Contacts of the helix formed by residues 185 - 189 (chain A) in PDB entry 1SOT
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183A PRO* 3.9 0.8 - - - +
184A THR* 1.3 80.8 + - - +
186A ARG* 1.3 66.7 + - - +
187A GLN* 3.3 6.5 - - - -
188A ASN* 3.1 15.9 + - - +
189A PHE* 4.0 17.7 + - - -
220A PHE* 6.4 0.4 - - - -
221A ASP* 4.7 4.9 - - - -
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Residues in contact with ARG 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A GLY* 1.3 71.0 - - - -
187A GLN* 1.3 65.4 + - - +
188A ASN 2.9 1.7 + - - -
189A PHE* 2.9 29.6 + - - +
191A GLN* 4.8 0.2 - - - +
220A PHE* 3.6 23.4 - - + +
221A ASP* 3.4 34.6 + - + +
234A PHE* 3.6 27.7 - - + -
164C LEU* 4.8 2.0 - - + -
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Residues in contact with GLN 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A ALA* 5.6 2.1 - - - +
177A GLY* 5.2 1.2 - - - -
184A THR 3.6 12.4 + - - +
185A GLY 3.5 2.6 - - - -
186A ARG* 1.3 77.1 + - - +
188A ASN* 1.3 78.8 + - - +
189A PHE 3.5 3.0 - - - +
191A GLN* 3.8 13.7 - - - +
221A ASP* 3.1 21.8 + - - +
163C ASN 4.2 13.5 + - - +
164C LEU* 3.7 31.9 - - + +
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Residues in contact with ASN 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A GLY* 3.1 5.8 - - - -
178A ARG* 2.7 62.7 + - + +
184A THR* 2.5 41.5 + - - +
185A GLY 3.1 5.0 + - - +
186A ARG 3.0 1.2 - - - -
187A GLN* 1.3 95.9 - - - +
189A PHE* 1.3 66.6 + - + +
237A PRO* 4.9 0.2 - - - +
316A LEU* 4.8 8.4 - - - +
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Residues in contact with PHE 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A LEU 3.7 23.1 - - - -
125A THR* 4.2 19.1 - - + -
175A ALA* 4.4 1.0 - - - +
177A GLY* 3.5 9.2 + - - -
185A GLY* 4.1 15.5 - - - -
186A ARG* 2.9 21.0 + - - +
187A GLN 4.0 2.3 - - - +
188A ASN* 1.3 89.1 - - + +
190A LEU* 1.3 68.6 + - - +
191A GLN* 3.6 11.6 + - - +
217A THR* 4.4 9.2 - - + -
220A PHE* 3.2 40.6 - + + -
234A PHE* 4.2 17.7 - - + -
235A ALA 3.5 11.4 - - - +
236A ILE* 5.1 5.8 - - + -
237A PRO* 4.5 9.2 - - + -
240A LEU* 5.5 5.8 - - + -
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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