Contacts of the helix formed by residues 358 - 372 (chain A) in PDB entry 3SPC
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 SER 358 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209A LEU* 4.5 0.9 - - - -
281A PHE 3.6 2.6 + - - -
282A GLY* 3.5 17.9 + - - -
283A ILE 3.3 33.2 - - - -
284A SER* 3.5 8.8 - - - -
323A TRP* 4.7 0.7 - - - -
357A CYS* 1.3 78.5 - - - +
359A ALA* 1.3 60.1 + - - +
360A LYS* 3.5 5.7 + - - +
361A ASP* 3.1 30.2 + - - -
362A LEU* 2.9 26.2 + - - +
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Residues in contact with ALA 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A LEU* 3.9 18.9 - - + +
274A ILE* 3.5 45.5 - - + +
280A LEU 5.2 0.2 + - - -
281A PHE* 3.5 12.1 + - + +
283A ILE 4.5 1.4 + - - -
358A SER* 1.3 73.8 - - - +
360A LYS* 1.3 57.8 + - - +
362A LEU* 3.1 11.0 + - + +
363A VAL* 2.9 33.5 + - + +
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Residues in contact with LYS 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A PHE* 3.0 53.9 + - + +
282A GLY* 4.4 8.3 - - - -
358A SER* 3.2 5.1 - - - +
359A ALA* 1.3 73.8 - - - +
361A ASP* 1.3 63.9 + - - +
363A VAL* 3.4 1.2 + - - +
364A GLU* 2.9 62.9 + - + +
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Residues in contact with ASP 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A SER* 5.1 2.9 - - - -
357A CYS* 3.7 19.8 - - + +
358A SER* 3.1 31.2 + - - +
360A LYS* 1.3 77.4 - - - +
362A LEU* 1.3 60.6 + - - +
364A GLU* 4.4 11.9 - - - +
365A ASN* 2.8 46.2 + - - +
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Residues in contact with LEU 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A MET* 4.2 30.1 - - + -
209A LEU* 4.4 21.3 - - + +
355A PRO* 4.3 18.4 - - + -
357A CYS* 4.1 19.0 - - - -
358A SER 2.9 8.7 + - - +
359A ALA* 3.2 11.7 - - + +
361A ASP* 1.3 78.3 - - - +
363A VAL* 1.3 63.3 + - + +
365A ASN* 3.9 5.8 - - + +
366A LYS* 3.4 35.0 + - + +
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Residues in contact with VAL 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A ASN* 6.3 0.2 - - - -
276A GLU* 6.1 3.6 - - + +
281A PHE* 4.3 19.7 - - + -
359A ALA* 2.9 20.5 + - + +
360A LYS* 3.8 4.7 - - - +
362A LEU* 1.3 76.8 - - + +
364A GLU* 1.3 67.9 + - + +
366A LYS* 3.0 30.7 + - + +
367A PHE* 3.3 34.6 + - + -
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Residues in contact with GLU 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360A LYS* 2.9 55.6 + - + +
361A ASP* 3.9 11.9 - - - +
363A VAL* 1.3 80.8 - - + +
365A ASN* 1.3 59.8 + - - +
367A PHE* 3.4 12.1 + - + +
368A LEU* 3.0 26.7 + - - +
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Residues in contact with ASN 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357A CYS* 4.6 9.3 - - - +
361A ASP* 2.8 37.3 + - - +
362A LEU* 3.9 6.9 - - + +
363A VAL 3.1 0.2 - - - -
364A GLU* 1.3 79.1 - - - +
366A LYS* 1.3 60.4 + - - +
368A LEU* 3.1 13.8 + - - +
369A LEU* 2.8 31.2 + - - +
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Residues in contact with LYS 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A GLY 4.7 11.7 + - - -
362A LEU* 3.4 29.2 - - + +
363A VAL* 3.0 15.3 + - + +
365A ASN* 1.3 78.3 - - + +
367A PHE* 1.3 65.8 + - + +
369A LEU* 2.6 34.0 - - - +
370A SER* 3.3 5.2 + - - -
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Residues in contact with PHE 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363A VAL* 3.3 36.8 + - + -
364A GLU* 3.8 9.9 - - + +
365A ASN 3.3 0.4 - - - -
366A LYS* 1.3 83.5 - - + +
368A LEU* 1.3 58.0 + - - +
370A SER* 3.8 9.1 + - - -
371A ASN* 2.9 36.5 + - - +
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Residues in contact with LEU 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364A GLU 3.0 16.5 + - - +
365A ASN* 3.1 15.7 + - - +
367A PHE* 1.3 78.6 - - - +
369A LEU* 1.3 61.3 + - + +
370A SER 3.4 3.1 + - - -
371A ASN* 4.2 3.8 + - - +
372A SER* 3.1 24.2 + - - +
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Residues in contact with LEU 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365A ASN 2.8 16.8 + - - +
366A LYS* 2.6 19.3 - - - +
368A LEU* 1.3 76.1 - - + +
370A SER* 1.3 53.9 + - - +
372A SER* 4.4 14.8 - - - +
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Residues in contact with SER 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366A LYS 3.6 9.4 - - - -
367A PHE* 4.0 9.2 - - - -
368A LEU 3.3 0.8 - - - -
369A LEU* 1.3 75.8 - - - +
371A ASN* 1.3 73.0 + - - +
372A SER 3.0 19.8 + - - +
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Residues in contact with ASN 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367A PHE* 2.9 25.6 + - - +
368A LEU* 4.2 4.7 + - - +
370A SER* 1.3 82.7 + - - +
372A SER* 1.3 56.7 + - - +
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Residues in contact with SER 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A LEU* 3.1 26.0 + - - +
369A LEU* 4.4 13.2 - - - +
370A SER* 3.0 15.5 + - - +
371A ASN* 1.3 80.4 - - - +
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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