Contacts of the helix formed by residues 182 - 194 (chain N) in PDB entry 5X6E
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 HIS 182 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172N GLN* 5.8 0.4 - - - -
180N ILE* 3.4 15.3 - - + +
181N ALA* 1.3 92.4 + - + +
183N SER* 1.3 66.3 + - - +
184N SER* 3.1 0.4 - - - +
185N ALA* 3.0 12.1 + - + -
186N VAL* 3.4 3.7 + - - +
18P G 3.6 19.3 - - + -
19P T 2.9 69.0 + + + -
20P T 4.0 31.1 - - + +
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Residues in contact with SER 183 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171N MET* 3.9 11.3 - - - +
172N GLN* 3.4 34.3 - - - +
181N ALA 4.2 1.2 + - - -
182N HIS* 1.3 70.7 - - - +
184N SER* 1.3 61.2 + - - +
186N VAL* 3.4 12.3 + - - +
187N SER* 3.2 16.6 + - - -
7O C 6.5 0.7 - - - -
8O G 5.3 9.6 - - - -
9O T 4.6 8.7 - - - -
20P T 5.8 0.4 - - - +
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Residues in contact with SER 184 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182N HIS* 4.2 0.3 - - - +
183N SER* 1.3 76.2 - - - +
185N ALA* 1.3 62.7 + - - +
187N SER* 3.3 2.9 + - - -
188N ARG* 3.0 28.8 + - - +
9O T 4.3 10.7 - - - +
10O T 3.3 25.2 - - - +
11O A 4.5 2.5 - - - -
19P T 3.6 5.6 - - - +
20P T 2.5 43.5 + - - +
21P A 3.4 6.5 - - - -
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Residues in contact with ALA 185 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180N ILE* 3.6 17.7 - - + -
182N HIS* 3.0 12.8 + - + +
184N SER* 1.3 81.8 + - - +
186N VAL* 1.3 61.4 + - - +
188N ARG* 3.5 24.9 + - - +
189N ILE* 3.3 27.1 + - + +
17P T 5.2 6.7 - - - +
18P G 5.1 2.2 - - + -
19P T 3.6 22.4 - - + -
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Residues in contact with VAL 186 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143N ILE* 4.9 8.1 - - + -
171N MET* 3.3 40.4 - - + +
172N GLN* 5.3 0.2 - - - -
174N LEU* 4.9 6.3 - - + -
175N GLY* 3.8 16.2 - - - +
180N ILE* 3.7 23.6 - - + -
182N HIS 3.6 13.9 - - - +
183N SER* 3.5 8.3 - - - +
184N SER 3.2 0.6 - - - -
185N ALA* 1.3 74.1 - - - +
187N SER* 1.3 55.3 + - - +
189N ILE* 3.0 5.6 + - - +
190N ILE* 2.7 56.0 + - + +
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Residues in contact with SER 187 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171N MET* 3.5 23.5 - - - +
183N SER 3.2 3.0 + - - -
184N SER 3.6 7.2 - - - -
186N VAL* 1.3 79.3 - - - +
188N ARG* 1.3 56.3 + - - +
190N ILE* 4.4 1.6 - - - -
191N SER* 2.6 40.4 + - - -
9O T 3.1 53.5 + - - +
10O T 3.9 8.7 - - - +
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Residues in contact with ARG 188 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184N SER 3.0 12.0 + - - +
185N ALA* 3.5 20.4 + - - +
187N SER* 1.3 74.3 - - - +
189N ILE* 1.3 66.4 + - - +
191N SER* 2.9 18.4 + - - -
192N LYS* 3.0 20.6 + - + +
10O T 4.4 8.2 - - + +
12O A 4.4 8.5 - - - +
17P T 3.2 59.9 + - - +
18P G 2.7 37.4 + - - -
19P T 3.4 17.8 + - - +
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Residues in contact with ILE 189 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139N LYS* 4.3 16.6 - - + -
140N LEU* 4.2 20.2 - - + +
143N ILE* 4.1 18.6 - - + -
180N ILE* 4.0 26.5 - - + -
185N ALA 3.3 10.3 + - - +
186N VAL* 3.0 8.6 + - - +
188N ARG* 1.3 85.3 - - - +
190N ILE* 1.3 58.5 + - + +
192N LYS* 3.0 9.2 + - + +
193N LEU* 2.4 62.0 + - + +
17P T 4.6 13.0 - - - +
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Residues in contact with ILE 190 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143N ILE* 4.3 14.4 - - + -
147N LEU* 4.7 3.1 - - + -
171N MET* 4.1 12.6 - - - -
174N LEU* 4.4 9.9 - - + -
186N VAL* 2.7 37.1 + - + +
187N SER* 4.0 4.5 - - - +
189N ILE* 1.3 71.3 - - + +
191N SER* 1.3 63.4 + - - +
193N LEU* 4.2 7.6 - - + -
194N LYS* 2.8 53.4 + - + +
199N ILE* 4.0 15.0 - - + -
201N TYR* 4.8 9.2 - - + -
206N PHE* 4.1 21.3 - - + -
9O T 4.9 5.6 - - - +
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Residues in contact with SER 191 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187N SER* 2.6 28.2 + - - -
188N ARG* 2.9 10.6 + - - -
190N ILE* 1.3 73.7 - - - +
192N LYS* 1.3 71.6 + - - +
194N LYS* 3.1 13.6 + - - +
195N GLN* 3.4 10.9 + - - +
9O T 5.4 3.9 + - - -
10O T 3.3 26.0 + - - -
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Residues in contact with LYS 192 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140N LEU* 5.1 20.6 - - + +
188N ARG* 3.2 17.7 - - + +
189N ILE* 3.0 7.2 + - + +
191N SER* 1.3 76.4 + - - +
193N LEU* 1.3 56.4 + - + +
194N LYS 2.6 16.7 + - - -
195N GLN* 3.0 15.5 + - - +
196N GLU* 3.1 30.9 + - - +
213N TYR* 6.1 0.2 - - - -
16P T 3.3 32.7 + - - -
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Residues in contact with LEU 193 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140N LEU* 3.9 21.8 - - + -
143N ILE* 3.7 23.1 - - + -
144N CYS* 4.0 8.1 - - - -
147N LEU* 4.3 5.8 - - + -
189N ILE* 2.4 53.5 + - + +
190N ILE* 3.3 1.8 + - + -
192N LYS* 1.3 67.6 - - - +
194N LYS* 1.3 88.4 + - + +
196N GLU* 3.2 8.2 - - + +
198N VAL* 3.1 38.6 + - + +
213N TYR* 4.0 25.1 - - + +
214N LEU* 5.7 0.7 - - + -
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Residues in contact with LYS 194 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147N LEU* 4.2 3.9 - - - +
190N ILE* 2.8 46.4 - - + +
191N SER* 3.1 8.3 + - - +
192N LYS 2.6 6.9 + - - -
193N LEU* 1.3 115.3 - - - +
195N GLN* 1.3 54.4 + - - +
197N LYS* 3.0 25.9 + - - +
198N VAL* 3.8 3.8 - - - -
199N ILE* 2.9 74.6 - - + +
200N VAL* 5.7 0.2 - - - -
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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