Contacts of the helix formed by residues 399 - 413 (chain A) in PDB entry 1SNX
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 399 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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398A MET* 1.3 86.9 - - - +
400A GLU* 1.3 65.1 + - - +
401A GLU* 3.8 13.6 + - - -
402A ASP* 3.1 28.1 + - - +
403A PHE* 3.2 16.6 + - - +
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Residues in contact with GLU 400 (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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399A SER* 1.3 74.2 - - - +
401A GLU* 1.3 53.8 + - - +
403A PHE* 3.3 10.5 - - - -
404A ILE* 2.7 48.3 + - + +
428A GLN* 4.5 16.3 + - - +
431A ILE* 4.7 18.7 - - + +
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Residues in contact with GLU 401 (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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399A SER* 3.8 15.7 + - - -
400A GLU* 1.3 77.0 - - - +
402A ASP* 1.3 82.6 + - - +
404A ILE* 2.6 29.6 + - + +
405A GLU* 2.8 13.5 + - - +
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Residues in contact with ASP 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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398A MET* 2.7 34.8 - - + +
399A SER* 3.1 26.9 + - - -
401A GLU* 1.3 87.2 - - + +
403A PHE* 1.3 56.7 + - - +
405A GLU* 3.0 29.6 - - - +
406A GLU* 3.7 4.2 + - - +
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Residues in contact with PHE 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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393A ILE* 3.9 28.9 - - + -
398A MET* 3.0 38.8 - - + +
399A SER 3.2 6.7 + - - +
400A GLU* 3.3 13.9 - - - -
401A GLU 3.2 0.6 - - - -
402A ASP* 1.3 75.7 - - - +
404A ILE* 1.3 74.8 + - + +
405A GLU 3.2 0.7 - - - -
406A GLU* 3.9 3.7 + - - +
407A ALA* 3.3 20.5 + - + +
424A VAL* 3.9 13.9 - - + -
426A LEU* 3.3 31.2 - - + -
431A ILE* 3.3 32.5 - - + -
432A CYS 4.8 3.4 - - - -
433A LEU* 4.6 14.1 - - + -
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Residues in contact with ILE 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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400A GLU* 2.7 36.1 + - + +
401A GLU* 2.6 22.2 + - + +
403A PHE* 1.3 86.7 - - + +
405A GLU* 1.3 64.0 + - - +
407A ALA* 3.2 6.1 + - - +
408A GLU* 2.9 42.0 + - + +
426A LEU* 4.9 16.4 - - + -
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Residues in contact with GLU 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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401A GLU 2.8 8.3 + - - +
402A ASP* 3.0 18.6 - - - +
404A ILE* 1.3 74.4 - - - +
406A GLU* 1.3 58.8 + - - +
408A GLU* 2.6 43.3 + - - +
409A VAL* 3.3 4.7 + - + +
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Residues in contact with GLU 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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374A PHE* 6.1 0.7 - - - -
398A MET* 5.7 10.4 - - + +
402A ASP 3.7 5.4 + - - +
403A PHE* 4.4 7.2 - - - +
404A ILE 3.7 0.4 - - - -
405A GLU* 1.3 82.2 - - + +
407A ALA* 1.3 61.9 + - - +
409A VAL* 3.2 11.6 + - + +
410A MET* 3.1 44.8 + - + +
501A PHE 3.6 6.9 - - - +
502A GLY* 2.7 40.8 - - - +
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Residues in contact with ALA 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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403A PHE* 3.3 21.0 + - + +
404A ILE* 3.2 12.5 + - - +
405A GLU 2.9 0.8 + - - -
406A GLU* 1.3 77.7 - - - +
408A GLU* 1.3 64.2 + - + +
410A MET* 3.2 23.1 + - - +
411A MET* 3.4 21.5 + - + +
421A LEU* 5.1 1.8 - - + +
424A VAL* 5.1 7.6 - - + -
426A LEU* 5.9 1.1 - - + -
433A LEU* 4.4 23.3 - - + -
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Residues in contact with GLU 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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404A ILE* 2.9 40.6 + - + +
405A GLU* 2.6 22.7 + - - +
407A ALA* 1.3 72.3 - - - +
409A VAL* 1.3 56.6 + - - +
411A MET* 3.7 28.1 + - + +
412A LYS* 3.7 10.0 + - - +
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Residues in contact with VAL 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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405A GLU 3.3 3.9 + - - +
406A GLU* 3.2 17.8 + - + +
408A GLU* 1.3 75.9 - - - +
410A MET* 1.3 72.9 - - + +
411A MET 3.1 2.0 - - - -
412A LYS* 3.1 33.6 + - + +
413A LEU* 3.5 23.2 + - + +
478A VAL* 5.6 11.2 - - + -
502A GLY* 5.4 8.1 - - - +
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Residues in contact with MET 410 (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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406A GLU* 3.1 54.8 + - + +
407A ALA 3.2 7.4 + - - +
409A VAL* 1.3 82.9 - - + +
411A MET* 1.3 58.0 + - - +
413A LEU* 3.2 24.8 + - - +
421A LEU* 4.5 17.2 - - + +
433A LEU* 4.0 19.7 - - + -
435A PHE* 4.2 24.9 - - + -
500A ASP* 5.8 2.0 - - - -
501A PHE* 4.0 46.1 - - + +
502A GLY* 5.1 1.8 - - - -
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Residues in contact with MET 411 (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 VAL* 4.1 35.9 - - - +
358A ILE* 5.5 7.0 - - + -
407A ALA* 3.5 11.7 - - + +
408A GLU* 3.8 30.5 - - + +
409A VAL 3.1 0.4 - - - -
410A MET* 1.3 76.6 - - - +
412A LYS* 1.3 62.9 + - - +
413A LEU 4.4 2.3 - - - +
414A SER* 5.7 1.7 - - - -
421A LEU* 4.8 13.9 - - + -
424A VAL* 5.1 12.8 - - + -
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Residues in contact with LYS 412 (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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408A GLU 3.7 4.8 + - - +
409A VAL* 3.1 30.4 + - + +
411A MET* 1.3 83.2 - - - +
413A LEU* 1.3 73.4 + - + +
414A SER* 3.9 2.9 + - - -
472A TYR* 4.1 3.5 + - - -
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Residues in contact with LEU 413 (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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409A VAL* 3.5 24.3 + - + +
410A MET* 3.2 17.3 + - - +
411A MET 4.4 1.6 - - - -
412A LYS* 1.3 92.0 - - + +
414A SER* 1.3 64.0 + - - +
418A LEU* 4.7 5.4 - - + +
472A TYR* 3.2 20.6 - - + +
473A LEU* 3.1 27.8 - - + -
476A ALA* 3.8 21.3 - - + +
478A VAL* 4.1 21.8 - - + -
501A PHE* 4.5 13.4 - - + -
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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