Contacts of the helix formed by residues 182 - 190 (chain M) in PDB entry 6NR8
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 M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173M LEU* 4.1 8.9 - - + +
178M VAL* 3.4 41.4 - - + +
180M SER 4.0 0.2 - - - -
181M CYS* 1.3 76.8 - - - +
183M ARG* 1.3 64.8 + - - +
184M GLN* 3.0 27.2 + - - +
185M MET* 3.5 38.8 + - + +
186M ALA 3.9 7.3 + - - -
219M LEU* 3.2 37.3 + - + +
220M GLU* 3.1 33.8 + - - -
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Residues in contact with ARG 183 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166M ILE* 2.8 44.8 + - - +
170M LYS* 3.5 32.7 - - - +
181M CYS* 3.1 19.5 + - - +
182M HIS* 1.3 71.0 - - - +
184M GLN* 1.3 68.8 + - - +
185M MET 3.3 0.7 + - - -
186M ALA* 3.4 20.5 + - - +
187M GLU* 3.3 49.4 + - - +
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Residues in contact with GLN 184 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182M HIS* 3.0 33.5 + - - +
183M ARG* 1.3 82.5 + - - +
185M MET* 1.3 61.0 + - - +
187M GLU* 4.2 5.4 - - - -
188M ILE* 3.2 36.2 + - + +
220M GLU* 2.5 43.6 + - - +
222M THR* 3.7 21.5 + - - +
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Residues in contact with MET 185 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173M LEU* 3.7 29.2 - - + -
182M HIS* 3.5 36.1 + - + +
183M ARG 3.2 1.0 - - - -
184M GLN* 1.3 79.4 - - - +
186M ALA* 1.3 64.7 + - - +
187M GLU 3.2 0.2 - - - -
188M ILE* 3.5 2.1 + - - +
189M ALA* 3.1 26.0 + - - +
219M LEU 3.3 27.4 - - - +
221M ASP 4.7 1.1 - - - +
222M THR* 3.3 34.4 - - + +
387M ILE* 4.9 10.8 - - + -
388M ARG 4.8 5.2 - - - +
398M ALA* 5.2 12.8 - - + -
402M LEU* 4.7 17.1 - - + +
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Residues in contact with ALA 186 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166M ILE* 3.9 8.4 - - - +
169M ALA* 3.7 34.4 - - + +
170M LYS* 4.9 0.7 - - - -
173M LEU* 4.3 8.3 - - + -
181M CYS* 5.3 0.4 - - - -
182M HIS 3.9 3.9 + - - +
183M ARG* 3.4 29.4 + - - +
184M GLN 3.6 0.2 - - - -
185M MET* 1.3 79.1 - - - +
187M GLU* 1.3 60.8 + - - +
189M ALA* 4.0 3.8 - - - +
190M VAL* 3.5 26.2 + - - +
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Residues in contact with GLU 187 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166M ILE* 3.7 29.0 - - + +
183M ARG* 3.3 49.8 + - - +
184M GLN* 4.7 4.4 - - - +
185M MET 3.2 0.6 - - - -
186M ALA* 1.3 78.6 - - - +
188M ILE* 1.3 57.6 + - + +
189M ALA 3.3 0.2 - - - -
190M VAL* 3.3 11.9 - - - +
191M ASN* 2.4 36.0 + - - +
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Residues in contact with ILE 188 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184M GLN* 3.2 24.4 + - + +
185M MET 4.1 2.7 - - - +
187M GLU* 1.3 79.4 - - + +
189M ALA* 1.3 57.7 + - - +
191M ASN* 2.8 26.2 + - - +
192M ALA* 3.0 11.6 + - - +
222M THR* 3.4 36.8 - - + +
223M LYS* 4.0 10.5 - - - +
224M LEU* 3.7 27.9 - - + +
385M ILE* 3.7 17.9 - - + -
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Residues in contact with ALA 189 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169M ALA* 5.8 2.9 - - + -
185M MET 3.1 18.7 + - - +
186M ALA* 4.2 7.0 - - - +
187M GLU 3.3 0.6 - - - -
188M ILE* 1.3 79.1 - - - +
190M VAL* 1.3 61.5 + - + +
191M ASN 3.5 0.3 + - - -
192M ALA* 3.9 3.6 + - - +
193M VAL* 3.4 21.5 - - - +
385M ILE* 4.6 13.0 - - + -
402M LEU* 5.2 7.2 - - + -
405M ALA* 5.6 5.2 - - + -
406M LEU* 3.8 28.2 - - + +
409M ILE* 4.4 1.3 - - - +
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Residues in contact with VAL 190 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162M THR* 4.2 28.8 - - + +
165M LEU* 3.8 32.8 - - + +
166M ILE* 4.3 7.2 - - + +
169M ALA* 5.9 1.8 - - + -
186M ALA 3.5 16.1 + - - +
187M GLU* 3.3 20.9 - - - +
189M ALA* 1.3 78.8 - - + +
191M ASN* 1.3 67.6 + - - +
192M ALA 3.5 0.4 - - - -
193M VAL 4.0 3.7 + - - -
194M LEU* 3.3 25.8 - - - +
409M ILE* 3.8 18.8 - - + +
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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