Contacts of the helix formed by residues 442 - 449 (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 CYS 442 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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441A GLY* 1.3 74.5 - - - -
443A LEU* 1.3 69.1 + - - +
444A SER* 2.6 11.3 + - - +
445A ASP* 2.9 45.2 + - - +
446A TYR* 3.1 8.1 + - - -
485A ALA 4.4 1.1 - - - +
486A ARG* 4.4 17.0 - - - +
488A CYS 3.4 11.4 - - - +
489A LEU* 3.3 14.8 - - + +
490A VAL* 4.3 1.8 - - - -
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Residues in contact with LEU 443 (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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442A CYS* 1.3 70.3 - - - +
444A SER* 1.3 68.7 + - - +
446A TYR* 4.2 5.4 - - + -
447A LEU* 2.7 54.7 + - + +
462A MET* 4.5 14.4 - - + -
466A VAL* 5.0 4.3 - - + -
485A ALA* 3.6 12.8 - - - +
488A CYS* 3.4 19.8 + - + -
489A LEU 4.9 0.2 - - - +
490A VAL* 3.6 28.0 - - + +
496A ILE* 4.8 16.4 - - + -
547A LEU* 4.0 15.3 - - + -
551A VAL* 3.7 27.1 - - + -
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Residues in contact with SER 444 (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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442A CYS* 2.6 11.0 + - - -
443A LEU* 1.3 83.2 - - - +
445A ASP* 1.3 56.8 + - - -
447A LEU* 2.6 26.8 + - - +
448A ARG* 3.2 18.0 + - - +
485A ALA* 3.3 17.3 + - - +
486A ARG* 3.6 34.8 + - - +
550A GLU* 5.3 1.4 + - - -
555A GLY* 4.9 2.2 - - - -
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Residues in contact with ASP 445 (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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441A GLY* 5.6 2.2 - - - -
442A CYS* 2.9 30.3 + - - +
444A SER* 1.3 80.1 + - - +
446A TYR* 1.3 56.7 + - - +
448A ARG* 2.8 40.0 + - - +
449A THR* 3.2 18.3 + - + +
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Residues in contact with TYR 446 (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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440A HIS* 4.1 36.3 - + + +
441A GLY* 5.3 0.8 - - - -
442A CYS 3.1 11.3 + - - +
443A LEU* 3.7 14.6 - - + +
444A SER 3.0 0.2 + - - -
445A ASP* 1.3 76.5 - - - +
447A LEU* 1.3 58.2 + - - +
449A THR* 2.9 23.4 - - + +
450A GLN* 3.7 37.0 - - + +
454A PHE* 3.8 22.9 - + - -
462A MET* 5.7 3.6 - - - -
490A VAL* 3.7 35.5 - - + +
494A GLN* 4.6 22.1 + - - -
496A ILE* 6.1 0.7 - - + -
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Residues in contact with LEU 447 (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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443A LEU* 2.7 55.0 + - + +
444A SER* 2.6 18.3 + - - +
446A TYR* 1.3 73.9 - - + +
448A ARG* 1.3 64.4 + - - +
449A THR 3.3 3.6 - - - +
451A ARG* 4.2 3.1 - - - +
454A PHE* 4.5 17.8 - - + -
459A LEU* 4.5 12.1 - - + -
462A MET* 4.8 4.0 - - - -
485A ALA* 4.7 2.0 - - + -
550A GLU* 4.1 9.4 - - + +
551A VAL* 3.7 39.3 - - - +
554A GLU* 3.0 25.0 - - - +
555A GLY* 3.7 16.8 - - - +
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Residues in contact with ARG 448 (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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444A SER* 3.2 13.2 + - - +
445A ASP* 2.8 33.9 + - - +
447A LEU* 1.3 77.6 - - - +
449A THR* 1.3 66.4 + - + +
451A ARG* 3.2 29.5 + - - +
554A GLU 4.2 3.6 - - - -
555A GLY* 3.9 24.4 + - - +
556A LYS* 5.5 0.4 - - - +
557A ILE* 4.6 23.2 - - - +
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Residues in contact with THR 449 (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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445A ASP* 3.3 18.2 - - + +
446A TYR* 2.9 17.7 - - + +
447A LEU 3.3 2.4 - - - +
448A ARG* 1.3 75.4 - - + +
450A GLN* 1.3 93.3 + - - +
451A ARG 2.5 18.6 + - - -
454A PHE* 4.0 0.2 - - - -
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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