Contacts of the helix formed by residues 183 - 190 (chain A) in PDB entry 1N3Y
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 183 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169A PHE 3.8 1.7 - - - +
170A SER* 3.7 8.1 - - - -
180A THR* 4.1 9.9 - - + -
182A PHE* 1.3 76.9 - - - +
184A PHE* 1.3 66.2 + - - +
185A GLU* 3.4 7.1 + - - +
186A GLU* 2.9 36.2 + - - +
187A PHE* 3.0 22.0 + - - +
225A TYR* 3.5 43.5 + - + -
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Residues in contact with PHE 184 (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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132A ASP* 3.5 24.5 - - + +
133A ILE 3.4 29.2 - - - -
134A VAL* 3.6 23.1 - - + -
168A GLN* 3.5 14.3 + - + -
169A PHE 3.5 24.5 - - - -
170A SER* 3.7 7.7 - - - -
183A THR* 1.3 74.2 - - - +
185A GLU* 1.3 59.0 + - - +
187A PHE* 3.2 2.5 + - - +
188A ARG* 2.8 36.6 + - - +
220A LEU 3.2 27.6 - - - -
221A PHE* 3.8 15.7 - + - -
225A TYR 3.2 7.2 + - - +
226A GLY 3.7 14.4 - - - +
227A ALA* 4.1 15.3 - - + -
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Residues in contact with GLU 185 (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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183A THR* 3.2 5.1 - - - +
184A PHE* 1.3 76.9 - - - +
186A GLU* 1.3 62.4 + - + +
188A ARG* 3.4 24.1 + - - +
189A ARG* 3.1 50.9 + - - +
224A SER 5.3 2.7 - - - +
225A TYR 3.0 18.3 + - - +
226A GLY* 3.8 10.1 - - - -
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Residues in contact with GLU 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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180A THR 5.6 0.2 - - - +
181A HIS 4.1 2.6 - - - +
182A PHE* 3.1 19.1 - - + -
183A THR* 2.9 44.1 + - - +
185A GLU* 1.3 77.5 - - + +
187A PHE* 1.3 63.1 + - - +
189A ARG* 3.5 36.2 + - - +
190A SER* 3.2 24.3 + - - -
196A LEU* 3.8 11.9 - - + +
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Residues in contact with PHE 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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159A ILE* 3.8 19.5 - - + -
164A ARG* 2.9 47.8 + - + -
167A THR 4.4 0.7 - - - -
168A GLN* 3.2 21.8 - - - -
169A PHE* 3.1 57.9 - + + +
182A PHE* 3.5 26.7 - + + -
183A THR 3.0 7.1 + - - +
184A PHE 3.2 5.4 + - - +
186A GLU* 1.3 79.7 - - - +
188A ARG* 1.3 57.2 + - - +
190A SER* 3.4 5.4 + - - -
193A PRO* 3.5 31.5 - - + +
196A LEU* 3.8 11.4 - - + +
197A LEU* 5.1 0.4 - - + -
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Residues in contact with ARG 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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132A ASP* 4.8 0.6 + - - -
164A ARG* 3.4 13.1 + - - +
165A PRO* 6.1 1.7 - - + +
168A GLN* 3.5 36.6 + - - +
184A PHE* 2.8 24.3 + - - +
185A GLU* 3.7 23.2 + - - +
187A PHE* 1.3 78.0 - - - +
189A ARG* 1.3 62.1 + - - +
190A SER 4.3 0.2 - - - +
226A GLY* 3.2 20.0 + - - -
228A ARG* 3.1 43.8 - - - +
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Residues in contact with ARG 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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185A GLU* 3.1 43.7 + - - +
186A GLU* 3.5 39.8 + - - +
188A ARG* 1.3 77.0 - - + +
190A SER* 1.3 66.4 + - - +
191A SER* 3.6 2.4 + - - -
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Residues in contact with SER 190 (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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164A ARG* 2.7 30.5 + - - -
186A GLU 3.2 18.3 + - - -
187A PHE 3.6 8.7 - - - -
188A ARG 3.3 1.7 - - - +
189A ARG* 1.3 79.8 - - - +
191A SER* 1.3 58.9 + - - +
192A ASN 3.0 27.9 + - - -
193A PRO* 3.5 10.9 - - - +
195A SER* 4.7 0.9 + - - -
196A LEU* 4.1 12.8 - - - +
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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