Contacts of the helix formed by residues 442 - 449 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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441B GLY* 1.3 70.1 - - - -
443B LEU* 1.3 54.3 + - - +
444B SER* 2.3 39.5 + - - -
445B ASP* 2.9 32.2 + - - +
446B TYR 3.4 4.4 + - - -
486B ARG* 4.0 22.7 - - - +
488B CYS 3.0 18.4 - - - +
489B LEU* 3.2 15.4 - - + +
490B VAL* 4.3 0.7 - - - -
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Residues in contact with LEU 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441B GLY 3.5 0.2 + - - -
442B CYS* 1.3 67.7 - - - +
444B SER* 1.3 66.6 + - - +
446B TYR* 3.2 6.7 + - + -
447B LEU* 2.8 49.9 + - + +
462B MET* 4.6 13.7 - - + -
466B VAL* 5.2 4.7 - - + -
485B ALA* 3.6 8.1 - - - +
488B CYS* 3.0 25.5 + - + +
490B VAL* 3.4 28.6 - - + +
496B ILE* 4.6 17.5 - - + -
547B LEU* 4.2 15.3 - - + -
551B VAL* 4.0 24.0 - - + -
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Residues in contact with SER 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442B CYS* 2.3 26.0 + - - -
443B LEU* 1.3 74.1 - - - +
445B ASP* 1.3 65.8 + - - -
447B LEU* 2.9 20.7 + - - +
448B ARG* 3.3 13.6 + - - +
485B ALA* 2.6 35.5 + - - +
486B ARG* 3.4 15.7 + - - +
550B GLU* 5.5 0.5 + - - -
555B GLY* 4.9 1.8 - - - -
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Residues in contact with ASP 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441B GLY* 6.0 2.0 - - - -
442B CYS* 2.9 21.7 + - - +
444B SER* 1.3 84.2 + - - +
446B TYR* 1.3 58.8 + - - +
447B LEU 3.2 0.4 + - - -
448B ARG* 3.5 30.4 + - - +
449B THR* 3.0 28.4 + - + +
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Residues in contact with TYR 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440B HIS* 3.8 42.3 + + + +
441B GLY 5.6 0.2 - - - -
442B CYS 3.4 2.4 + - - +
443B LEU* 3.6 11.4 - - + +
444B SER 3.0 1.4 + - - -
445B ASP* 1.3 76.4 - - - +
447B LEU* 1.3 64.7 + - - +
449B THR* 3.2 15.1 - - + +
450B GLN* 3.8 39.0 + - + +
454B PHE* 3.8 17.7 - + - -
462B MET* 5.9 2.7 - - - -
490B VAL* 3.5 43.2 - - + +
494B GLN* 3.9 27.6 + - - -
496B ILE* 5.9 0.2 - - + -
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Residues in contact with LEU 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443B LEU* 2.8 53.5 + - + +
444B SER 3.2 7.2 - - - +
446B TYR* 1.3 77.4 - - - +
448B ARG* 1.3 70.6 + - - +
449B THR 2.7 5.7 - - - +
451B ARG* 3.8 7.4 + - - -
454B PHE* 4.1 23.2 - - + -
459B LEU* 4.7 6.7 - - + -
462B MET* 4.8 4.3 - - - -
485B ALA* 4.6 5.2 - - + -
550B GLU* 3.5 30.5 - - + +
551B VAL* 3.8 21.5 - - - +
554B GLU* 3.0 22.8 - - - +
555B GLY* 3.6 7.0 - - - +
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Residues in contact with ARG 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444B SER* 4.0 10.8 + - - +
445B ASP* 3.5 35.0 + - - +
447B LEU* 1.3 79.1 - - - +
449B THR* 1.3 71.5 + - + +
451B ARG* 2.8 28.9 + - - +
554B GLU 3.7 4.9 + - - -
555B GLY 3.9 20.8 + - - +
557B ILE* 5.3 15.6 - - - +
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Residues in contact with THR 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445B ASP* 3.0 21.3 - - + +
446B TYR* 3.2 7.7 - - + +
447B LEU 2.7 7.3 - - - +
448B ARG* 1.3 81.9 - - + +
450B GLN* 1.3 91.5 + - - +
451B ARG* 2.4 20.4 + - - +
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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