Contacts of the helix formed by residues 183 - 191 (chain B) in PDB entry 3NX4
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B SER* 3.6 18.1 - - - +
178B SER* 2.9 22.0 + - - -
180B ARG* 3.0 52.8 + - + +
181B GLU 3.1 0.4 - - - -
182B SER* 1.3 82.3 - - - +
184B HIS* 1.3 58.8 + - - +
185B GLY 3.5 0.9 - - - -
186B TYR* 3.3 6.4 + - - +
187B LEU* 2.9 35.9 + - - +
316B GLN* 3.8 18.2 - - - +
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Residues in contact with HIS 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B SER* 4.7 7.6 + - - -
180B ARG 3.4 23.1 + - - -
181B GLU* 3.6 23.8 + - + +
182B SER 3.4 2.4 - - - -
183B THR* 1.3 78.2 - - - +
185B GLY* 1.3 67.0 + - - +
187B LEU* 3.0 7.6 + - + +
188B LYS* 2.9 29.1 + - + +
195B ILE* 3.2 42.4 - - + +
196B LEU 5.4 2.8 + - - -
197B SER* 5.9 2.8 - - - -
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Residues in contact with GLY 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B SER 4.8 2.6 + - - -
183B THR 3.5 0.2 - - - -
184B HIS* 1.3 77.4 - - - +
186B TYR* 1.3 61.0 + - - +
188B LYS* 3.4 9.0 + - - +
189B SER* 3.1 23.4 + - - -
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Residues in contact with TYR 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B SER* 3.9 16.8 - - - -
161B SER* 2.7 34.3 + - - -
182B SER 5.2 2.1 + - - +
183B THR* 3.3 13.6 + - - +
184B HIS 3.1 0.4 - - - -
185B GLY* 1.3 77.0 - - - +
187B LEU* 1.3 67.8 + - + +
189B SER* 2.7 25.9 + - - -
190B LEU* 3.1 31.5 + - + +
293B GLN* 3.6 27.4 - - + -
294B ALA* 3.6 8.4 - - - +
316B GLN* 3.4 38.4 - - + +
317B GLY* 3.2 20.9 - - - -
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Residues in contact with LEU 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B ALA* 3.5 36.6 - - + +
156B SER* 3.8 7.4 - - - +
164B VAL* 4.3 5.2 - - + +
176B ALA* 4.2 9.4 - - + -
178B SER* 3.9 19.7 - - - -
183B THR* 2.9 36.1 + - - +
184B HIS 3.0 1.3 + - - +
186B TYR* 1.3 80.3 - - + +
188B LYS* 1.3 66.5 + - - +
190B LEU* 3.2 19.5 + - + +
191B GLY 3.3 1.0 + - - -
192B ALA* 3.2 22.6 + - + +
195B ILE* 3.4 32.3 - - + -
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Residues in contact with LYS 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184B HIS* 2.9 22.8 + - + +
185B GLY* 3.7 8.5 - - - +
187B LEU* 1.3 76.2 - - - +
189B SER* 1.3 58.6 + - - +
191B GLY* 3.1 19.2 + - - -
192B ALA 3.6 19.7 + - - +
193B ASN* 3.2 25.8 + - - +
194B ARG* 4.7 1.9 - - - +
195B ILE* 4.2 18.2 - - + -
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Residues in contact with SER 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185B GLY 3.1 13.2 + - - -
186B TYR* 2.7 25.8 + - - -
188B LYS* 1.3 78.2 - - - +
190B LEU* 1.3 59.8 + - - +
191B GLY* 3.5 0.7 + - - -
293B GLN* 2.7 38.7 + - - +
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Residues in contact with LEU 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161B SER* 3.7 24.9 - - - +
164B VAL* 3.9 13.0 - - + -
165B ALA* 3.7 24.4 - - + +
168B HIS* 4.1 7.7 - - - +
186B TYR* 3.1 55.0 + - + +
187B LEU* 3.2 17.9 + - + +
189B SER* 1.3 78.5 + - - +
191B GLY* 1.3 55.7 + - - +
192B ALA 3.8 0.4 - - - -
290B PHE* 4.0 24.9 - - + -
293B GLN* 3.9 29.8 - - + +
294B ALA* 4.9 0.4 - - + -
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Residues in contact with GLY 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164B VAL* 4.1 4.0 - - - -
168B HIS* 3.4 40.4 + - - +
174B VAL* 4.6 1.8 - - - +
188B LYS 3.1 10.9 + - - -
189B SER 3.2 1.1 - - - -
190B LEU* 1.3 80.7 - - - +
192B ALA* 1.3 68.4 + - - +
193B ASN* 3.2 10.9 + - - +
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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