Contacts of the helix formed by residues 350 - 367 (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 ASP 350 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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345C SER* 2.9 20.8 + - - +
348C VAL* 3.3 15.6 + - + -
349C GLY* 1.3 73.6 - - - +
351C LYS* 1.3 60.2 + - - +
352C SER* 3.1 10.0 + - - -
353C GLY* 2.5 33.7 + - - -
354C GLU* 3.0 16.9 + - - +
30F ARG* 5.8 1.9 + - - -
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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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349C GLY 2.8 11.8 + - - +
350C ASP* 1.3 71.0 + - - +
352C SER* 1.3 57.4 + - - +
354C GLU* 3.4 15.1 + - - +
355C LEU* 3.0 27.4 + - - +
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Residues in contact with SER 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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350C ASP* 3.1 6.8 + - - -
351C LYS* 1.3 76.3 - - - +
353C GLY* 1.3 60.2 + - - +
355C LEU* 3.3 6.4 + - - +
356C THR* 2.9 44.3 + - - +
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Residues in contact with GLY 353 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319C TRP* 6.4 2.0 - - - -
341C HIS* 3.8 9.1 + - - -
345C SER* 3.4 15.2 + - - -
350C ASP* 2.5 26.7 + - - -
352C SER* 1.3 70.6 - - - +
354C GLU* 1.3 56.4 + - - +
356C THR* 3.3 7.5 + - - -
357C ALA* 2.8 37.2 + - - +
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Residues in contact with GLU 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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342C LEU* 3.6 19.1 - - + +
345C SER* 3.4 15.3 - - - +
346C ARG* 2.5 42.8 + - + +
350C ASP 3.0 12.7 + - - +
351C LYS* 3.6 16.3 - - - +
353C GLY* 1.3 75.6 - - - +
355C LEU* 1.3 58.8 + - - +
358C ARG* 3.1 28.6 + - + +
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Residues in contact with LEU 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 3.0 14.8 + - - +
352C SER* 3.5 11.4 - - - +
353C GLY 3.1 0.2 - - - -
354C GLU* 1.3 75.5 - - - +
356C THR* 1.3 67.6 + - + +
357C ALA 3.3 0.3 + - - -
358C ARG* 3.3 6.9 + - - +
359C LEU* 3.1 21.5 + - - +
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Residues in contact with THR 356 (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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319C TRP* 4.5 14.6 + - + -
341C HIS* 3.8 9.5 + - - -
352C SER* 2.9 24.3 + - - +
353C GLY* 3.3 11.8 + - - -
355C LEU* 1.3 77.8 - - + +
357C ALA* 1.3 63.7 + - - +
359C LEU* 3.5 7.1 + - - +
360C ASN* 2.9 34.1 + - - -
26F ASP* 5.0 10.5 - - + +
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Residues in contact with ALA 357 (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* 4.3 3.6 - - - +
341C HIS* 3.4 27.6 - - + -
342C LEU* 3.6 31.4 - - + +
353C GLY 2.8 19.8 + - - +
354C GLU 3.9 2.7 - - - +
356C THR* 1.3 75.3 + - - +
358C ARG* 1.3 65.6 + - - +
360C ASN* 3.2 7.5 + - - +
361C LEU* 3.0 24.0 + - - +
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Residues in contact with ARG 358 (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* 4.3 16.5 - - + +
346C ARG* 5.8 1.8 - - - +
354C GLU* 3.1 19.5 + - + +
355C LEU* 3.7 5.2 - - - +
357C ALA* 1.3 75.4 - - - +
359C LEU* 1.3 65.1 + - - +
361C LEU* 3.1 17.0 + - - +
362C SER* 3.4 14.7 + - - -
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Residues in contact with LEU 359 (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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355C LEU 3.1 13.0 + - - +
356C THR* 3.6 12.6 - - - +
358C ARG* 1.3 78.5 - - - +
360C ASN* 1.3 64.0 + - - +
362C SER* 3.4 8.0 + - - -
363C ASP* 3.1 23.2 - - - +
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Residues in contact with ASN 360 (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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319C TRP* 4.7 18.6 - - - +
323C ASN* 4.8 11.4 + - - +
338C ALA* 4.7 11.2 - - + +
341C HIS* 4.9 2.6 - - - -
356C THR* 2.9 24.6 + - - +
357C ALA* 3.2 9.2 + - - +
359C LEU* 1.3 79.1 - - - +
361C LEU* 1.3 63.9 + - - +
362C SER 3.4 0.2 + - - -
363C ASP* 3.5 9.2 + - - +
364C LEU* 3.3 30.3 + - + +
26F ASP* 4.8 2.8 + - - -
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Residues in contact with LEU 361 (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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335C MET* 3.8 20.2 - - + -
338C ALA* 4.3 12.3 - - + +
339C GLU* 3.6 39.3 - - + +
342C LEU* 3.7 32.5 - - + -
357C ALA 3.0 11.8 + - - +
358C ARG* 3.1 10.5 + - - +
360C ASN* 1.3 77.0 - - - +
362C SER* 1.3 57.9 + - - +
364C LEU* 3.4 3.2 + - - +
365C GLN* 2.8 55.7 + - + +
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Residues in contact with SER 362 (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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358C ARG 3.4 8.3 + - - -
359C LEU* 3.9 9.2 - - - -
360C ASN 3.3 0.6 - - - -
361C LEU* 1.3 75.7 - - - +
363C ASP* 1.3 70.5 + - - +
365C GLN* 3.1 13.1 + - - +
366C MET* 2.9 27.0 + - - +
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Residues in contact with ASP 363 (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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359C LEU 3.1 19.0 - - - +
360C ASN* 3.5 8.8 + - - +
361C LEU 3.5 0.2 - - - -
362C SER* 1.3 78.8 - - - +
364C LEU* 1.3 62.0 + - + +
366C MET* 2.8 32.4 - - - +
367C VAL* 3.1 14.8 - - + +
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Residues in contact with LEU 364 (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* 6.3 0.2 - - - -
326C THR* 4.1 23.1 - - + +
331C HIS* 4.0 32.1 - - + +
334C ALA* 3.8 13.2 - - + +
335C MET* 3.5 50.7 - - + +
338C ALA* 3.9 13.7 - - + -
360C ASN* 3.3 20.1 + - + +
361C LEU 3.7 3.6 - - - +
362C SER 3.1 0.4 - - - -
363C ASP* 1.3 80.4 - - + +
365C GLN* 1.3 60.0 + - - +
366C MET 3.4 0.2 + - - -
367C VAL* 2.8 28.0 + - + +
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Residues in contact with GLN 365 (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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335C MET* 4.4 19.7 - - + +
339C GLU* 5.3 3.8 + - - -
361C LEU* 2.8 55.5 + - + +
362C SER* 3.7 10.5 + - - +
364C LEU* 1.3 76.2 - - - +
366C MET* 1.3 63.6 + - - +
367C VAL 3.1 6.8 - - - +
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Residues in contact with MET 366 (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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362C SER 2.9 14.0 + - - +
363C ASP* 2.8 35.7 - - - +
365C GLN* 1.3 73.9 - - - +
367C VAL* 1.3 85.8 + - + +
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Residues in contact with VAL 367 (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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331C HIS* 4.7 29.8 - - + +
335C MET* 5.5 1.4 - - - +
363C ASP* 3.1 20.1 + - + +
364C LEU* 2.8 19.1 - - + +
365C GLN 3.1 6.4 - - - +
366C MET* 1.3 104.2 - - + +
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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