Contacts of the helix formed by residues 185 - 192 (chain C) in PDB entry 3G1Q
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 185 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184C PHE* 1.3 78.7 - - - +
186C GLU* 1.3 65.3 + - - -
187C ASP* 3.3 4.3 - - - -
188C LEU* 3.1 10.8 + - - +
189C ARG* 3.2 12.5 + - - +
247C ARG* 4.1 0.6 - - - +
258C THR* 3.8 18.8 - - - -
259C SER 5.7 0.7 - - - -
260C ASP* 2.7 25.7 + - - +
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Residues in contact with GLU 186 (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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185C GLY* 1.3 69.6 - - - -
187C ASP* 1.3 64.9 + - - +
189C ARG* 2.9 38.2 + - - +
190C LYS* 3.0 49.1 + - - +
258C THR* 4.7 6.0 - - - +
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Residues in contact with ASP 187 (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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185C GLY 3.8 1.2 - - - -
186C GLU* 1.3 75.5 - - - +
188C LEU* 1.4 75.5 + - - +
190C LYS* 3.0 28.0 + - + +
191C ARG* 3.3 13.3 + - - +
243C ILE* 3.8 13.1 - - + +
246C ALA* 5.6 2.2 - - + +
247C ARG* 2.9 53.8 + - - +
250C GLU* 4.5 14.2 - - - +
258C THR* 3.6 15.0 + - - +
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Residues in contact with LEU 188 (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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184C PHE* 3.4 43.5 - - + -
185C GLY 3.1 8.2 + - - +
187C ASP* 1.4 86.6 + - - +
189C ARG* 1.3 58.9 + - - +
191C ARG* 3.3 1.6 + - - -
192C LEU* 2.9 53.0 + - + +
239C ILE* 4.7 1.8 - - + -
240C LEU* 4.1 18.2 - - + -
243C ILE* 3.6 31.0 - - + -
247C ARG* 4.3 4.9 - - - +
260C ASP* 4.0 10.5 - - - +
262C LEU* 4.4 18.8 - - + -
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Residues in contact with ARG 189 (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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180C CYS* 3.6 20.4 - - + -
181C GLN* 3.2 54.3 + - - +
184C PHE* 2.8 42.8 + - + +
185C GLY* 3.2 15.1 + - - +
186C GLU* 2.9 47.2 + - - +
188C LEU* 1.3 74.4 - - - +
190C LYS* 1.3 62.7 + - - +
192C LEU 3.6 12.1 - - - +
193C ASP* 3.3 30.7 + - + +
194C ALA 5.9 0.7 - - - +
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Residues in contact with LYS 190 (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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186C GLU* 3.0 42.4 + - - +
187C ASP* 3.0 18.1 + - - +
189C ARG* 1.3 78.0 - - - +
191C ARG* 1.3 60.8 + - + +
193C ASP* 5.0 1.6 + - - +
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Residues in contact with ARG 191 (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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187C ASP 3.3 8.6 + - - +
188C LEU 3.8 6.7 - - - +
190C LYS* 1.3 80.5 - - + +
192C LEU* 1.3 56.6 + - - +
193C ASP 4.1 0.4 - - - -
196C ARG* 2.7 49.1 + - - +
239C ILE* 3.7 32.5 + - + +
242C GLU* 2.5 46.8 + - - +
243C ILE* 4.0 12.9 - - + +
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Residues in contact with LEU 192 (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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180C CYS* 5.8 2.3 - - - +
184C PHE* 5.2 7.8 - - + -
188C LEU* 2.9 35.1 + - + +
189C ARG* 3.4 14.6 - - - +
190C LYS 3.3 0.2 - - - -
191C ARG* 1.3 79.8 - - - +
193C ASP* 1.3 64.6 + - - +
196C ARG* 4.4 7.9 - - - +
197C PHE* 3.9 48.0 - - + +
200C LEU* 3.9 28.7 - - + -
236C LEU* 4.5 12.1 - - + -
239C ILE* 4.1 20.2 - - + -
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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