Contacts of the helix formed by residues 330 - 348 (chain C) in PDB entry 3SF4
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 ASN 330 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325C TYR* 3.0 27.4 + - + +
328C LEU* 3.6 26.0 + - - +
329C GLY* 1.3 77.0 + - - +
331C HIS* 1.3 58.3 + - - +
332C ASP* 3.5 4.9 - - - -
333C GLN* 3.1 17.3 + - + +
334C ALA* 2.9 26.0 + - - +
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Residues in contact with HIS 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326C THR* 4.4 16.3 + - + -
329C GLY* 2.8 38.4 + - - -
330C ASN* 1.3 70.7 - - - +
332C ASP* 1.3 59.0 + - - +
334C ALA* 3.1 6.8 + - - +
335C MET* 2.8 31.6 + - + +
364C LEU* 4.0 27.6 - - + +
367C VAL* 4.7 28.4 - - + +
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Residues in contact with ASP 332 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330C ASN* 4.8 1.9 - - - -
331C HIS* 1.3 74.7 + - - +
333C GLN* 1.3 72.7 + - - +
334C ALA 3.2 0.2 - - - -
335C MET* 3.8 16.7 - - + +
336C HIS* 3.1 21.5 + - - +
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Residues in contact with GLN 333 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325C TYR* 3.5 40.3 + - + -
330C ASN* 3.1 16.5 + - + +
332C ASP* 1.3 84.6 + - - +
334C ALA* 1.3 63.6 + - - +
336C HIS* 3.4 15.6 + - - +
337C PHE* 3.3 37.8 + - - -
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Residues in contact with ALA 334 (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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322C GLY* 3.8 7.9 - - - +
325C TYR* 3.7 17.2 - - + +
326C THR* 3.3 28.5 - - - +
330C ASN 2.9 12.4 + - - +
331C HIS* 3.3 12.8 - - - +
333C GLN* 1.3 76.3 - - - +
335C MET* 1.3 59.2 - - - +
337C PHE* 3.0 5.7 + - - +
338C ALA* 2.8 26.5 + - - +
364C LEU* 3.8 10.5 - - + +
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Residues in contact with MET 335 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331C HIS* 2.8 18.4 + - + +
332C ASP* 3.9 17.5 - - + +
334C ALA* 1.3 73.0 - - - +
336C HIS* 1.3 64.5 + - - +
338C ALA* 3.7 1.1 - - - +
339C GLU* 3.0 38.4 + - - +
361C LEU* 3.8 20.0 - - + -
364C LEU* 3.5 36.1 - - + +
365C GLN* 4.4 20.9 - - + +
367C VAL 5.5 1.3 - - - +
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Residues in contact with HIS 336 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332C ASP 3.1 16.1 + - - +
333C GLN* 3.5 18.4 - - - +
335C MET* 1.3 79.8 - - - +
337C PHE* 1.3 90.3 + + - +
339C GLU* 3.6 7.8 + - - +
340C LYS* 3.2 54.6 + - - +
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Residues in contact with PHE 337 (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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299C LEU* 4.6 6.5 - - + -
302C LEU* 3.7 19.5 - - + -
318C CYS* 3.6 41.4 - - - +
321C LEU* 3.6 27.6 - - + -
322C GLY 4.1 7.2 - - - +
325C TYR* 3.4 32.1 - + - -
333C GLN* 3.3 27.8 + - - -
334C ALA 3.0 7.3 + - - +
336C HIS* 1.3 101.5 - + - +
338C ALA* 1.3 60.7 + - - +
339C GLU 3.2 1.3 - - - -
340C LYS* 4.2 4.9 - - + -
341C HIS* 2.9 28.1 + - - +
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Residues in contact with ALA 338 (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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318C CYS 5.2 1.1 - - - -
322C GLY* 5.0 5.1 - - - -
334C ALA 2.8 15.9 + - - +
335C MET* 3.2 5.6 + - - +
337C PHE* 1.3 76.9 - - - +
339C GLU* 1.3 58.7 + - - +
341C HIS* 3.0 11.5 - - - +
342C LEU* 3.0 25.8 + - - +
357C ALA* 4.3 4.8 - - - +
360C ASN* 4.7 15.5 - - + -
361C LEU* 4.3 15.7 - - + +
364C LEU* 3.9 20.0 - - + -
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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 MET* 3.0 37.4 + - - +
336C HIS* 3.7 6.5 - - - +
338C ALA* 1.3 73.5 - - - +
340C LYS* 1.3 65.8 + - + +
341C HIS 3.0 1.3 - - - -
342C LEU* 3.0 4.7 + - - +
343C GLU* 2.9 38.2 + - - +
361C LEU* 3.6 31.5 - - + +
365C GLN* 5.3 3.6 + - - -
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Residues in contact with LYS 340 (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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318C CYS* 3.8 22.2 - - - -
336C HIS* 3.2 43.4 + - + +
337C PHE* 3.4 12.5 + - + +
339C GLU* 1.3 79.9 - - + +
341C HIS* 1.3 61.7 + - - +
343C GLU* 4.1 23.8 + - - +
344C ILE* 2.8 41.6 + - + +
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Residues in contact with HIS 341 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315C GLY* 3.4 18.1 + - - -
318C CYS* 4.2 8.3 - - + -
319C TRP* 3.4 54.0 - + + +
337C PHE 2.9 14.6 + - - +
338C ALA* 3.0 16.4 - - - +
339C GLU 3.0 0.2 - - - -
340C LYS* 1.3 75.6 - - - +
342C LEU* 1.3 60.1 + - - +
344C ILE* 4.0 2.1 - - - +
345C SER* 2.7 47.5 + - - -
353C GLY* 3.8 15.3 + - - -
356C THR* 3.8 6.2 + - - -
357C ALA* 3.4 24.0 - - + -
360C ASN* 4.9 3.6 - - - -
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Residues in contact with LEU 342 (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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338C ALA 3.0 11.8 + - - +
339C GLU* 3.0 8.5 + - - +
341C HIS* 1.3 76.1 - - - +
343C GLU* 1.3 65.6 + - + +
345C SER* 3.7 2.2 - - - -
346C ARG* 3.3 62.0 + - - +
354C GLU* 3.6 32.8 - - + +
357C ALA* 3.6 11.8 - - + +
358C ARG* 4.3 11.9 - - + +
361C LEU* 3.7 25.4 - - + -
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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
----------------------------------------------------------
311C ARG* 5.4 3.4 + - - +
339C GLU* 2.9 31.8 + - + +
340C LYS* 3.7 32.0 + - - +
342C LEU* 1.3 77.8 - - + +
344C ILE* 1.3 70.0 + - + +
346C ARG* 3.0 19.1 + - - +
347C GLU* 3.1 13.1 + - - +
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Residues in contact with ILE 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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311C ARG* 3.2 54.5 - - + +
312C ILE* 5.0 1.8 - - - -
314C GLU* 4.8 4.0 - - + +
315C GLY* 3.7 31.0 - - - +
318C CYS* 5.1 4.9 - - - -
340C LYS* 2.8 40.9 + - + +
341C HIS 4.1 1.6 - - - +
343C GLU* 1.3 84.8 - - + +
345C SER* 1.3 67.4 + - - +
347C GLU* 2.9 19.7 + - - +
348C VAL* 3.1 24.7 + - + +
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Residues in contact with SER 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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315C GLY* 5.9 0.2 - - - -
341C HIS* 2.7 38.9 + - - -
342C LEU 3.7 5.6 - - - -
344C ILE* 1.3 78.4 - - - +
346C ARG* 1.3 59.8 + - - +
348C VAL* 4.2 7.0 - - - -
349C GLY 3.3 2.6 + - - -
350C ASP* 2.9 38.5 + - - +
353C GLY* 3.4 15.9 + - - -
354C GLU* 3.4 26.4 - - - +
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Residues in contact with ARG 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 LEU* 3.3 45.3 + - - +
343C GLU* 3.0 10.7 + - - +
345C SER* 1.3 72.9 - - - +
347C GLU* 1.3 67.5 + - - +
348C VAL 3.0 3.0 + - - -
349C GLY* 3.0 13.4 + - - -
354C GLU* 2.5 39.5 + - + +
358C ARG* 5.8 2.2 - - - +
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Residues in contact with GLU 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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311C ARG* 3.2 49.0 + - - +
343C GLU 3.1 9.3 + - - +
344C ILE* 2.9 11.5 + - - +
346C ARG* 1.3 77.4 - - - +
348C VAL* 1.3 62.1 + - + +
349C GLY 3.6 0.2 - - - -
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Residues in contact with VAL 348 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311C ARG* 4.3 24.5 - - + -
312C ILE* 3.4 36.4 - - + +
344C ILE* 3.1 21.7 + - + +
345C SER* 3.8 8.7 - - - +
347C GLU* 1.3 83.1 - - + +
349C GLY* 1.3 63.0 + - - +
350C ASP* 3.4 16.3 + - + +
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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