Contacts of the helix formed by residues 192 - 198 (chain C) in PDB entry 5D0A
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 THR 192 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154C LYS* 4.2 7.0 - - - +
190C SER 3.7 8.2 + - - +
191C CYS* 1.3 81.3 - - - +
193C LYS* 1.3 67.3 + - - +
194C CYS 3.3 2.7 - - - -
195C LEU* 3.3 28.9 + - + -
196C ASP* 3.1 39.3 + - - -
206C PRO* 6.1 0.4 - - + -
501C SF4 4.1 5.2 - - - -
284D LYS* 5.4 1.4 - - - +
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Residues in contact with LYS 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191C CYS* 3.6 12.5 - - - -
192C THR* 1.3 78.9 - - - +
194C CYS* 1.3 58.1 + - - +
196C ASP* 3.8 6.6 - - - +
197C ALA* 2.9 32.1 + - - +
246C VAL* 3.9 23.1 + - + +
248C PRO* 4.1 20.9 - - + +
501C SF4 3.9 11.4 - - - -
285D GLU* 4.4 25.0 + - - +
289D HIS* 6.2 2.2 - - - -
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Residues in contact with CYS 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155C ASN* 3.7 38.1 - - + -
193C LYS* 1.3 78.0 - - - +
195C LEU* 1.3 84.8 + - - +
197C ALA* 3.9 0.9 - - - +
198C CYS* 3.0 25.1 + - - +
203C LEU* 3.8 5.0 - - + +
243C CYS* 3.7 17.1 - - + +
246C VAL* 3.9 10.8 - - - -
501C SF4 2.3 44.6 - - - -
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Residues in contact with LEU 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154C LYS* 3.6 29.4 - - + +
192C THR* 3.3 32.3 + - + +
194C CYS* 1.3 87.6 - - - +
196C ASP* 1.3 67.5 + - - +
197C ALA 3.5 0.2 + - - -
198C CYS* 3.7 13.0 + - - +
201C GLY* 5.3 4.0 - - - -
203C LEU* 3.8 34.5 - - + +
205C ASN 4.2 2.9 - - - +
206C PRO* 4.1 35.9 - - + -
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Residues in contact with ASP 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192C THR* 3.1 35.1 + - - +
193C LYS* 3.9 6.5 - - - +
195C LEU* 1.3 82.5 - - - +
197C ALA* 1.3 59.3 + - - +
198C CYS 3.5 4.4 + - - +
281D ARG* 6.0 8.5 - - + +
284D LYS* 3.4 43.6 + - + +
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Residues in contact with ALA 197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193C LYS 2.9 19.2 + - - +
194C CYS 4.0 1.8 - - - +
195C LEU 3.3 0.2 - - - -
196C ASP* 1.3 77.4 - - - +
198C CYS* 1.3 66.9 + - - +
199C PRO* 3.1 9.4 - - - +
242C THR* 4.0 13.2 - - + +
246C VAL* 3.8 32.3 - - + -
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Residues in contact with CYS 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194C CYS 3.0 16.5 + - - +
195C LEU 3.9 9.9 - - - +
196C ASP 3.5 5.4 - - - +
197C ALA* 1.3 75.3 - - - +
199C PRO* 1.3 70.1 - - - +
200C THR* 3.2 7.5 + - - -
201C GLY* 3.5 12.4 + - - +
202C ALA 3.5 27.4 - - - +
203C LEU* 4.1 9.2 - - + +
502C SF4 2.3 43.7 - - - -
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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