Contacts of the helix formed by residues 335 - 355 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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326A GLU* 4.0 17.9 + - - +
328A PHE* 3.2 35.9 - - + -
334C GLY* 1.3 70.0 - - - -
336C GLU* 1.3 70.5 + - - +
338C PHE* 3.0 18.1 + - + +
339C GLU* 3.3 21.9 + - + +
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Residues in contact with GLU 336 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334C GLY* 5.0 2.0 - - - -
335C ARG* 1.3 81.4 - - - +
337C ARG* 1.3 77.0 + - + +
338C PHE 3.2 0.5 + - - -
339C GLU* 3.3 22.9 + - - +
340C MET* 3.4 9.4 + - - +
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Residues in contact with ARG 337 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A ASN* 4.8 5.0 - - - +
348A LEU* 3.7 34.3 + - + +
349A GLU* 3.7 28.0 + - - +
352A ASP* 3.0 34.2 + - - +
332C ILE* 4.1 4.7 - - - -
333C ARG* 3.6 32.8 + - - +
334C GLY* 3.8 4.0 + - - +
335C ARG 3.2 0.2 - - - -
336C GLU* 1.3 85.9 - - + +
338C PHE* 1.3 66.6 + - - +
340C MET* 3.0 26.6 + - + +
341C PHE* 3.2 29.0 + - + -
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Residues in contact with PHE 338 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A PHE* 3.5 34.5 - + + -
329A THR 2.7 38.8 - - - -
330A LEU* 3.7 16.2 - - + -
332C ILE* 3.4 32.3 - - + +
334C GLY 3.1 15.4 + - - +
335C ARG* 3.0 11.8 + - + +
337C ARG* 1.3 76.9 - - - +
339C GLU* 1.3 71.8 + - + +
340C MET 2.9 0.9 + - - -
341C PHE* 3.0 13.0 + - - +
342C ARG* 3.0 33.3 + - + +
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Residues in contact with GLU 339 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335C ARG* 3.7 29.1 + - + +
336C GLU* 3.3 14.3 + - - +
338C PHE* 1.3 85.2 - - + +
340C MET* 1.3 62.1 + - - +
342C ARG* 3.5 26.3 + - - +
343C GLU* 3.0 23.4 + - - +
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Residues in contact with MET 340 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A LEU* 3.9 28.5 - - + -
340B MET* 4.6 30.3 - - + +
343B GLU* 6.4 2.0 - - - -
344B LEU* 4.9 12.8 - - + -
336C GLU 3.4 5.8 + - - +
337C ARG* 3.0 18.5 + - + +
338C PHE 2.9 0.2 + - - -
339C GLU* 1.3 80.0 - - - +
341C PHE* 1.3 81.5 + - + +
343C GLU* 3.1 20.4 + - + +
344C LEU* 3.3 19.6 + - + +
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Residues in contact with PHE 341 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A LEU* 4.3 6.1 - - + -
341A PHE* 4.1 24.3 - + - -
344A LEU* 3.9 14.4 - - + -
345A ASN* 3.5 42.6 - - + -
348A LEU* 3.8 28.7 - - + -
330C LEU* 4.8 3.8 - - + -
332C ILE* 3.3 38.8 - - + -
337C ARG* 3.2 30.0 + - - -
338C PHE 3.0 2.7 + - - +
340C MET* 1.3 87.1 - - + +
342C ARG* 1.3 66.5 + - - +
344C LEU* 2.9 22.7 + - + +
345C ASN* 3.0 10.7 + - - +
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Residues in contact with ARG 342 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A LEU* 4.1 23.9 - - + +
332C ILE* 5.1 0.4 - - - +
338C PHE* 3.0 33.6 + - + +
339C GLU* 3.8 27.4 + - - +
341C PHE* 1.3 78.1 - - - +
343C GLU* 1.3 64.6 + - - +
345C ASN* 3.1 11.3 + - + +
346C GLU* 3.0 35.3 + - - +
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Residues in contact with GLU 343 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339C GLU 3.0 14.1 + - - +
340C MET* 3.2 14.4 - - + +
341C PHE 3.0 0.2 - - - -
342C ARG* 1.3 79.4 - - - +
344C LEU* 1.3 66.2 + - + +
345C ASN 3.2 0.2 + - - -
346C GLU* 3.2 6.8 + - - +
347C ALA* 3.0 19.8 + - - +
348D LEU* 3.8 22.4 - - + +
351D LYS* 3.2 29.2 + - - +
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Residues in contact with LEU 344 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341A PHE* 4.0 14.1 - - + -
344A LEU* 4.4 16.6 - - + -
340B MET* 5.0 9.2 - - + -
344B LEU* 4.3 22.9 - - + -
340C MET* 3.3 22.6 + - + +
341C PHE* 2.9 13.4 + - + +
343C GLU* 1.3 77.7 - - + +
345C ASN* 1.3 64.4 + - - +
347C ALA* 3.1 13.3 + - + +
348C LEU* 3.2 18.4 + - - +
344D LEU* 4.2 26.9 - - + -
348D LEU* 4.1 31.0 - - + -
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Residues in contact with ASN 345 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330A LEU* 3.8 30.3 - - + +
331A GLN 3.9 18.7 + - - +
332A ILE* 4.4 12.3 - - - +
333A ARG 5.3 0.2 - - - +
337A ARG* 4.8 4.9 + - - +
341A PHE* 3.6 24.0 - - + -
341C PHE 3.0 5.4 + - - +
342C ARG* 3.1 12.7 + - - +
344C LEU* 1.3 79.6 - - - +
346C GLU* 1.3 65.9 + - - +
348C LEU* 4.1 1.9 - - - +
349C GLU* 3.1 44.8 + - - +
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Residues in contact with GLU 346 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342C ARG* 3.0 24.7 + - - +
343C GLU* 3.8 5.6 - - - +
345C ASN* 1.3 83.1 - - - +
347C ALA* 1.3 63.1 + - - +
349C GLU* 3.7 8.8 - - + +
350C LEU* 2.9 24.3 + - - +
351D LYS* 3.8 26.1 + - + +
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Residues in contact with ALA 347 (chain C).
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 3.0 13.8 + - - +
344C LEU* 3.1 16.5 + - + +
346C GLU* 1.3 76.9 - - - +
348C LEU* 1.3 64.9 + - - +
350C LEU* 3.0 19.3 + - - +
351C LYS 3.3 4.0 + - - -
344D LEU* 5.8 0.2 - - + -
347D ALA* 3.3 41.5 - - + +
348D LEU* 3.9 13.5 - - + +
350D LEU* 5.0 0.2 - - - +
351D LYS* 3.9 10.5 - - - +
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Residues in contact with LEU 348 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337A ARG* 3.8 22.4 - - + +
340A MET* 3.9 19.3 - - + -
341A PHE* 3.8 33.0 - - + -
344C LEU 3.2 6.3 + - - +
345C ASN 4.2 1.8 - - - +
347C ALA* 1.3 75.4 - - - +
349C GLU* 1.3 64.8 + - - +
351C LYS* 3.0 17.2 + - + +
352C ASP* 3.1 17.8 + - - +
343D GLU* 3.7 35.9 - - + +
344D LEU* 4.1 17.0 - - + -
347D ALA* 4.1 13.2 - - + -
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Residues in contact with GLU 349 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331A GLN 5.5 1.0 - - - +
333A ARG* 5.2 11.1 + - - +
337A ARG* 3.8 25.4 + - - +
345C ASN* 3.1 37.7 + - - +
346C GLU* 3.7 10.5 - - + +
348C LEU* 1.3 76.8 - - - +
350C LEU* 1.3 63.6 + - - +
352C ASP* 3.4 5.5 + - - +
353C ALA* 3.0 22.7 + - - +
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Residues in contact with LEU 350 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346C GLU 2.9 14.0 + - - +
347C ALA* 3.2 11.2 - - - +
349C GLU* 1.3 78.1 - - - +
351C LYS* 1.3 63.1 + - - +
353C ALA* 3.2 18.8 + - + +
354C GLN* 3.3 11.7 + - - +
350D LEU* 3.5 13.9 - - + +
351D LYS* 3.4 46.9 - - + +
354D GLN* 3.3 38.8 - - + +
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Residues in contact with LYS 351 (chain C).
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 2.9 + - - +
348C LEU* 3.0 14.0 + - - +
350C LEU* 1.3 79.3 - - - +
352C ASP* 1.3 66.7 + - - +
354C GLN* 3.0 14.8 + - - +
355C ALA* 3.1 11.2 + - + +
343D GLU* 3.2 36.0 + - - +
346D GLU* 3.6 30.3 + - + +
347D ALA* 3.8 29.2 - - - +
350D LEU* 3.4 24.1 - - + +
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Residues in contact with ASP 352 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337A ARG* 3.0 28.2 + - - +
348C LEU* 3.1 9.3 + - - +
349C GLU* 3.8 9.6 - - - +
351C LYS* 1.3 81.0 - - - +
353C ALA* 1.3 62.6 + - - +
355C ALA* 3.1 22.8 + - - +
356C GLY 3.9 2.4 + - - -
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Residues in contact with ALA 353 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349C GLU 3.0 13.5 + - - +
350C LEU* 3.3 20.6 - - + +
351C LYS 3.0 0.4 + - - -
352C ASP* 1.3 80.7 - - - +
354C GLN* 1.3 61.6 + - + +
355C ALA 3.1 0.7 + - - -
356C GLY* 3.6 8.8 + - - -
357C LYS* 4.5 3.5 + - - +
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Residues in contact with GLN 354 (chain C).
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 8.3 + - - +
351C LYS* 3.0 8.5 + - - +
353C ALA* 1.3 76.2 - - + +
355C ALA* 1.3 64.4 + - - +
356C GLY 3.1 2.9 - - - -
357C LYS* 3.2 37.8 + - + +
350D LEU* 3.2 40.2 - - + +
354D GLN* 3.4 27.2 + - - +
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Residues in contact with ALA 355 (chain C).
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 3.1 10.2 + - - +
352C ASP* 3.2 22.0 - - - +
353C ALA 3.1 0.8 - - - -
354C GLN* 1.3 79.9 - - - +
356C GLY* 1.3 59.8 + - - +
357C LYS 3.2 4.6 + - - +
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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