Contacts of the helix formed by residues 193 - 200 (chain C) in PDB entry 6PAI
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 193 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189C PRO* 4.3 9.3 - - + +
191C GLY 4.3 0.2 - - - -
192C ARG* 1.3 71.3 - - - +
194C ALA* 1.3 61.0 + - - +
195C ALA* 3.6 15.9 - - - -
196C CYS* 3.3 37.9 - - + +
197C GLN* 2.8 32.2 + - - +
211C CYS* 3.9 3.8 - - - -
213C ARG* 5.2 4.0 - - - -
214C HIS* 3.4 34.5 - - + +
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Residues in contact with ALA 194 (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 ARG* 3.6 8.1 + - - +
193C CYS* 1.3 73.1 - - - +
195C ALA* 1.3 57.2 + - - +
197C GLN* 3.2 22.3 + - - +
198C ASP* 3.0 33.6 + - - +
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Residues in contact with ALA 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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193C CYS* 3.2 10.2 - - - -
194C ALA* 1.3 80.0 - - - +
196C CYS* 1.3 55.9 + - - +
198C ASP* 3.1 15.1 + - - +
199C ALA* 3.0 24.9 + - - +
211C CYS* 3.6 21.5 - - + +
213C ARG* 5.9 2.2 - - - +
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Residues in contact with CYS 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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189C PRO* 4.6 6.1 - - + -
193C CYS* 3.0 35.4 + - + +
195C ALA* 1.3 74.3 - - - +
197C GLN* 1.3 65.1 + - - +
199C ALA* 3.1 12.8 + - - +
200C SER* 3.2 12.6 + - - -
209C ALA 4.1 4.7 - - - +
210C GLN* 3.5 23.3 - - + -
211C CYS* 3.2 33.0 - - - +
214C HIS* 3.8 13.7 - - - -
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Residues in contact with GLN 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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984A THR* 4.3 16.0 + - - +
988A GLU* 4.7 3.7 - - - +
192C ARG* 3.2 45.7 + - + +
193C CYS 2.8 12.8 + - - +
194C ALA* 3.3 23.7 + - - +
196C CYS* 1.3 73.8 - - - +
198C ASP* 1.3 56.5 + - - +
200C SER* 3.0 9.2 + - - +
201C ARG* 2.8 36.5 + - - +
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Residues in contact with ASP 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 ALA* 3.0 22.4 + - - +
195C ALA* 3.2 13.8 - - - +
197C GLN* 1.3 76.1 - - - +
199C ALA* 1.3 55.9 + - - +
201C ARG* 2.6 40.4 + - - -
202C ALA* 2.6 41.3 + - + +
203C HIS 3.4 0.9 + - - -
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Residues in contact with ALA 199 (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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195C ALA 3.0 11.5 + - - +
196C CYS 3.1 12.3 + - - +
198C ASP* 1.3 76.6 - - - +
200C SER* 1.3 58.5 + - - +
201C ARG 3.4 0.4 - - - -
203C HIS* 2.9 28.4 - - + +
205C GLY 4.4 1.2 + - - -
209C ALA* 4.4 13.1 - - + +
210C GLN 3.9 27.8 - - - +
211C CYS* 4.0 3.8 - - - +
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Residues in contact with SER 200 (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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196C CYS 3.2 6.5 + - - -
197C GLN* 3.0 11.6 + - - -
199C ALA* 1.3 74.0 - - - +
201C ARG* 1.3 57.3 + - - +
203C HIS 3.0 10.9 - - - +
204C PRO* 3.9 14.6 - - - +
205C GLY 5.0 0.2 - - - +
206C ASP 3.8 16.8 + - - -
209C ALA* 3.6 19.6 + - - +
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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