 22.1 - - + +
351A LYS* 3.1 29.9 + - - +
339B GLU 3.0 14.0 + - - +
340B MET* 3.2 14.4 - - + +
341B PHE 3.0 0.4 - - - -
342B ARG* 1.3 79.6 - - - +
344B LEU* 1.3 66.9 + - + +
345B ASN 3.2 0.2 + - - -
346B GLU* 3.2 7.3 + - - +
347B ALA* 3.0 19.9 + - - +
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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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344A LEU* 4.3 26.5 - - + +
348A LEU* 4.1 31.9 - - + -
340B MET* 3.3 22.9 + - + +
341B PHE* 2.9 13.9 + - + +
343B GLU* 1.3 78.4 - - + +
345B ASN* 1.3 65.6 + - - +
347B ALA* 3.1 13.2 + - + +
348B LEU* 3.2 18.5 + - - +
340C MET* 4.9 9.9 - - + -
341C PHE* 6.1 0.2 - - + -
344C LEU* 4.3 23.3 - - + -
341D PHE* 4.1 14.1 - - + -
344D LEU* 4.6 15.0 - - + -
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Residues in contact with ASN 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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341B PHE 3.0 5.4 + - - +
342B ARG* 3.1 12.7 + - - +
344B LEU* 1.3 78.6 - - - +
346B GLU* 1.3 65.3 + - - +
348B LEU* 3.5 1.7 + - - +
349B GLU* 3.1 46.3 + - - +
330D LEU* 3.8 33.6 - - + +
331D GLN 3.9 19.1 + - - +
332D ILE* 4.4 9.3 - - - +
333D ARG 5.3 0.6 - - - +
337D ARG* 4.9 3.9 + - - +
341D PHE* 3.7 23.6 - - + -
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Residues in contact with GLU 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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351A LYS* 3.9 22.8 + - + +
342B ARG* 3.0 23.4 + - - +
343B GLU* 3.8 9.1 - - - +
345B ASN* 1.3 83.3 - - - +
347B ALA* 1.3 64.0 + - - +
349B GLU* 3.7 8.8 - - + +
350B LEU* 2.9 24.6 + - - +
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Residues in contact with ALA 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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347A ALA* 3.3 40.8 - - + +
348A LEU* 4.0 12.1 - - + +
351A LYS* 3.9 10.9 - - - +
343B GLU 3.0 13.2 + - - +
344B LEU* 3.1 16.8 + - + +
346B GLU* 1.3 77.3 - - - +
348B LEU* 1.3 65.3 + - - +
350B LEU* 3.0 19.1 + - - +
351B LYS* 3.3 5.5 + - - +
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Residues in contact with LEU 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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343A GLU* 3.7 36.3 - - + +
344A LEU* 4.1 15.7 - - + -
347A ALA* 4.1 14.4 - - + -
344B LEU 3.2 8.0 + - - +
345B ASN 4.2 2.2 - - - +
347B ALA* 1.3 74.6 - - - +
349B GLU* 1.3 63.5 + - - +
351B LYS* 3.0 17.1 + - + +
352B ASP* 3.1 18.2 + - - +
337D ARG* 3.9 22.4 - - + +
340D MET* 4.0 17.9 - - + -
341D PHE* 3.7 34.1 - - + -
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Residues in contact with GLU 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B ASN* 3.1 37.6 + - - +
346B GLU* 3.7 10.8 - - + +
348B LEU* 1.3 77.0 - - - +
350B LEU* 1.3 63.1 + - - +
352B ASP* 3.4 5.7 + - - +
353B ALA* 3.0 22.3 + - - +
331D GLN 5.4 1.6 - - - +
333D ARG* 5.3 11.0 + - - +
337D ARG* 3.9 25.5 + - - +
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Residues in contact with LEU 350 (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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350A LEU* 3.6 12.3 - - + +
351A LYS* 3.5 45.5 - - + +
354A GLN* 3.2 39.7 - - + +
346B GLU 2.9 14.7 + - - +
347B ALA* 3.0 12.3 + - - +
349B GLU* 1.3 77.0 - - - +
351B LYS* 1.3 63.6 + - - +
353B ALA* 3.2 19.2 + - + +
354B GLN* 3.3 12.0 + - - +
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Residues in contact with LYS 351 (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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343A GLU* 3.3 36.0 + - - +
346A GLU* 3.7 28.6 + - + +
347A ALA* 3.8 28.7 - - - +
350A LEU* 3.4 25.3 - - + +
347B ALA 3.3 2.9 + - - +
348B LEU* 3.0 13.8 + - + +
350B LEU* 1.3 80.1 - - - +
352B ASP* 1.3 66.6 + - - +
354B GLN* 3.0 15.1 + - - +
355B ALA* 3.1 10.7 + - - +
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Residues in contact with ASP 352 (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 LEU* 3.1 9.1 + - - +
349B GLU* 3.8 10.3 - - - +
351B LYS* 1.3 82.4 - - - +
353B ALA* 1.3 62.0 + - - +
355B ALA* 3.1 24.0 + - - +
356B GLY 3.9 2.8 + - - -
337D ARG* 2.9 29.2 + - - +
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Residues in contact with ALA 353 (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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349B GLU 3.0 14.1 + - - +
350B LEU* 3.3 20.2 - - + +
351B LYS 3.0 0.2 - - - -
352B ASP* 1.3 79.7 - - - +
354B GLN* 1.3 61.7 + - + +
355B ALA 3.1 0.7 + - - -
356B GLY* 3.6 8.7 + - - -
357B LYS* 4.5 3.6 + - - +
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Residues in contact with GLN 354 (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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350A LEU* 3.3 38.6 - - + +
354A GLN* 3.3 27.6 + - - +
350B LEU* 3.3 7.9 + - - +
351B LYS* 3.0 8.7 + - - +
353B ALA* 1.3 77.8 - - + +
355B ALA* 1.3 64.0 + - - +
356B GLY 3.1 2.9 - - - -
357B LYS* 3.2 38.5 + - + +
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Residues in contact with ALA 355 (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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351B LYS 3.1 10.3 + - - +
352B ASP* 3.2 22.0 - - - +
353B ALA 3.1 1.2 - - - -
354B GLN* 1.3 79.9 - - - +
356B GLY* 1.3 59.1 + - - +
357B LYS 3.5 3.8 + - - +
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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