Contacts of the helix formed by residues 401 - 409 (chain A) in PDB entry 3SM9
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 401 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A GLN* 4.3 5.6 - - - +
382A MET* 3.5 13.6 - - + +
386A LEU* 6.2 0.7 - - + -
396A ALA 5.3 1.0 + - - -
399A ILE 3.5 5.6 + - - +
400A LEU* 1.3 71.8 - - - +
402A GLY* 1.3 61.2 + - - +
403A LYS* 3.1 22.2 + - - +
404A LYS* 3.3 43.0 + - + +
405A LEU* 3.1 18.7 + - - +
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Residues in contact with GLY 402 (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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140A GLN* 3.2 26.7 + - - +
142A PRO* 3.7 8.1 - - - +
161A TYR* 3.6 15.0 - - - -
400A LEU* 3.3 12.9 + - - -
401A ASP* 1.3 70.8 + - - +
403A LYS* 1.3 58.4 + - - +
405A LEU* 3.7 8.2 - - - +
406A TYR* 3.0 24.6 + - - +
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Residues in contact with LYS 403 (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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140A GLN* 4.0 15.6 + - - +
161A TYR* 3.3 28.3 + - + +
401A ASP* 3.1 12.0 + - - +
402A GLY* 1.3 76.2 - - - +
404A LYS* 1.4 59.1 + - + +
406A TYR* 4.0 0.5 - - - +
407A LYS* 3.1 56.9 + - + +
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Residues in contact with LYS 404 (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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382A MET* 4.1 11.7 - - + -
386A LEU* 5.5 14.8 - - + +
401A ASP* 3.3 35.2 + - + +
403A LYS* 1.4 75.8 - - + +
405A LEU* 1.4 61.0 + - - +
408A ASP* 2.8 46.5 + - - +
409A TYR* 3.3 17.3 - - + -
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Residues in contact with LEU 405 (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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118A ALA 3.5 25.1 - - - +
142A PRO* 3.8 14.6 - - + -
375A MET* 4.6 9.9 - - - -
378A ALA* 4.0 27.1 - - + +
379A LEU* 3.7 33.4 - - + -
382A MET* 3.8 18.0 - - - +
400A LEU* 3.9 11.0 - - + -
401A ASP 3.1 14.0 + - - +
402A GLY* 3.7 9.2 - - - +
403A LYS 3.5 0.2 - - - -
404A LYS* 1.4 75.7 - - - +
406A TYR* 1.3 52.5 + - - +
409A TYR* 3.4 10.5 + - + +
410A LEU* 2.7 35.4 + - + +
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Residues in contact with TYR 406 (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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142A PRO* 4.3 7.6 - - + -
159A TYR 4.4 3.1 + - - -
160A ASP* 3.2 26.9 + - - -
161A TYR* 3.6 38.8 - + + -
162A PHE 2.7 28.3 + - - -
163A ALA* 4.2 6.5 - - + -
402A GLY 3.0 17.3 + - - +
403A LYS 4.0 2.2 - - - +
405A LEU* 1.3 77.1 - - - +
407A LYS* 1.3 74.6 + - + +
410A LEU* 3.6 17.2 - - + +
411A LEU* 3.0 69.0 + - + +
433A THR 5.1 0.3 + - - -
434A PHE 4.0 9.2 + - - -
435A GLY* 4.2 0.2 - - - -
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Residues in contact with LYS 407 (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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160A ASP 5.6 0.2 - - - +
161A TYR* 6.5 1.1 - - + -
403A LYS* 3.1 47.6 + - + +
406A TYR* 1.3 93.8 - - + +
408A ASP* 1.3 72.5 + - - +
411A LEU* 3.9 18.2 - - + +
412A LYS* 3.8 12.5 - - - +
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Residues in contact with ASP 408 (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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381A LYS* 5.2 2.6 - - - +
404A LYS* 2.8 39.2 + - - +
407A LYS* 1.3 85.4 - - - +
409A TYR* 1.3 81.2 + - + +
412A LYS* 3.4 24.7 - - + +
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Residues in contact with TYR 409 (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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378A ALA* 3.6 21.1 - - + +
381A LYS* 3.7 33.7 - - + +
382A MET* 3.7 50.0 - - + -
385A THR* 3.4 30.1 - - + +
386A LEU* 4.4 9.6 - - + +
404A LYS* 3.3 26.2 - - + -
405A LEU* 3.4 10.6 + - + +
407A LYS 3.6 0.2 - - - -
408A ASP* 1.3 95.0 - - + +
410A LEU* 1.4 66.3 + - - +
411A LEU 3.4 1.1 - - - -
412A LYS* 3.0 13.9 + - - +
413A ILE* 3.1 15.5 + - - +
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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