Contacts of the helix formed by residues 335 - 355 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326B GLU* 4.0 22.2 + - - +
328B PHE* 3.2 30.4 - - + -
334D GLY* 1.3 69.2 - - - -
336D GLU* 1.3 69.4 + - - +
338D PHE* 3.0 18.4 + - + +
339D GLU* 3.3 21.6 + - + +
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Residues in contact with GLU 336 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334D GLY* 5.0 1.8 - - - -
335D ARG* 1.3 81.4 - - - +
337D ARG* 1.3 75.8 + - + +
338D PHE 3.2 0.3 + - - -
339D GLU* 3.3 22.6 + - - +
340D MET* 3.4 9.5 + - - +
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Residues in contact with ARG 337 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B ASN* 4.9 3.8 - - - +
348B LEU* 3.8 30.5 + - + +
349B GLU* 3.9 25.8 + - - +
352B ASP* 2.9 35.4 + - - +
332D ILE* 4.1 5.6 - - - -
333D ARG* 3.6 36.8 + - - +
334D GLY* 3.8 4.9 + - - +
335D ARG 3.2 0.6 - - - -
336D GLU* 1.3 85.9 - - + +
338D PHE* 1.3 65.1 + - - +
340D MET* 3.0 29.5 + - + +
341D PHE* 3.2 28.5 + - + -
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Residues in contact with PHE 338 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B PHE* 3.4 35.2 - + + -
329B THR 2.7 39.7 - - - -
330B LEU* 3.9 15.7 - - + -
332D ILE* 3.4 31.4 - - + +
334D GLY 3.1 15.2 + - - +
335D ARG* 3.0 12.0 + - + +
337D ARG* 1.3 76.9 - - - +
339D GLU* 1.3 72.4 + - + +
340D MET 2.9 1.2 + - - -
341D PHE* 3.0 12.0 + - - +
342D ARG* 3.0 33.5 + - + +
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Residues in contact with GLU 339 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335D ARG* 3.7 29.1 + - + +
336D GLU* 3.3 14.3 + - - +
338D PHE* 1.3 85.7 - - + +
340D MET* 1.3 62.1 + - - +
342D ARG* 3.6 27.6 + - - +
343D GLU* 3.0 23.6 + - - +
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Residues in contact with MET 340 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340A MET* 4.4 32.5 - - + +
343A GLU* 6.4 2.5 - - - -
344A LEU* 5.0 11.0 - - + -
348B LEU* 4.0 26.7 - - + -
336D GLU 3.4 6.0 + - - +
337D ARG* 3.0 19.1 + - + +
339D GLU* 1.3 79.3 - - - +
341D PHE* 1.3 82.4 + - + +
343D GLU* 3.1 20.4 + - + +
344D LEU* 3.3 20.8 + - + +
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Residues in contact with PHE 341 (chain D).
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* 6.0 0.2 - - + -
330B LEU* 4.3 6.5 - - + -
341B PHE* 4.3 22.0 - + - -
344B LEU* 4.1 13.5 - - + -
345B ASN* 3.7 44.0 - - + -
348B LEU* 3.7 29.6 - - + -
330D LEU* 4.8 4.7 - - + -
332D ILE* 3.3 39.3 - - + -
337D ARG* 3.2 30.0 + - - -
338D PHE 3.0 2.9 + - - +
340D MET* 1.3 88.2 - - + +
342D ARG* 1.3 65.4 + - - +
344D LEU* 2.9 23.6 + - + +
345D ASN* 3.0 10.0 + - - +
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Residues in contact with ARG 342 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B LEU* 4.1 21.6 - - + +
332D ILE* 5.1 0.2 - - - +
338D PHE* 3.0 34.7 + - + +
339D GLU* 3.8 27.6 + - - +
341D PHE* 1.3 77.8 - - - +
343D GLU* 1.3 63.1 + - - +
345D ASN* 3.1 11.7 + - + +
346D GLU* 3.0 35.7 + - - +
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Residues in contact with GLU 343 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348C LEU* 3.7 24.6 - - + +
351C LYS* 3.2 28.9 + - - +
339D GLU 3.0 14.7 + - - +
340D MET* 3.2 13.7 - - + +
341D PHE 3.0 0.4 - - - -
342D ARG* 1.3 78.8 - - - +
344D LEU* 1.3 66.4 + - + +
345D ASN 3.2 0.3 + - - -
346D GLU* 3.2 6.8 + - - +
347D ALA* 3.0 19.6 + - - +
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Residues in contact with LEU 344 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340A MET* 4.9 9.6 - - + -
344A LEU* 4.3 23.3 - - + -
341B PHE* 4.0 14.8 - - + -
344B LEU* 4.6 11.2 - - + -
344C LEU* 4.2 31.4 - - + -
348C LEU* 4.1 32.3 - - + -
340D MET* 3.3 22.4 + - + +
341D PHE* 2.9 14.1 + - + +
343D GLU* 1.3 78.4 - - + +
345D ASN* 1.3 64.7 + - - +
347D ALA* 3.1 12.8 + - + +
348D LEU* 3.2 17.8 + - - +
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Residues in contact with ASN 345 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330B LEU* 3.8 31.0 - - + +
331B GLN 3.8 19.5 + - - +
332B ILE* 4.4 11.7 - - - +
333B ARG 5.3 0.2 - - - +
337B ARG* 4.9 3.8 - - - +
341B PHE* 3.6 22.9 - - + -
341D PHE 3.0 5.8 + - - +
342D ARG* 3.1 12.5 + - - +
344D LEU* 1.3 79.2 - - - +
346D GLU* 1.3 65.2 + - - +
348D LEU* 3.5 2.1 + - - +
349D GLU* 3.1 46.0 + - - +
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Residues in contact with GLU 346 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351C LYS* 3.6 27.1 + - + +
342D ARG* 3.0 24.4 + - - +
343D GLU* 3.8 5.4 - - - +
345D ASN* 1.3 81.5 - - - +
347D ALA* 1.3 64.1 + - - +
349D GLU* 3.7 9.3 - - + +
350D LEU* 2.9 24.8 + - - +
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Residues in contact with ALA 347 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347C ALA* 3.3 41.6 - - + +
348C LEU* 3.9 12.8 - - + +
351C LYS* 3.8 10.0 - - - +
343D GLU 3.0 13.8 + - - +
344D LEU* 3.1 16.5 + - + +
346D GLU* 1.3 77.0 - - - +
348D LEU* 1.3 64.5 + - + +
350D LEU* 3.0 19.4 + - - +
351D LYS* 3.3 5.2 + - - +
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Residues in contact with LEU 348 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B ARG* 3.8 23.8 - - + +
340B MET* 4.0 17.9 - - + -
341B PHE* 3.7 34.3 - - + -
343C GLU* 3.8 35.2 - - + +
344C LEU* 4.1 14.4 - - + -
347C ALA* 4.1 14.1 - - + -
344D LEU 3.2 8.1 + - - +
345D ASN 4.2 2.2 - - - +
347D ALA* 1.3 75.2 - - - +
349D GLU* 1.3 64.7 + - - +
351D LYS* 3.0 17.3 + - + +
352D ASP* 3.1 17.7 + - - +
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Residues in contact with GLU 349 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331B GLN 5.4 1.4 - - - +
333B ARG* 5.2 12.9 + - - +
337B ARG* 3.9 25.0 + - - +
345D ASN* 3.1 37.8 + - - +
346D GLU* 3.7 11.0 - - + +
348D LEU* 1.3 76.8 - - - +
350D LEU* 1.3 63.5 + - - +
352D ASP* 3.4 5.7 + - - +
353D ALA* 3.0 22.3 + - - +
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Residues in contact with LEU 350 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350C LEU* 3.5 12.2 - - + +
351C LYS* 3.4 46.4 - - + +
354C GLN* 3.2 40.2 - - + +
346D GLU 2.9 13.6 + - - +
347D ALA* 3.2 11.4 - - - +
349D GLU* 1.3 78.0 - - - +
351D LYS* 1.3 63.6 + - - +
353D ALA* 3.2 18.1 + - + +
354D GLN* 3.3 11.9 + - - +
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Residues in contact with LYS 351 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343C GLU* 3.2 36.3 + - - +
346C GLU* 3.8 27.1 + - + +
347C ALA* 3.9 29.6 - - - +
350C LEU* 3.4 24.8 - - + +
347D ALA 3.3 2.9 + - - +
348D LEU* 3.0 15.1 + - + +
350D LEU* 1.3 80.4 - - - +
352D ASP* 1.3 65.2 + - - +
354D GLN* 3.0 15.3 + - - +
355D ALA* 3.1 11.4 + - + +
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Residues in contact with ASP 352 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337B ARG* 2.8 29.3 + - - +
348D LEU* 3.1 8.2 + - - +
349D GLU* 3.8 9.2 - - - +
351D LYS* 1.3 81.8 - - - +
353D ALA* 1.3 63.5 + - - +
355D ALA* 3.1 23.5 + - - +
356D GLY 3.9 2.3 + - - -
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Residues in contact with ALA 353 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349D GLU 3.0 14.1 + - - +
350D LEU* 3.3 20.4 - - + +
351D LYS 3.0 0.4 - - - -
352D ASP* 1.3 79.7 - - - +
354D GLN* 1.3 61.7 + - + +
355D ALA 3.3 0.5 + - - -
356D GLY* 3.6 8.7 + - - -
357D LYS* 4.5 3.6 + - - +
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Residues in contact with GLN 354 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350C LEU* 3.3 39.4 - - + +
354C GLN* 3.4 27.5 + - - +
350D LEU* 3.3 7.7 + - - +
351D LYS* 3.0 8.3 + - + +
353D ALA* 1.3 77.8 - - + +
355D ALA* 1.3 62.8 + - - +
356D GLY 3.1 2.9 - - - -
357D LYS* 3.2 39.2 + - + +
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Residues in contact with ALA 355 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351D LYS* 3.1 9.9 + - + +
352D ASP* 3.2 20.9 - - - +
353D ALA 3.1 0.8 - - - -
354D GLN* 1.3 80.7 - - - +
356D GLY* 1.3 59.0 + - - +
357D LYS 3.2 4.2 + - - +
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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
------------------------------------------------------------
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