Contacts of the helix formed by residues 181 - 188 (chain A) in PDB entry 1N0W
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 SER 181 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179A GLY 4.3 0.2 + - - -
180A LEU* 1.3 70.2 - - - +
182A GLY* 1.3 57.9 + - - +
183A SER* 2.9 23.6 + - - -
184A ASP* 3.2 29.0 + - - +
185A VAL* 2.9 31.7 + - - +
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Residues in contact with GLY 182 (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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172A LEU* 3.6 21.8 - - - +
175A ALA* 4.1 14.4 - - - -
180A LEU 3.2 5.3 + - - -
181A SER* 1.3 72.1 + - - +
183A SER* 1.3 61.7 + - - +
185A VAL* 3.3 2.1 + - - +
186A LEU* 3.0 29.1 + - - +
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Residues in contact with SER 183 (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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181A SER* 2.9 16.1 + - - -
182A GLY* 1.3 73.8 - - - +
184A ASP* 1.3 66.9 + - - +
186A LEU* 3.4 8.3 + - - +
187A ASP* 3.0 33.0 + - - +
1528B SER* 5.5 0.2 - - - -
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Residues in contact with ASP 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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181A SER* 3.2 27.1 + - - +
183A SER* 1.3 85.0 + - - +
185A VAL* 1.3 63.9 + - + +
187A ASP* 3.1 10.4 + - - +
188A ASN* 2.9 39.3 + - - +
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Residues in contact with VAL 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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142A VAL* 3.8 27.1 - - + -
145A GLN* 3.3 28.1 + - - +
171A LEU* 4.4 13.0 - - + +
172A LEU* 5.9 0.2 - - - -
175A ALA* 3.7 22.7 - - + -
180A LEU* 3.9 22.9 - - + -
181A SER 2.9 21.0 + - - +
182A GLY 3.6 4.9 - - - +
184A ASP* 1.3 77.7 - - + +
186A LEU* 1.3 62.6 + - + +
188A ASN 3.1 8.8 + - - -
189A VAL* 3.3 16.9 - - + +
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Residues in contact with LEU 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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168A PRO* 3.8 26.2 - - + +
171A LEU* 3.9 16.4 - - + -
172A LEU* 3.6 28.3 - - + -
182A GLY 3.0 19.5 + - - +
183A SER* 3.8 6.5 - - - +
185A VAL* 1.3 76.9 - - + +
187A ASP* 1.3 63.0 + - - +
188A ASN 3.2 0.7 + - - -
189A VAL* 3.3 5.9 + - - -
1527B ALA* 3.1 51.6 + - + +
1528B SER* 4.0 22.0 - - - +
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Residues in contact with ASP 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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156A LYS* 5.0 5.4 + - - +
183A SER* 3.0 27.7 + - - +
184A ASP* 3.1 11.6 + - - +
186A LEU* 1.3 75.9 - - - +
188A ASN* 1.3 63.7 + - - +
189A VAL 3.4 0.9 + - - -
1526B THR* 3.7 19.8 - - + +
1528B SER* 2.7 30.8 + - - -
1530B LYS* 3.3 21.7 + - + +
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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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145A GLN* 3.2 30.5 + - + +
155A GLY 6.2 0.2 - - - -
156A LYS* 3.3 40.3 - - + +
157A ALA 3.0 23.4 + - - +
184A ASP* 2.9 28.1 + - - +
185A VAL 3.8 0.4 - - - +
186A LEU 3.1 0.8 - - - -
187A ASP* 1.3 82.9 - - - +
189A VAL* 1.3 60.5 + - - +
190A ALA 4.0 0.7 - - - -
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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