Contacts of the helix formed by residues 190 - 197 (chain C) in PDB entry 4BZ5
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 GLY 190 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141C HIS* 3.6 10.8 - - - -
182C TYR* 5.0 3.1 - - - -
184C ASP* 3.1 26.9 + - - -
188C HIS 3.4 1.6 + - - -
189C HIS* 1.3 72.3 + - - +
191C ASP* 1.3 63.0 + - - -
192C GLY 3.5 2.2 + - - -
193C VAL* 3.6 5.6 + - - +
194C GLU* 3.1 23.6 + - - +
207C SER* 3.2 16.6 + - - -
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Residues in contact with ASP 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142C HIS* 2.8 30.3 + - - -
144C LYS* 3.5 20.8 + - - -
149C SER* 4.8 4.7 + - - -
189C HIS* 2.9 30.4 + - + +
190C GLY* 1.3 70.0 - - - +
192C GLY* 1.3 65.4 + - - -
194C GLU* 3.4 1.1 + - - +
195C GLU* 2.9 46.5 + - + +
217C PRO* 3.4 24.7 - - - +
219C THR* 3.6 9.1 + - - +
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Residues in contact with GLY 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C PHE* 4.5 3.1 - - - -
141C HIS 3.0 13.9 + - - -
142C HIS 4.2 0.2 - - - -
143C ALA 3.8 7.9 - - - +
144C LYS* 3.7 24.8 - - - +
155C ASN* 3.9 6.3 - - - -
158C VAL* 4.2 0.9 - - - +
191C ASP* 1.3 85.2 + - - +
193C VAL* 1.3 61.2 + - - +
195C GLU* 3.9 2.0 - - - +
196C ALA* 3.1 24.4 + - - +
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Residues in contact with VAL 193 (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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141C HIS* 3.4 18.1 + - + +
155C ASN* 4.0 7.2 - - - +
157C ILE* 3.9 21.1 - - + -
158C VAL* 3.9 8.1 - - + -
161C ILE* 3.9 22.7 - - + -
182C TYR* 3.7 46.7 - - + +
190C GLY 3.6 2.0 + - - +
191C ASP 3.3 0.4 - - - -
192C GLY* 1.3 74.2 - - - +
194C GLU* 1.3 66.5 + - - +
196C ALA 3.3 8.5 + - - -
197C PHE* 3.3 24.7 + - + +
205C THR* 4.3 4.2 - - + +
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Residues in contact with GLU 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189C HIS* 2.9 26.8 + - - -
190C GLY 3.1 18.8 + - - +
191C ASP 3.7 3.9 - - - +
193C VAL* 1.3 78.8 - - - +
195C GLU* 1.3 65.5 + - + +
197C PHE* 3.4 2.3 + - - +
198C TRP* 3.1 52.7 + - + +
205C THR* 4.0 19.7 + - - +
207C SER* 5.4 1.4 - - - -
219C THR* 5.3 1.6 - - - -
220C GLY* 5.1 1.0 + - - -
244C ALA* 4.0 12.9 - - + +
245C PHE 4.6 1.2 - - - +
246C ASN* 2.9 31.0 + - - +
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Residues in contact with GLU 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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62C PHE* 6.5 0.2 - - + -
144C LYS* 3.1 42.1 + - + +
191C ASP* 2.9 32.5 + - + +
192C GLY 3.9 3.1 - - - +
194C GLU* 1.3 78.7 - - + +
196C ALA* 1.3 65.8 + - - +
197C PHE 3.2 0.9 + - - -
198C TRP* 3.2 23.6 + - + +
199C TYR* 5.5 1.2 - - - -
219C THR* 5.7 4.2 - - - +
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Residues in contact with ALA 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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62C PHE* 3.6 31.0 - - + -
158C VAL* 3.6 24.9 - - + -
192C GLY 3.1 17.9 + - - +
193C VAL 3.3 3.5 + - - +
195C GLU* 1.3 76.7 - - - +
197C PHE* 1.3 68.9 + - + +
198C TRP 3.9 0.2 + - - -
199C TYR 5.3 0.3 + - - -
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Residues in contact with PHE 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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158C VAL* 3.8 33.7 - - + -
161C ILE* 3.4 38.8 - - + -
162C HIS* 4.3 12.8 - + + -
165C VAL* 5.3 3.4 - - + -
193C VAL* 3.3 29.7 + - + +
194C GLU 3.6 3.1 - - - +
195C GLU 3.1 0.6 - - - -
196C ALA* 1.3 85.1 - - + +
198C TRP* 1.3 63.7 + - - +
199C TYR 3.1 3.4 - - - -
200C SER* 2.9 32.5 + - - +
203C VAL* 3.6 47.1 - - + +
205C THR* 4.6 5.4 - - + -
243C SER* 4.7 2.3 + - - -
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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